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Transmission of disease from mother to fetus
Can  parasite, microbes be passed from mother to fetus through the placenta ?
I know some like HIV can be.

HIV rarely crosses the placenta and almost exclusively where it has been left untreated leading to vary high viral load - a greater risk is in delivery itself leading to many HIV+ve mothers chose to undergo elective Caesarean sections

Pregnant mothers can indeed pass on various microbes to their fetuses but it is not always directly through the placenta, as the placenta can be protective.  Although the blood of the mother and fetus do not mix directly, the two can interact.  Maternal proteins can flow across to the fetus, as maternal antibodies are actually the source of a newborn's immune system for a few months, and maternal immune cells have even been found in fetuses, which of course means other cells or viruses can get across.
HIV is a good example for your question, actually.  HIV can infect newborns through the placenta, but the majority of infections occur during birth, not in utero.  Birth is a pretty bloody process, and the rupturing of the amniotic sac exposes the infant to anything in the mother's blood, which is when most infections occur.  For HIV specifically, physicians can all but prevent mother-to-infant transmission by administering anti-HIV drugs just before birth.
Here is a list from the CDC of some STDs which details how infections may be passed on to newborns; most clarify that it mainly happens during the birthing process.  That being said, plenty of diseases will cause transplacental infections.  Usually they are viruses, as viruses are simply smaller, but there are definitely bacterial and parasitic examples, such as Borrelia duttonii, Trypanosoma cruzi, and Toxoplasma gondii.  Here's a list of bacterial ones and here's a list of viral ones.

Parasite are organisms, and they can pass through mother to her child while its in hers womb. Toxoplasma gondii is an example, it passed from mother to child as it moves through her body, and since child is present inside her, of course it will get into the child.
You can diagnose for the parasites, or can even get them treated well just like getting your self treated, but measurements should be taken while treating as the their might be a danger of miscarriage.
So the answer is Yes, parasites can pass through the body of mother to her baby. Since the baby is inside her being a part of her body.
There is an infection called toxoplasmosis which doesnot passed from person to person, yet it can pass while in pregnancy.
Chagas disease is a disease that can get transferred from Mother to her child, during pregnancy. Which is called by a Parasite called Trypanosoma cruzi.
Reference:
http://voices.yahoo.com/can-parasite-passed-unborn-children-via-their-4839156.html?cat=70
http://kidshealth.org/parent/infections/parasitic/toxoplasmosis.html
http://www.livescience.com/21432-chagas-disease-mother-child-pregnancy.html


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How is saltatory conduction faster than conduction of unmyelinated fibers?
It's always the same explanation that currents are able to "hop" along Ranvier nodes instead of passing continuously along the axon making saltatory conduction more efficient than continuous conduction.
However, if we take this down to the molecular level, I cannot understand how they are different. Conduction in unmyelinated nerve fibers are first triggered by an effective stimulus, changing the cell membrane potential and thus opening the voltage gated sodium channels, causing an explosive influx of sodium ions. The action potential is conducted along the fiber through stimulating sodium channels in nearby regions, causing rapid flow of sodium ions into the cell in membrane immediately near the segment of stimulation and this process repeats as the action potential passes unidirectionally along the axon.
Conduction in myelinated nerve fibers are usually described as hopping along the axon, but on the molecular basis, sodium channels are congregated at the site of Ranvier nodes, large numbers of sodium ions that made its way into the cell swim down the axon in the cytoplasma of the nerve fiber reaching the next ranvier node, changing the membrane potential in that specific site therefore triggering another influx of sodium ions.
So to put the question simply, the mechanism of continuous conduction is triggering voltage gated sodium channels continuously along the way, whereas the mechanism of saltatory conduction is triggering-swimming-triggering-swimming...how does this difference essentially make saltatory conduction faster?

Possible duplicate of Why is saltatory conduction faster than continuous conduction?

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Sources for common laboratory Saccharomyces strains?
I'm used to working with bacteria - some of the more common laboratory strains sometimes come with an order from some vendors.  What's the most convenient source to order common straings of Saccharomyces for lab work?

The Saccharomyces Genome Database has a list of sources here. One of them is the Japanese Yeast Genetic Stock Center: I checked their site out and found that they charge ¥390 per strain which is around USD4. There is also a USD5 fee on all orders. I searched for a couple of standard strains, and these were in the catalogue, so it looks like a good possibility.
(Incidentally I have used USD here rather than $ because there seems to be a bug when typing that symbol  twice in a post - try it and you'll see what I mean.)

thanks this looks good @AlanBoyd.  that's close enough to free for me!

ATCC is the place I would go to, just like purchasing cell lines or bacterial lines. The reference ATCC catalog numbers are also listed with each of the common strains you have linked. Depending on the purpose, you could just go to your local grocery store for baker's yeast.

ATCC costs $300 per sample.  When you work with e.coli some of the catalog give strains away free with a purchase.  hoping there is a similar tip for yeast...

Do they really charge that? They took over the Yeast Genetic Stock Center collection and as I recall the YGSC used to provide strains at a nominal price. My suggestion would be to contact the PI in a smaller/midsize lab and explain what you need. As long it is just a few strains I can't imagine that there would be a problem.

And that's exactly why people ask others for their cell lines to make their own stocks. ;) There are rare mamallian cell lines that ca cost tens of thousands of dollars from ATCC.

One very important resource is EUROSCARF. http://web.uni-frankfurt.de/fb15/mikro/euroscarf/
It is one of the very famous and dedicated strain repository for yeast (S. cerevisiae) strains. You can even find some very useful yeast plasmids here.
Another resource I would recommend will be the original labs, which made the mutant strains/plasmids. Yeast researchers as a community are very nice, I have almost always obtained the strains and plasmids that requested from the original labs.
Hope it helps,
Cheers!!

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A number of questions regarding chemotaxis assay using PBMCs
In our lab we would like to study the chemotaxis of PBMCs towards conditioned medium obtained following treatment of cancer cells with different compounds.
My questions are regarding the method of purification of PBMCs from whole blood:

I have read a number of protocols saying that during the isolation process the buffers used should not contain calcium or magnesium ions, as these can cause the activation of the PBMCs. Is that so? From my knowledge Ca+2 is a second messenger only in TCR signaling. I am not sure reegarding the other cells present, and how magnesium is relevant at all.
Even if I use PBS (without any calcium or magnesium ions) to isolate the PBMCs from blood, in the end I resuspend the isolated PBMCs in medium which does contain these ions. Is there any rationale to use calcium and magnesium-free buffers for the isolation when  the final medium contains these ions anyway?
When I begin the assay, should the PBMCs be activated or not? In other words, do chemokines also activate the PBMCs or are chemotaxis and activation two totally independent processes? How should activation/no activation affect my results?

Thank you in advance.


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Bioinformatics tool for "pairwise alignment" of complementary sequences?
I'm currently working on some ribozyme binding, and I'm looking for a tool that will essentially analyze the regions of the degree of complementarity in two sequences in order to extrapolate efficiency of binding. After thinking about it, I'm essentially looking for "the opposite" of BLAST, in that BLAST looks for regions of similarity in sequences in the same orientation, while I'm looking for  regions of complementarity in sequence in the opposite orientation.
Does such a tool exist?
EDIT 1
To clarify, I'm looking for a tool that can detect the most optimal regions of complementarity in two sequences when both are aligned as such:

5' TCGAAUAACTCGTCUGAUGAGUCGCUGAAAUGCGACGAAACCGTTAACGGA 3'
3'   GTTTTACGCAAAGCAGCGTAAAGTCGCTGAGTAGTCACTTTAATGAC   5'

The opposite? You mean regions of low similarity or actually complementary? If the latter, just use translated blast flavors. If you post an example sequence to clarify, I should be able to give you a precise answer.

Sorry for the confusion: looking for regions of high complementarity. Will edit question in a moment.

I'm not sure this is what you need since the sequences you posted are not actually complementary as far as I can tell. However, exonerate is one of the most powerful tools out there and can do this as well. Using these sequences as examples:

>query
  TAGCTTATTGATGGGAGGAGAGTCCGTGCACATGACAGACCTTGGCTGTCCCAGACTGCAGGAAGCCCAGG
  >target
  CCTGGGCTTCCTGCAGTCTGGGACAGCCAAGTCTGTTATGTGCACGTACTCTCCTCCCCTCAATAAGCTA

And this command (should be run on a *nix system):
exonerate -m coding2coding -q qq.fa -t test.fa -s 0

I get this output:
C4 Alignment:
------------
         Query: query [revcomp]
        Target: target
         Model: genome2genome
     Raw score: 312
   Query range: 71 -> 0
  Target range: 0 -> 70

 71 :                                                          CCA       :  6
      CCTGGGCTTCCTGCAGTCTGGGACAGCCAAGGTCTGTCATGTGCACGGACTCTCCTCProTCAATA
      |||||||||||||||||||||||||||||| |||||| ||||||||| |||||||||||+||||||
      CCTGGGCTTCCTGCAGTCTGGGACAGCCAA-GTCTGTTATGTGCACGTACTCTCCTCProTCAATA
  1 :                                                          CCC       : 65

  5 : AGCTA :  1
      |||||
 66 : AGCTA : 70

vulgar: query 71 0 - target 0 70 + 312 M 30 30 G 1 0 M 26 26 C 3 3 M 11 11

C4 Alignment:
------------
         Query: query
        Target: target [revcomp]
         Model: genome2genome
     Raw score: 309
   Query range: 0 -> 71
  Target range: 70 -> 0

  1 :                      GTC                                           : 66
      TAGCTTATTGATGGGAGGAGAValCGTGCACATGACAGACCTTGGCTGTCCCAGACTGCAGGAAGC
      ||||||||||| |||||||||||+||||||||| ||||| ||||||||||||||||||||||||||
      TAGCTTATTGAGGGGAGGAGAValCGTGCACATAACAGA-CTTGGCTGTCCCAGACTGCAGGAAGC
 70 :                      GTA                                           :  6

 67 : CCAGG : 71
      |||||
  5 : CCAGG :  1

vulgar: query 0 71 + target 70 0 - 309 M 21 21 C 3 3 M 15 15 G 1 0 M 31 31

Basically it gives you two alignments, one reading the target 3->5 and the query 5->3 and one the other way around.
Alternatively, you could do a translated blast search, tBLASTx which will translate both target and query sequence and so, should find complementary regions.

Is that where you grabbed yours?  I just installed it and got different results.  Some of it is visual (AA names, 1 versus 0-based indexing) but the scores are pretty different.

@Amory I'm using the one from the Debian repos, v. 2.2.0. Yes, the page you linked to is the homepage, so I'm guessing you just got a newer version and they've changed the algorithm a bit. Perhaps a different scoring matrix. In any case, the score here is irrelevant since it will depend directly on the length of the sequence.

@terdon On second thought, would doing a regular pairwise alignment with the reverse-complement of only of the sequences yield the same result?

@LanceLafontaine probably but it will be slower and perhaps less accurate. If you are looking for possibly complementary sequences that can bind to each other I would use something like exonerate or blast rather than a sequence aligner.

@terdon: I dont understand why you suggested tblast. Translation has got no relation to complementarity.

@WYSIWYG I recommended tBLASTx. tBLASTx will translate input sequences in all 6 frames which includes the - strand which is the reverse complement of the + strand. Therefore, it can be used to find complementary sequences since the 5'->3' translation of the plus strand will be the 3'->5' translation of the - strand.

yes but same translational product can arise with different codons and therefore you wont be able to assess complementarity..

@WYSIWYG indeed, I am just very used to translated blast searches and it was the first thing I thought of because they will also show weaker complimentarity. Since most homonymous codons change only in the wobble position, you might be able to spot complimentarity more easily precisely because of the code's redundancy. In any case, exonerate was my first suggestion, and I agree that your simple nucleotide blast is probably better than translations.

You could try using a tool to estimate the binding affinities of the two sequences, i.e. OligoCalc
http://www.basic.northwestern.edu/biotools/OligoCalc.html

Just run blast with only the Plus-Minus alignments. See this post in biostar; it is similar to what you are interested in. This is for the standalone version. I am not sure about how to do it in the online blast.
If you have just two sequences then you can use UNAfold for checking complementarity.


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Reassociation of DNA
What is the order in which this DNA samples would would reassociate ?
e.coli DNA
plasmid DNA
viral DNA
satellite DNA
DNA-RNA hybrid
This is a homework question and I have not been given any information about the condition in which they are reassociated.

RNA-DNA hybrids have a higher thermodynamic stability compared to DNA-DNA hybrids (deltaG(hybridization)) is low. However that doesn't really mean they will form faster. Just that the equilibrium is towards association.

The rate is determined by the size and complexity of the sequence. Short, non-repetitive sequences should re-associate (at a given r.t.p.) faster than longer, repetitive DNA.
I'm guessing that that is what this question is getting at.


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What is meant by 73 hour birth
I was reading an article, when I read a sentence saying, His mother ... nearly died less than three years later during Mathers' 73-hour birth.
What does mean by 73-hour birth?

This isn't really a Biology question, it just means that Mathers took 73 hours to be born.  If you need further explanation, I'd suggest trying English Language Learners http://ell.stackexchange.com/

This question appears to be off-topic because it is about use of the English Language

I could find that topic related to Eminem's mother, Debbie Mathers-Briggs, who almost died delivering her first son(Eminem) at the end of a 73-hour labor or 73-hour birth. That "73 hour birth" means she was in labor(to undergo the efforts of childbirth) for "73 hours".

yah, anyone can find that article by reading Mathers :D and yes, thanks for the answer :)


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Do brain cells shrink during REM sleep or a lucid dream?
In this BBC news article a study shows that during sleep brain cells shrink to open up the gaps between neurons and allow fluid to wash the brain clean.  But do the cells shrink and undergo the whole procedure during REM sleep and lucid dreaming?

According to the research(M. Nedergaard and team) it only says it was tested when mice were asleep but there is no information about which stage of the sleep. It would be interesting to know which stage of sleep in future.

For those who have access, here's the full text.
Having read the paper, I can't give you a good answer.  This study was performed in mice, not humans, and "sleep" was achieved in a few ways.  Mice normally sleep most of the day, so it was easy to get mice sleeping normally.  They also induced "sleep" through anesthesia (incidentally, they saw these same results in anesthetized mice, which I think is quite interesting).  The state of "sleep" was confirmed mainly through the measurement of brain waves, in particular the delta wave.  Delta waves correlate to deep sleep, and that's what they measured.  Panels D and G from figure 1 (below) basically confirm just that - the mice were asleep - and that's all we know so far.  More exciting research to be done!

I have to add that the authors do not show any evidence for cell shrinkage. In fact, the word shrink is not mentioned even once in the article. Therefore the BBC article is not correct. To answer your question, all we know is that there is more fluid clearance; the authors do not show the mechanisms for this.


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Are there known 3- or 4-nucleotide RNA linkers with no RE sites?
Question is rather self-explanatory. I'm looking for a non-cleavable RNA sequence to act as an RNA linker.
I mention 3- or 4-nucleotides only, but making such a sequence with 2 nucleotides is rather easy as seen below, but I've encountered some difficulties in transcription.

GAGGAAGGGAAAGGGGAAAAGGGGGAAAAA...

This also works for just about any random sequence of G's and A's.

Used as a linker, I don't know if the second part of the question, "secondary structure" can be answered.  This could be very dependent on the flanking regions.  Using poly-A is nice for flexibility, but you will get slipping in your transcription.

I don't know the answer, but you could simply brute force the answer by generating all possible combinations of 3- or 4-nt length sequences, and comparing against the restriction enzyme database (REbase).
It would not take long to do. There are $ 3^4 $ and $ 4^4 $ combinations, respectively. Depending on your purpose, it might be possible when not considering engineered restriction enzymes (which are not likely to have recognition sequences found in nature).

3 nucleotides are so short that many of them can be RE sites or not, depending on the other nucleotides around them.   the brute force method here is the best shot, but the chance that an enzyme that includes your linker may later be discovered.  some restriction enzymes do not cleave the sequence they bind to either.  so not clear whether this is really possible at all.

Those are fair comments. I'm unclear why it's necessary to find such a sequence, unless it's just an exercise. If this is for expression in a particular system, then maybe only its restriction enzymes need to be avoided.


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Which hydroxyl from either the phosphate or the glycerol is taken during synthesis of a phospholipid head?
The oxygen anion in the phosphate group is likely to be bonded with a hydrogen cation and thus forming a hydroxyl.
When the phosphate group is condensed with glycerol to make a phospholipid, is the hydroxyl from the glycerol molecule taken or the hydroxyl from the phosphate group taken?
I believe it's related to the difference of electronegativity of oxygen and phosphorus which causes unequal sharing of electrons between atoms, thus making a hydroxyl from one side easier to get taken off than the hydroxyl from the other side is.

I'm trying to figure out where in the process you are talking about.  Are you asking about the creation of Glucose 6-phosphate, phosphatidic acid, or phospholipids down stream of DAG?  I was originally thinking the creation of phosphatidic acid, but I'm not sure.

In all phosphorylation reactions, the oxygen of the hydroxyl group in the substrate attacks P of phosphate. This is because of high partial positive charge on P which is bonded to four highly electronegative oxygen atoms. When the bond forms between the substrate oxygen atom and phosphorus of terminal phosphate, electrons are transferred to the O that bridges the ester bond between 2nd and 3rd phosphate. Therefore the O of the substrate is retained and that of the terminal phosphate (of ATP) becomes the part of the 2nd phosphate (now terminal phosphate of ADP).

See this

My recollection is that the formation of a phospholipid normally involves acylation of glycerol 3-phosphate. Glycerol 3-phosphate is a glycolytic intermediate, and so there is no actual phosphorylation of a glycerol; the phosphate on the glycerol will have come from the phosphorylation of glucose or of fructose 6-phosphate.
In a kinase reaction the oxygen of the -OH in the acceptor acts as a nucleophile at the P of the phosphate, so in terms of your question the O atom comes from the acceptor, not the donor. Presumably if there was a glycerol kinase (I expect there is) it would have the same mechanism so the O would come from the glycerol.


text:
Isotropy of sarcomere bands in skeletal muscle cells
As seen under a polarization microscope, the A-Band in skeletal muscle fibres is so named because it is anisotropic in its refractive index which is a characteristic of orderly crystalline structure. On the other hand, the I-Band is so named because of its isotropic nature, as far as its refractive index is considered, which is characteristic of Amorphous substances or substances which lack long-range order. Both are filamentous (as opposed to globular) in the sarcomere (Actin is present as F-Actin).

But then why this difference in the characteristics of refractive index,
  which is indicative of order (i.e crystalline or amorphous?) in their
  molecular structure?

Moreover, is the H-Band anisotropic?
If not, then the anisotropy of the remaining part of A-Band must be a consequence of the relative arrangement of Actin and Myosin which are independently isotropic, and hence cannot give a possible isotropic arrangement.
If yes, then that indicates that the myosin filaments are anisotropic in themselves and actin filaments are isotropic. But, in the region of their overlapping (A-Band minus H-Band), the overlap is between an anisotropic (myosin) and an isotropic (actin) component which shouldn't be anisotropic because the randomness of actin filaments (i.e. its isotropicity) should make the entire configuration isotropic?
I am sorry if I am wrong in my understanding of isotropic and anisotropic characteristics, or if my question sounds too "physics-related", but this has been bothering me for quite some while now.
Here is a directly related question I asked on physics.se. It partly solves the problem of possible arrangement of isotropic elements to generate anisotropy.

I am not sure if the "biochemistry" tag applies here. Please edit the tags if it doesn't.

refractive index is not just a property of an amorphous material. Crystalline solids also have refractive index but it may vary with different planes. And i dont think the A-band is in crystalline form. The anisotropy refers to polarization effects. You cannot deduce that myosin conributes to anisotropy. It is a property of a material as a whole (even same substances can exhibit different optical properties in different structural forms)

@WYSIWYG I know refractive index is not the property of amorphous substances. I meant isotropic refractive index is a property of amorphous substances. And I was just saying, that normally, crystalline substances have anisotropic refractive index. Therefore, I wanted to know what property of the molecular structure of actin and myosin contributes to such a division of isotropic and anisotropic bands in the sarcomere

I am not sure about this but if you just take different sections and see how the 2D arrangement looks like then the A-Band region will look different in different sections (x-y and x-z planes). This may be the reason for the observed anisotropy.

This is sort of technical answer, but I hope its helpful I hope.
All these bands in the sarcomere are anisotropic.  Isotropy would imply that the structure/properties of something is equally ordered or coherent in all 3 directions.  The sarcomere has definite structure along its longer axis so the H band is anisotropic.
Since the H band is a small structure compared to the actin and myosin components of the sarcomere, much of the signal that one measures via diffraction or polarization experiments is from those two fibers and less information would be discernible from the anchoring portion (H band) of the myosin filament.
In the case of the A and H bands, which are identified by electron microscopy, the structure along the sarcomere axis is not very strong - they are thin sections of the sarcomere and tend to function structurally to connect the actin and myosin axes.
Because of this the information that you might get from A and H band segment studies will be that 'these bands are not very ordered along the axis of the sarcomere'.  That's not a lot of information, and we know this from other experiments.  But it is information nonetheless because they have some spatial organization.


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What are examples of genes succesfully reproducing in ways that is in conflict with helping the individual creating offspring
Most of the time, our genes have common interests with our "self".
We reproduce well if and only if our genes reproduce well.
In some cases, like in bees, the haploid bees can survive better if they help their queen reproduce.
In humans and other species, are there samples that give individuals "incentive" to help non family member to reproduce for the sake of their genes.
So

No filial altruism
No reciprocal altruism

So I need a sample between individual based evolution and gene base evolution.
For example, many genocide are done against the best and brightest. I wonder what sort of genes encode "kill the best and brightest" and how does that kind of gene survive well in the gene pool?

The prototypical example of this is t, whose existence was predicted by Robert Trivers and featured prominently in the Selfish Gene.  The current dominant point of view in evolutionary biology is that genes act in their own interest and even the 'self' is just a manifestation of the gene's reproductive properties.
t is a locus in some male mice. The t gene characterizes very well the selfishness of a selfish gene.  While most paternal genes are found in 50% of offspring, t is found in over 3/4 of offspring.  Somehow it manages to reproduce at the expense of the other loci in the male mouse.  t itself is not known to convey any advantages to its host organism.  the males tend to be smaller and sometimes even reproductively disadvantaged.
Does that go some way to answering this question?
Animal behavior such as cheating or adopting are often interpretable as reproductive advantages.  Killing the best and brightest definitely are to the advantage of those who are doing the killing.  This SNL Skit has always said it best to me. "... and now I am smart!".  Such kill offs so rarely include killing one's own offspring.  I'm not sure they can be called in conflict with reproductive advantage.  EO Wilson's essay "On Human Nature" does a reasonable case for saying that wars and famines are in fact produced by evolutionary advantage, however cruel and ugly they may be.

And what stops t from dominating and be found in all mice? Oh because it creates weaker male?

you got it.  that's in fact the most famous thing about Selfish Genes - they propagate themselves at the expense of the organism that contains them.  This parasitic case of the gene is not a great strategy but it proves that genes compete directly.  Are there other types of competition?  not everyone agrees :)

Complex behaviours like altruism rarely boil down to a single gene, so it's hard to find a concrete example.
This is one lead:
http://scan.oxfordjournals.org/content/early/2010/10/28/scan.nsq083.full
If you think about it, being altruistic is detrimental to your personal fitness, but inproves the fitness of the population (within certain parameters).
I've only ever heard of clear examples of this in simple game-theoretic simulations.
There may be some good examples here:
http://en.wikipedia.org/wiki/Kin_selection
HTH


text:
Ventral stream pathway and architecture proposed by Poggio's group
Please can you give me a very brief explanation about all functions in the ventral stream architecture summarized in this figure:
This figure is from Serre et al.'s A quantitative theory of immediate visual recognition. Prog Brain Res. 2007.
I read multiple articles about this model, but I still don't understand the basic aim, especially behind the two operations (Gaussian-like and max-like operations).. So please can someone explain to me in details the ventral stream pathway (from V1-V2-V4-IT-PFC) including the two operations in this model.
For example : I don't understand how the cells in S1 are constructed...

The title is misleading. This is just ONE model of the ventral stream processing among many possibilities. Can you be more as to which references you read? Looks like a convolutional deep learning architecture, but you need to tell us more.

thank you for your response. Can you tell me in details what's happen in this picture ? (in S1, C1, etc. ) . Thank you in advance.

The picture doesn't tell much. It seems like it's alternating finding local linear features then aggregating same features across space. You need to point us to where you got the picture, and if you could also write down the equations that would help. Not enough information from the picture!

i edited my picture.. i need only the concept

where did you get the picture?

in my question above

I think @Memming is asking you to give credit to the source of the image, from where did you download this?

http://serre-lab.clps.brown.edu/wp-content/uploads/2012/08/Serre_etal_PBR07_wfig.pdf

I made edits to your question to include proper references. I hope you agree with my changes.

This is a typical architecture of computation proposed as a model for ventral stream of visual processing in primates. It has a long history (e.g., Neocognitoron by Fukushima was 1980) and still widely accepted in machine learning (e.g., deep learning) and neuroscience.

It is motivated by the organization of V1 simple cells and complex cells. Simple cells in V1 can be approximately thought of as edge detectors at a specific retinal location. This is why on the figure you cite, they are represented as a circle with a bar (a cartoon receptive field). The simple cells can only detect things very locally, meaning if the edge appears at a different location in your field of view, it will not respond.
Mathematically, you can think of a spatial filter that detects an edge (e.g., oriented Gabor patch) multiplied to your retinal image, and summed. For example the filter below will detect match a 45 degree bar aligned on the hot-colored area, but will have less activity if the bar is shifted out of the specific position.

The complex cells in V1, on the other hand is still an edge detector, but has some location invariance. In other words, when the edge is slightly displaced, the response of complex cells does not seem to change. It is believed that this is because complex cells pull from multiple simple cells with the same orientation. This is what you see in your figure where a single complex cell pulls information from the same orientation simple cells but at different locations.
Mathematically, a soft-max operation or a max operation over the simple cell outputs can lead to a good complex cell model. But, it is not limited to such operations. In fact, quadratic or other nonlinear models are also widely used in computational neuroscience.
The full hierarchy for ventral stream is then simply obtained by extending repeatedly using the simple-cell-complex-cell analogy. For each stack simple cell layer extracts some local feature (by computing on the previous layer's complex cell's output), and complex cell layer makes it invariant over space. From edges in V1, one can get corners on the next layer, then complex contours, and all the way up to objects. At least that's how the story goes.

I don't know how to thank you about this response. I really appreciate it very much... But i still don't understand some details, i will tell you my opinion in the second comment.

I know that in area v1, we have simple and complex cells. each simple cell receive some inputs from the Lateral Geniculate Nucleus (LGN).These inputs are combined with a bell-shaped tuning (gaussian-Like tuning) with the preferred orientation. And all we know that each simple cell can response to a specific oriented bar (in the case of gaussian-like tuning, the response of the cell must be optimal?? because we are making a tuning with the preferred orientation of the receptive field of the cell ?).

However, if we consider such an image, please can you explain to me in details what happen in order to get the tuned simple cells in v1 ? In other words, and in case of the considered image, what we mean about the inputs of such a simple cell? is there a segmentation of the image before the tuning operation? i didn't understand the phenomenon...is there a convolution of the image with a specific filter in order to obtain the image as a form of bars ?? please i need your appreciated help :) and thank you very very much Dear.

@Liszt You're welcome. The orientation tuning curve can be thought of as a consequence of LN model. If you ask this in a separate question, I could write down the equations for you.

@Liszt In fact, the tuning curve would have a cosine shape, not exactly Gaussian or von Meises...but they look very similar. This comes from the relation between dot product and cosine.

for the first step (tuning the simple cells in v1), can you give me an example which can include in details and step by step the operation of this tuning in order to obtain the simple cells (the S1 layer). So please can you give me this example in a specific image that you choose ... I will appreciate very much your response !! :) if yes, please put your example in a second answer :) you don't need to make calculation, you can only give me a brief example (cartoon scheme).

@Liszt I suggest you ask a completely separate question. Each question should have only one question in it. That's how SE works. :)

ahh sorry, so i can ask another question in this site, and can you response me (to give me an example ) ? :):)

@Liszt Yes, I'll answer your question. (unless someone else does) :P

Dear Memming, can you explain to me how the euclidean distance in S2 layer is computed between a patch X of size nxn (but contains nxnx4 C1 units) and a stored prototype? how the result must be an S2 image? please i need your help :) thank youu


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How much can you learn about species variation from a skeleton?
I just read about the discovery of the 1.8-million-year-old human skull in Georgia, and how it suggests that early humans were all one species instead of distinct ones. Would an archaeologist unearthing dog bones a million years from now know that a Great Dane and a Chihuahua are the same species?

It seems as if this article is purely speculative. They didn't mention any DNA testing, but instead discussed physical features.
There are two "types" of archaeologists: clumpers and splitters. Clumpers (like the author of this article) believe that there is wide variety among members of the same species, and so it is often wrong to categorize every new hominid fossil as being a different species. Splitters like to "split" their findings into new species, even though there is no evidence that speciation had ever occurred; they just decide that since the remains look different, they must have speciated.
In the future, I hope that archaeologists will have more sophisticated means of sequencing the DNA of ancient remains, allowing them to construct an accurate phylogeny


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How to measure bacterial content
I´m using water container placed on a radiator to humidify room air. Someone might argue that it is a perfect nest for bacteria. I have to put copper coins into the water to kill the bacteria.
I would like to do an experiment, have two similair containers filled with water one with copper coins, the other without them.
I would like to compare how many bacteria are living in those containers, how can I do that? (in home conditions)

There is evidence that copper pots have antibacterial effects when used for storing drinking water (Sudha, et al. 2012), so the copper coins will probably have a similar effect.
The easiest way to test this at home would probably be to buy a test kit from an online vendor - these are relatively inexpensive.
Some Googling produced this website [appslabs.com.au], which has some tests for common types of bacteria. There are undoubtedly others too, if these don't sound suitable

Anything I can get in Europe? Do you have any recommendation on type/brand?

@Hurda I'm afraid not - I've not used them myself, just found them by searching on the internet. Find one with some good reviews!

I would first like to address a couple of your underlying assumptions:
1) Most "copper" looking coins (in North America anyway) are actually a bronze alloy, reflecting a change from ~95% Cu to ~95% steel. As a result, I don't think that there would be much antimicrobial effect from the coins. Now, if you did really have copper in the water (like copper piping), then the best antimicrobial effects are likely to come from regular stirring/agitation to make sure the bacteria contact the copper.
2) Having some tap water sitting in a warm area is not really a "perfect" breeding ground for bacteria. A perfect breeding ground would contain nutrients (at the very least, sugar). Whatever bacteria you would find is likely the bacteria that circulates in your home air, or other contaminants (like sneezing).
As for your question, how to measure the bacterial load in each bowl, I think the simplest method to do at home would be as @Alan Boyd suggests. Take a small sample of water from each dish, and plate them out on some kind of growth plate (such as a LB agar). After 16-18 hours of growth on the plate, you would just count the number of colonies on each plate, and get a simple measurement of bacterial load from each bowl.
The drawback to this method is that it does not tell you what kind of bacteria are growing, or whether they are likely to cause illness (pathogenic).
Edit:
For reference, here is a detailed overview of the most common types of agar plates used for microbiology purposes. This is also a protocol for how to make your own plates at home, using readily available gelatin as a gelling agent, rather than using agar (which can be found in some ethnic supermarkets, but is less available).

It,s Euro cents, they claim copper coating of Fe body. I'm trying to measure the antibacterial effect (instead of just assuming something) - compared to no additive and based on suggestion also real copper (old GPU heatsink)

Sounds good, I was just pointing out a few things for you to consider.

@Hurda, I added two references for commonly used agar plates, as well as a method to make your own plates at home with readily available home ingredients.

I think you might be better advised to try plating out samples of the water and counting bacterial colonies. There has been some good advice on doing basic microbiology at home elsewhere on this site.

I don't understand how this should help me to determine, which sample (container) conatined more bacteria before I started cultivation (and put any number to that)? Is it the speed at which the cultivation progress?

Thanks to leonardo for answering this before I got a chance to!

I have no idea, how your containers look like [and I doubt that's the best way to humidify air] and I don't think there is any chance to get rid of bacteria by putting some copper coins inside, but any-case:
The easiest way to measure concentration of bacteria utilized in laboratory practice is with the aid of a spectrophotometer. There are lots of protocols on-line, but basically you need a spectrophotometer able to measure absorption at 600 nm, special cuvettes and pipettes. One major drawback is that this way you get relative amounts of bacteria, and to get an idea, of how much cells in one unit of volume you actually have, you need calibration. [Calibration curves are unfortunately not transferable from photometer to photometer or from one bacterial culture to another one]. Calibration is generally performed by measuring absorption of media with different a priori known concentrations of bacteria. To get such control media, one needs a more laborious trick: measure individual cells from a known volume under a microscope (pour, say 1 mkl of the medium on a glass and "just" count all cells).
Moreover, you likely need a centrifuge, capable of rotating at 5000 g, because bacterial content in your water is not going to be high enough and you have to collect the cells and re-suspend them later in much smaller volume.

Few homes have a spectrophotometer, so this is not suitable approach "in home conditions" as was asked for.

Yes, perfect reason for a down-vote. I wrote: "in laboratory practice". E.g., I also don't have LB in my kitchen or a thermostate.


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Which of Perutz et al's protein structures other than 3₁₀ helix were correct?
In 1950, Bragg, Kendrew and Perutz published "Polypeptide chain configurations in crystalline proteins" (open access) and were famously 'proved wrong' by Pauling, Corey and Branson the following year, in the paper that documented the alpha and gamma helices, "Two Hydrogen-Bonded Helical Configurations of the Polypeptide Chain" (also OA)
I'm reading about this (as reviewed here for example) where the idea is that Bragg et al were disproved - in the words of the Pauling paper:

None of these authors propose either our 3.7-residue [α] helix or our 5.1- residue [γ] helix. On the other hand, we would eliminate by our basic postulates all of the structures proposed by them. The reason for the difference in results obtained by other investigators and by us through essentially similar arguments is that both Bragg and his collaborators . . . discussed in detail only helical structures with an integral number of residues per turn, and moreover assume only a rough approximation to the requirements about interatomic distances bond angles, and planarity of the conjugated amide group, as given by our investigations of simpler substances. We contend that these stereochemical features must be very closely retained in stable configurations of polypeptide chains in proteins, and that there is no special stability associated with an integral number of residues per turn in the helical molecule.

There was one however, the 310 helix which was correctly identified by Perutz's group in 1950. I don't have any access to library facilities at present and online resources aren't quite the same as a solid textbook. I'm wondering if any of the other forms described were in fact correct?
To list, these were:

27a
27b
28
213
214
38
( 310 )
411
413
213

I'll continue looking in the meantime but it's hard to search when there are subscripts in names, and I would think more experienced protein scientists could give me a quicker answer (or just direct me to where I should be reading)

I'm pretty sure you have it right because Pauling made a big splash with his alpha helix and both beta sheet models years later.

ok i had the time to expand into an answer....

nice reference! I've not read Perutz' book yet - I really need to! Note how Astbury's data had not been correctly evaluated; giving the wrong pitch for the alpha helix, misleading Kendrew and Perutz.  One of the reasons for so many of those crazy helix numbers.

I think you've got the list of good predictions from the Bragg, Perutz, and Kendrick paper.  And the 310 helix was not really right either - it did turn out to show up occasionally in protein structures though.
At the time all of these secondary structure elements were well evidenced from noncrystalline diffraction data and small molecule crystal structures. Examples being collagen from hair and spider silk fiber diffraction patterns. Fiber diffraction of hair, whose ordered structure consists mainly of alpha helices somewhat aligned to the fiber axis (along the length of the hair) or the mainly beta sheets which constitute silk.
Because it was known that these substances contain mainly protein, building models which would show how regular peptide polymers would produce these patterns.  This happened in chemistry and physics departments worldwide.  The paper you cite is representative to the field.
Pauling caused a splash in the spring of 1951 by publishing descriptions of the alpha helix and the beta sheet (both parallel and antiparallel).  The main advantage that Pauling had was that he had studied the structure of simple di-amino acid structures (notably glycyl-glycine) and understood that the peptide bond had some double bond like properties which prevented it from rotating freely.  As the discoverer of valence bond theory, which united quantum mechanics and chemistry and established the basis for at least most organic/biological chemical structures Pauling must have been practically alone in this insight at the time.
This next set the stage for the dramatic race to discover the structure of DNA. If you read Watsons' memoir, he describes how the MRC in Cambridge was still feeling the heat,  competing with CalTech and Pauling.  He and the young lab there was holding their own against the MRC Cambridge with its multiple nobel laureates; a lab which had established the relationship of x-ray diffraction and chemical structure (the notes on chapter 7 are interesting - follow the link).
Looking back on it, Pauling's main advantage was that he understood the peptide bond better than the rest of the world. By the time DNA was being resolved, the conformations of organic molecules were understood by many and the playing field should have been more level.  I'm not sure I buy the arguments that Pauling would have got the structure without seeing the diffraction patterns and even then maybe not. I might not give such strong credence to the idea that Pauling would have gotten the DNA structure so quickly if he had been able to travel.
Of course Perutz and Kendrew verified the peptide alpha helix themselves when they solved the first crystal structures of hemoglobin and myoglobin, having the final say.  The structures contain a small amount of 310 helix but are otherwise full of alpha helices.  I'm not sure that the secondary structure was entirely confirmed until the 1958 when myoglobin was resolved.

Wow nice essay haha! I thought Coulson proposed valence bond theory, thanks for the historical input though mate, v nice :-)

its a story I've enjoyed learning.  If you're reading that paper you are pretty deep into it yourself!

BTW Chemical valence was a term around before Pauling, but he formulated the quantum mechanical rationale for chemical bonding, which was adjusted by molecular orbital theory, but which we still use today.


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Question about production of CFTR protein
How do organelles such as ribosomes, ER, Golgi and vesicles produce CFTR protein and mucus?

Can you provide more context? Also can you unpack CFTR?

Also, what is your background knowledge and where are you stuck?

CFTR (cystic fibrosis transmembrane conductance regulator) is an integral glycoprotein of the plasma membrane, and mucous is rich in secreted glycoproteins. All proteins are made on ribosomes: CFTR will be cotranslationally inserted into the ER membrane while secretory glycoproteins are cotranslationally sent across the same membrane into the lumen of the ER. In the ER the initial glycans are added to specific amino acid residues. The folding of all proteins is carefully monitored by chaperones in the ER to avoid misfolded proteins reaching the cell surface. Various folding factors also come into play, including peptidyl proline isomerase and protein disulphide isomerase.
Proteins destined for the cell surface leave the ER in COPII-coated vesicles (CFTR will be in the vesicle membrane, secretory glycoproteins in the vesicle lumen) and are targetted to the Golgi where the glycosylation process is completed. Another round of vesicle transport gets the proteins to the cell surface - when these vesicles fuse with the inner surface of the plasma membrane the vesicle content is secreted into the surroundings, while the vesicle membrane proteins enter the plasma membrane.
The classic example of a CFTR defect, resulting in cystic fibrosis, is due to the ΔF508 mutation - the loss of a single amino acid results in misfolding, and the defective protein is held in the ER resulting in loss of CFTR function at the cell surface. Overcoming this retention is one of the targets for CFTR therapy, because if the ΔF508 protein does manage to pass through the secretory pathway to the cell surface it provides sufficient channel function to abolish cystic fibrosis symptoms.
I haven't cited any references here because this is all standard biochemistry/molecular cell biology textbook stuff, so should be easy to confirm.

There are a couple nice videos here: https://synbiota.com/projects/325/
You can also check out some DNA sequences and some protein structures (PDB files) if you want to learn more.


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Empirical evidence for species selection
Do we have any empirical evidence in favor of species (or lineage) selection? Do we know some cases that can only be explained (or seem to be only explained) by lineage selection? What are today the best study cases in favor of lineage selection?
If not, how could we find any evidence for lineage selection?
Note: I call lineage selection a differential in speciation and/or extinction rate that drive the proportion of lineage (species for example) displaying a given trait (emergent traits or not) to increase or decrease over time.

A commonly used empirical example of species selection (a.k.a clade selection, lineage selection) is pelagic larvae in sessile ocean species. See Maliska et al (2013) for a recent paper discussing this in Tunicata and Jablonski & Hunt (2006) for larval modes in gastropods. The idea is to some extent really intuitive - pelagic larvae means higher dispersal rates, so the species will be exposted to and can colonize new environments. This can lead to speciation through adaptive radiation. Larger ranges also means lower extinction rates (e.g. through less population synchrony). If the trait is fixed within a lineage, this lineage as a whole will, as compared to an sister lineage lacking the trait, contain more species (i.e. species selection).
However, you can also argue that pelagic larvae will lead to higher gene flow between populations, which could inhibit speciation. Therefore, the effect of pelagic larvae, and how these mechanisms are weighted in practice, is really an empirical question (see Duda & Palumbi, 1999 and Jablonski & Hunt, 2006 for discussions on this issue).
Jablonski (2008) provides a nice general review of species selection (concept, mechanisms, theoretical models and data), and Okasha (2006) (chap. 7) is good for a theoretical/philosophical treatment of levels of selection. Also remember that traits are selected for at the individual level, but can (especially if fixed) still act on a lineage level.


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Lyonization and X-linked disorders?
Lyonization or X-chromosome inactivation is the conversion of all but one, X-chromosomes in Females into non-coding heterochromatin (i.e. deactivated) leading to the formation of one or more Barr bodies. The selection of the X-chromosome to be inactivated is different in different animals. In female Marsupials, the inactivation is always of the Paternal X-chromosome while in placental mammals, the selection is random. (Although the extent of lyonization is not completely random and varies directionally with age).
My question is

If the X-chromosome to be inactivated is randomly selected in
  placental mammals (including humans), then why don't the females
  heterozygous for a X-linked recessive disorder do not show the
  phenotype of the disease though the functional gene is equally likely
  (as compared to the defective) to be the one to be lyonized?

There are some evidences of genes escaping inactivation and managing to exhibit themselves but I don't think they can account for all the recessive x-linked disorders.

The simple answer is that which X chromosome is inactivated varies in different cell lineages, so typically a female will have cells exhibiting either wild-type or mutant phenotypes. It was Mary Lyon's observation of mosaicism in heterozygous mouse coat colour that gave the phenomenon its name. So in the case of a recessive disease there will be a phenotype, but in many cases the 50% of cells expressing the normal gene will provide sufficient functional cells to get by. From the Wikipedia article about Mary Lyon:

Her research has allowed us to understand the genetic control mechanisms of chromosome X, which explains the absence of symptoms in numerous healthy women that are carriers of diseases associated with this chromosome.

Edit - response to comments:
Plug, I et al. (2006) Bleeding in carriers of hemophilia. Blood 108: 52-56
Abstract:

A wide range of factor VIII and IX levels is observed in heterozygous carriers of hemophilia as well as in noncarriers. In female carriers, extreme lyonization may lead to low clotting factor levels. We studied the effect of heterozygous hemophilia carriership on the occurrence of bleeding symptoms. A postal survey was performed among most of the women who were tested for carriership of hemophilia in the Netherlands before 2001. The questionnaire included items on personal characteristics, characteristics of hemophilia in the affected family members, and carrier testing and history of bleeding problems such as bleeding after tooth extraction, bleeding after tonsillectomy, and other operations. Information on clotting factor levels was obtained from the hospital charts. Logistic regression was used to assess the relation of carrier status and clotting factor levels with the occurrence of hemorrhagic events. In 2004, 766 questionnaires were sent, and 546 women responded (80%). Of these, 274 were carriers of hemophilia A or B. The median clotting factor level of carriers was 0.60 IU/mL (range, 0.05-2.19 IU/mL) compared with 1.02 IU/mL (range, 0.45-3.28 IU/mL) in noncarriers. Clotting factor levels from 0.60 to 0.05 IU/mL were increasingly associated with prolonged bleeding from small wounds and prolonged bleeding after tooth extraction, tonsillectomy, and operations. Carriers of hemophilia bleed more than other women, especially after medical interventions. Our findings suggest that not only clotting factor levels at the extreme of the distribution, resembling mild hemophilia, but also mildly reduced clotting factor levels between 0.41 and 0.60 IU/mL are associated with bleeding.

Bimler, D & Kirkland, J (2009) Colour-space distortion in women who are heterozygous for colour deficiency. Vision Research 49: 536-543
from the Introduction:

About 15% of women are heterozygous for some form of colour vision deficiency (CVD). That is, they possess a genetic abnormality on one of their two X chromosomes, affecting the photopigments (opsins) which subserve colour vision. The retina of a heterozygous woman is a mosaic in which some cone cells express the aberrant gene while others express the normal copy, depending on which X chromosome is active (inactivation of one X chromosome occurs randomly in retinal stem-cells at some stage of fetal development). The normal cells are sufficient to provide full trichromatic vision.

Thank you for the answer. In case of a female heterozygous for haemophilia, can we observe the defective $\beta$-Hb chain in atleast a part of the total RBCs? That, if possible, would greatly simplify identification of Heterozygous carriers.

I don't know the answer, but I think that you are getting your diseases mixed up - it's sickle cell anaemia that's a haemoglobin disorder. I seem to recall however that the most common genetic disease in humans, glucose 6-phosphate dehydrogenase deficiency (X-linked) is an example of a blood disorder in which heterozygous females have two populations of red cells.

I am sorry. I was in quite a haste and blundered because of it! Thank you anyway.

@SatwikPasani I got quite interested in what you said in the first comment if we apply it to some other disorder as sickle cell anaemia isn't X linked ( As alan boyd already pointed out). Why shouldn't the concentration of say, a clotting factor differ in haemophilia carriers from that of homozygous female ?

@biogirl Analysing the cone constitution in females heterozygous for color-blindness is equally intriguing since there is a possibility of there being a random distribution of color-blind and normal cones, in the retina. Anyway, I am looking up the Haemophilia case at the adjacent pathology centre and will keep updating here. P.s.( I know I did a mistake in my first comment but editing comments after 5 min is disallowed :))

@SatwikPasani Cool ! Would love to follow up !

@AlanBoyd Does extreme lyonization (in the first paper) mean inactivation of X chromosome carrying the normal allele in most of the cells ?

@AlanBoyd As a co-incidence, it was this very paper(first one) the pathology department asked me to look at (they didn't have the latest research papers directly on lyonization for they rarely came across haemophilia cases, let alone carriers). Though the link they gave was behind a paywall, I got a free link here.http://bloodjournal.hematologylibrary.org/content/108/1/52.full.pdf The second link was unknown. Thank you for it.


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Exotic Cell Shapes
As far as I know, plant cell shapes are a difficult thing to pin down. However plant cells have cell walls and so can be very rigid. However the only plant cells I've seen have been either block shaped or tube shaped. Are there more exotic examples of cell shapes, particularly in plants? For instance have plants ever used honeycomb patterns or other forms of tesselation?

Pavement cells should content you:

From http://dev.biologists.org/content/131/21/5215.full


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Whole genome amino acid composition tool?
I'm interested in a statistical tool to get bacterial codon usage at genomic level. Ideally, the tool should be flexible to analyse hundreds of bacterial genomes.
I've looked in MeSH terms database but I'm a bit lost when I search for "Genetic Code" and Software.
I'm looking for an output like this one:

Please clarify a little. What is "genetic code usage"? Do you mean the code that a species uses or are you thinking of codon biases? What are you trying to do with MESH? How do you get aa composition at the genome level? You mean the usage ratio of aas in the whole proteome? Please [edit] your post and include the actual scientific question you are trying to answer.

Just to amplify the comment from  @terdon - do you mean the amino acid composition of the proteome (i.e. taking into account protein abundance) or do you mean that simply calculated from the translation of all open reading frames?

In response to the comments, I edited my question and added my ideal output.

check this.
You can get the tables for multiple genomes and then apply your statistics. You can use a script to automate the download

You should also be aware that within subsets of the genome, there are different codon biases. For example, metabolic genes use a different codon bias than whole-genome transcript bias. Also, mitochondrial DNA has a different codon bias from genomic DNA codon bias.

@Masi could you clarify how you would like the answer to be improved? Perhaps edit the question to define a specific statistical calculation you would like to see?

More practical examples and more comparison to other existing tools. I have seen some in different laboratories and would like to have different views why to use some tools. This is a huge topic and I cannot see that my answer can answer this question.

I have written a script that will get you started. It downloads all protein coding transcripts of the species of interest from Ensembl and prints the codon use for each codon on each transcript.
You will need to install the Bio::EnsEMBL::Registry Perl module, see here for instructions. The script also uses the Math::Round module, everything else should be installed by default with your Perl distribution. Finally, the script expects to be run from a Unix/Linux operating system.
Example run
 ensembl_get_codon_count.pl human > human.csv

Example output
Gene Name   Gene ID      Transcript ID  Ala_GCC Ala_GCC_% Ala_GCA Ala_GCA_% Ala_GCG Ala_GCG_% Ala_GCT Ala_GCT_%
CRLF2   ENSG00000205755 ENST00000400841    6       40        6      40         0       0         3       20

In the example above, the transcript ENST00000400841 of the human CRLF2 gene, contains a total of 15 Alanine residues, 6 of which are coded for by the GCC codon (40%), 6 by the GCA codon (40%) and 3 by the GCT codon (20%). The GCG codon is not used (0%).
This is a cut version of the output, the actual output lines are much longer since they include all codons and there will be one line per protein coding transcript.
This script should at least get you started since it will provide you with the raw data needed to perform your statistical analyses. If you use it in published work, I would appreciate it if you could let me know (my email is included in the script) and perhaps mention me in the acknowledgements :).


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Is Zymase, A Complex of Enzymes? Which ones?

Some websites state that the enzyme zymase (which I understand to be a complex of several enzymes) is responsible for catalyzing glycolysis in order to produce pyruvate.
On the other hand, some other websites state that zymase is responsible for catalyzing the conversion of pyruvate to acetaldehyde, and acetaldehyde to ethanol and carbon dioxide.

Which one of the above is correct? And, what are the names of the enzymes that are collectively called zymase.
I thank you for your time and consideration. Good day!

This is all correct it seems, but maybe the term is more of historical interest rather than current science.
Zymase is a term which is no longer in use in the scientific literature.  It seems to have disappeared in the 1950s.   The latest reference I can see is 1970s.
The reason seems to be that Zymase was purifiable from yeast with 19th century techniques.  The term was coined in 1897.  This is probably because in brewers yeast the Zymase components are either in a protein complex or contained within a compartment in the cell that could be separated from the rest of the organism.  Here's an early reference - german isn't so great.
The Zymase activity was shown to vary from one strain of yeast to another, which makes the discovery seem more a manifestation of the physiology of that one strain of yeast.
Later work showed that Zymase activity was organizable into a more universal set of genes which are conserved in all living things and called the 'citric acid cycle' or the Krebs Cycle. Krebs performed his work without reference to Zymase, where biochemicals were added to a culture and their transformation tracked. So, Zymase seems more like a historical footnote...
Wikipedias' entry sounds as if the extraction was not very pure - its called a 'press juice' so I think it would be difficult to describe exactly which specific enzymes were in Zymase.  I'd naively assume that nearly all the citric acid cycle enzymes would be involved in Zymase activity, where observed.
Many of the enzymes in the citric acid cycle form large complexes with themselves and other of the enzymes, which might be responsible for the original discovery of Zymase.

The linked german paper is a reproduction from 1935, so I don't think it is evidence that the term is still used

good point - fixed.


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Breakdown current for human body
If I am not mistaken, during exposure to electricity sources it is the magnitude of the current and not the voltage that kills the human body.  If so, what is the order of magnitude of current that human body can sustain, and for what duration?  How do defibrillators exploit this?

It might be better to break this into two questions, the second one being how defibrillators exploit this.  I think you've got a good answer to the first half already.

A part of the answer can be found in Skeptics question: http://skeptics.stackexchange.com/questions/1664/is-it-the-current-that-kills-you-not-the-voltage

@AtlLED I thought one who answers the first question will most likely be able address then second one continuing the explanation and for this reason I clubbed the two questions

@PradeepS The linked post is insightful, thank you for sharing.

According to Wikipedia Electric shock, the Magnitude of electric shock to a body is mainly due to current as well as voltage. Various factor of the environment will also play a major role in damaging the body while under contact. The following quote explains it:

The minimum current a human can feel depends on the current type (AC or DC) and frequency. A person can feel at least 1 mA (rms) of AC at 60 Hz, while at least 5 mA for DC. At around 10 milliamperes, AC current passing through the arm of a 68 kg (150 lb) human can cause powerful muscle contractions; the victim is unable to voluntarily control muscles and cannot release an electrified object. This is known as the "let go threshold" and is a criterion for shock hazard in electrical regulations. The current may, if it is high enough, cause tissue damage or fibrillation which leads to cardiac arrest; more than 30 mA of AC (rms, 60 Hz) or 300 – 500 mA of DC can cause fibrillation.

To give a clear picture of how various current threshold will affect human body see the image below. (Complete data is available here "Electrical Safety").

Even High Voltage also can be fatal to human body which is enough to cause damage.

High voltage electrical energy greatly reduces the body's resistance by quickly breaking down human skin. Once the skin is punctured, the lowered resistance results in massive current flow. Ohm's law is used to demonstrate the action.
  At 1,000 volts, Current = Volts/Ohms = 1,000/500 = 2 Amps, which can cause cardiac arrest and serious damage to internal organs.

Now what is the length of time that body is under electrical contact. This length of time exposure is also critical.

When muscular contraction caused by stimulation does not allow the victim to free himself from the circuit, even relatively low voltages can be extremely dangerous, because the degree of injury increases with the length of time the body is in the circuit. LOW VOLTAGE DOES NOT IMPLY LOW HAZARD!
  100mA for 3 seconds = 900mA for .03 seconds
  in causing fibrillation

(Complete detail is available How Electrical Current Affects the Human Body)

This article deals with the issue in detail.

Please write a short summary of the information in the article.


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The Operation of tuning in the S1 layer of ventral model
According to my previous question in ventral Stream pathway and architecture, I want now to get a brief example about how the S1 layer is constructed. In other words, how all the simple units are tuned with the gaussian-Like tuning (for example). I am only interested to get such a cartoon example in step by step how this operation can be achieved in given of inputs (which inputs? and what we mean about these inputs?) in order to obtain the tuned simple units.
We all know that each simple unit is obtained after a tuning operation around their inputs (Subunits) in order to select an optimal output which corresponds to the preferred orientation for such a simple unit.
Moreover, I know that the S1 layer units perform a convolution on regions of the raw input image using gabor filters at different orientations and sizes. The entire population of S1 units represents a convolution map of Gabor filters of different sizes and orientations with the entire raw image (really I didn't understand this point) you can read the subsection 2.2 in this article
The image below contains the image to be recognized by the brain and some simple units obtained after the tuning operation. So what I want is to obtain a brief example which can include the details (step by step) of how the operation of tuning can be achieved.

i didn't understand well the concept. That's why i need a real example with a specific image which can contains all the steps described in my attached image (step by step) because i still don't understand what we mean about inputs x, etc.
So please if anyone can give me a real example with a specific image which can respond briefly to this attached image

I'm quite busy at the moment. Perhaps tonight I might have some time to answer this. :'(

ah don't worry :) thank you so much, anw i put an image in the answer below. But i didn't understand well the concept. That's why i need that you give me a real example with a specific image which can contains all the steps described in  my answer below (step by step) because i still don't understand what we mean about inputs x, etc.


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Function of papain in papaya
I know that papain is a proteolytic enzyme present in papaya. It is often used to tenderise meat.  What is the function of papain in papaya?  Is papain sweet? Does it function as an antibiotic?

Papain is a cysteine protease, for which Wikipedia should be sufficient:

Cysteine proteases play multi-faceted roles, virtually in every aspect of physiology and development in plants such as in growth and development, in senescence and apoptosis (programmed cell death), in accumulation and mobilization of storage proteins such as in seeds. In addition, they are involved in signalling pathways and in the response to biotic and abiotic stresses. In humans they are responsible for apoptosis, MHC class II immune responses, prohormone processing, and extracellular matrix remodeling important to bone development.


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Effect of pH on life? Use buffer or HCl? How about lactic acid?
I'm trying to find the effect of pH on living things like E. coli and such. At first I thought of using a buffer solution which maintains its level of pH, but it's possible that the inactive ions of each buffer have their own effect on living things that I can't account for. On the other hand, I could use hydrochloric acid and sodium hydroxide at different concentrations by diluting it. This will be a little bit more effort (I'll be diluting the acid and base myself), but much cheaper than the buffers, and I'll know that the only other ions present beside H+ and OH- are just Na+ and Cl-, the ingredients of table salt. According to this paper, the effect of pH on the population also depended on the acid (HCl vs lactic acid).
I would like a second opinion on this:
If I'm investigating the effect of pH on growth of living things, do I use specially made buffers or just properly diluted HCl and NaOH?

What makes you think that Na+ and Cl- can be ignored? Just because they're what makes up table salt does not mean they are harmless. I am not saying they can't be ignored for the purposes of this experiment either, just pointing out that you may be jumping to conclusions.

@terdon  Not saying they are to be ignored, but if anything, these are controls. I KNOW that they're there. OTOH, I have no idea what went into those buffers.

That is a variable that you have the pleasure defining yourself. Just know that using a buffer will introduce other atoms that could affect the "living things". Conversely, if you don't use a buffer, it is likely that the pH of your "living things" will be easily altered by the metabolism of your living things (IMHO, this is worse).
I don't know the details of your project, but recommend:
-use a buffer like.. Tris, phosphate...
-use 10 mM Tris-Cl without any extra electrolyte (aside of the HCl or NaOH that you use to modulate the pH of your buffer to different pH's that you want to test)
-e.g. Tris-Cl pH 7, 8, 9.. or Phosphate pH 2,3,4,5,6,7,8,9..


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Population Growth Rate Question?
A population of 600 birds faced a problem of biological magnification resulting in a large number of deaths reducing their population to 350. But 230 births also took place and 21 birds immigrated into the population while 13 birds migrated out. How many deaths took place in the population? What is the growth rate of this small population?
So I guess we need to use the
PGR = (BIRTHS + IMMIGRATION) - (DEATH + EMIGRATION) / INITIAL POPULATION x 100%
So.. I keep getting -2% as my answer, but apparently the correct answer is -41.7%
Thanks!

Tag as homework? Also, 350/600 -1 = -41.7% which is the alternative answer you are looking for. It all depends on whether the births, immigrations and emmigration are already included in the reduced population size at t+1.

You phrasing seems to imply that 350 remained after deaths, but that births etc also took place, making the population size at t+1 equal to 350+230+21-13=588. If so, the -2% would be correct.

@fileunderwater but how would I make it true so that it equals -41.7% using the full population growth equation?

Well, 250/600=41.7

As you have phrased it, the question can be understood in two ways.

The population size at t+1 is 350, after births, deaths and migration have taken place.
The population size is 350 after deaths, but you also have to take births and migration into account to calculate population size at t+1

For alternative 1 the growth rate is:
$pgr = \frac{(230+21)-(488+13)}{600} = -0.417$,
with $\Delta N=-250 \Rightarrow -250 = 230+21-deaths-13$
For alternative 2 the growth rate is:
$pgr = \frac{(230+21)-(250+13)}{600} = -0.02$


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Function of carapace
Majority of crustacean larvae have expanded carapace drawn out into processes as an adaptation for :
a. Protection from enemies
b. Planktonic habit
The answer given is b but I think it should be (a) as carapace functions as an exoskeleton.
Please help!

I don't know anything about this topic, but surely the key to this is that the question is actually asking about processes extending from the modified carapace, so this is function over and above exoskeleton function. I can imagine that such processes could help with dispersal in currents.

Preface:

Any question about adaptation on macro-level has very little meaning and no precise answer.
There are two types of larvae in invertebrates: primary ("original") and secondary (evolved from post-larval stages). Not digging into the details, nauplius (together with metanauplius) is the only type of primary larvae in Crustacea and it never has a carapace.
"Majority" is by far too strong term, even if we are talking about all larval types. If we just take the largest crustacean orders with species numbers > 1000, together comprising 92% of crustacean species (species numbers are from Ahyong et al, 2011, they seem to be largely correct):

Decapoda - 14.7 k species - rarely have nauplius, marine forms do have planktonic carapaced larvae (principally - zoea)
Isopoda - 10.7 k - no carapace
Amphipoda - 9.9 k - no carapace
Podocopida - 6.2 k - no carapace
Harpacticoida - 6.0 k - no carapace
Cyclopoida - 4.2 k - no carapace
Calanoida - 3.1 k - no carapace
Siphonostomatoida - 2.5 k - no carapace
Cumacea - 1.5 k - have carapace, but development is direct
Mysida - 1.2 k - have carapace, but development is direct
Tanaidacea - 1.1 k - have carapace, but development is direct

So, "majority" could be applied to Decapoda only.
Fabula:
If we substitute "adaptation" with "main biological function" (as you have done) or more correctly "main physiological role":
I would prefer the (a), because carapace does function as a protective structure in those decapod larvae which don't rely on behavioral anti-predatory defenses: see Morgan: "Fishes quickly learned to avoid spined prey, which ... may also increase the rate of evolution of the character". Non-carapaced larvae rely principally on behavior only.
The only contribution of carapace to planktonic life-style in zoea is participation of its spines [when they are pronounced] in parachuting (Chia et al).
[The above should be largely true also for the cypris larva of the cirripeadians, which are enclosed in a non-spined bivalve carapace.]
From the morphological point of view, [at least in adult forms of decapods] carapace creates a chamber for gills, so a morphologist would argue that this is the "main function" of carapace.


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What determines if an allele is dominant or recessive?
Going back to my high school days we were taught about dominant and recessive genes. We were taught how to calculate the geneotype and pheneotype of potential offspring using a small table (forgotten the actual table name). But it never occurred to me then what determines if a gene is dominant or recessive and how this is carried out biologically.
Take my example below, there is a 50% change that an offspring will carry both the tall (T) and short (t) genes. What determines that the tall gene T has a dominant effect over the short gene t.
Now, I know that there is going to be differences between the different genes (i.e. eye colour), but is there a general description any one and provide which states how a gene becomes dominant and how the dominant effect is carried out biologically.

A common cause is haplosufficiency, i.e. that a single copy of an allele will produce enought protein to create a heterozygote phenotype that is similar to the homozygote phenotype.

Which "why" are you asking? Do you mean "Why" like "why did it evolve that there is dominance rather that additivity?" or "why" like "what genetic mechanisms creates a relation of dominance between two alleles?"

If "why" meant "what evolutionary reasons" then, there are maybe two models that are worth talking about which are Fisher's model and Wright's model of the evolution of dominance

An interesting example I like is that horns on cattle is recessive, but having horns gives enough of an advantage that the trait became very common. But if you have a bull with two copies of the dominant no horns allele, none of your calves will have horns. Just an example that recessive traits aren't always rarer in nature.

Dominance is seldom complete. Owing to effects like co-dominance, incomplete dominance, collaborative (additive) effects of polygenes, our classical concept of dominance doesn't work. Having said that, there are certain ways in which a gene, if showing complete dominance can be analysed from the molecular level.
In an individual heterozygous for a certain trait, the following possibilities exist:

Both the alleles, though different, code for a protein (which might be an enzyme or a regulatory protein) which is functional and is indistinguishable atleast in terms of its functions. In this case, no matter if the person is heterozygous or homozygous for either allele, the concerned protein will be in sufficient amounts and will always be functional. These alleles can be treated as the same allele while performing Mendelian analysis though their products might differ slightly, leading to formation of two (or more) functionally similar Alloenzymes (as opposed to Isozymes which are similar enzymes produced by genes at different loci).
Haplosufficiency. In this case, one of the two alleles codes for a functional protein and the other either codes for a non-functional protein (or does not code at all). But, even in heterozygous condition where only one allele producing functional protein is present, the amount of protein produced is sufficient to show the phenotype and hence, even in heterozygous individuals, enough protein is coded for by the single functional allele exhibiting the normal phenotype. If the two non-functional alleles are present as a homozygous pair, no functional protein is synthesised and hence the phenotype is not shown (i.e a different phenotype is shown). Here, the functional allele is Haplosufficient (able to produce enough protein in heterozygous condition) and is called the dominant since it expresses its phenotype both in heterozygous and homozygous conditions. this is pretty common.
Complete Haploinsufficiency. Here again one allele codes for a functional protein while the other does not. But this time, if the functional allele is present in heterozygous condition, then the amount of the protein produced is not at all sufficient and hence the phenotype is not exhibited. Here the non-functional allele is said to be dominant because heterozygous phenotype resembles the phenotype of homozygous non-functional allele (where no protein is synthesized) since the functional allele is completely haploinsufficient (unable to produce enough protein in heterozygous condition). This method is pretty rare.(e.g rare autosomal dominant dyskeratosis congenita)

If there is partial haplosufficiency /partial haploinsufficiency, the phenomenon of incomplete dominance can be explained. (heterozygous individual produces protein not sufficient for a full-blown phenotype but just a partial expression of the phenotype)
Here, "functional" refers to being actually "functional" as in case of flower colour (anthocyanin synthesis) or just performing certain kind of a conversion leading to a particular effect on thephenotype.

Fisher and Wright provided two different models in order to explain why newly arisen mutations tend to be recessive. I am not sure though if this answer your question!
Fisher's model

"...there is a tendency always at work in nature which modifies the
  response of the organism to each mutant gene in such a way that the
  wild type tends to become dominant."
  Given that most mutations are deleterious, there is selection to make fixed mutations dominant over almost any mutations that could appear.

Wright's model

"...mutations are most frequently in the direction of inactivation and
  that for physiological reasons inactivation should generally behave as
  recessive."

There are 2 physiological reasons.
1) Deleterious mutations are mutations that usually cause a protein to not work properly. Given that the kinetics of reaction is usually not linear but is a function which derivative is decreasing over the number of enzyme, if we divide by 2 the number of functionning protein, we divide by less than two the reaction rate. Therefore, a deleterious mutation is usually recessive.
2) The reagents of a given reaction are often the products of another one. If this other reaction is slow compare to the reaction that followed, diminishing the rate the following reaction will not have a big impact on the rate of the overall metabolic pathway. Therefore, most deleterious mutations are recessive.
More information here
Note that there is a correlation between the impact a mutation has on fitness and its recessivity (the worst is a mutation, the higher is its recessivity).


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Does the Petri dish lid orientation on workbench affect aseptic technique?
When examining an incubated plate, it is rather clear that holding the plate in one hand and the lid in another is best for aseptic technique, or simply resting the lid on the plate as shown below.

However, I can't seem to find an answer for what to do with your Petri dish lid when doing manipulations like plating. It's pretty obvious that the above practice is, well, practically impossible.
Thus, I always went under the assumption that when placing the Petri dish lid on the workspace, the orientation of the lid did not particularly affect risk of contamination, assuming that you're technique is indeed aseptic (ethanoled workbench, Bunsen burner, etc). However, discussing with collegues has resulted in mixed answers. Some say it doesn't matter, some say the lid should be facing up, some say down.
When doing manipulations like plating, is there a common practice for exactly how to place your Petri dish lid?

What do you mean by plating here ?

Plating = Spreading.

If you are spreading then there isn't any need to put the lid down. One hand simultaneously opens the lid and holds the dish, the other does the spreading. That's what I used to do. However the best solution is to use glass beads - see http://www.youtube.com/watch?v=TACbj-ixW-U although ironically I don't think much of his lid technique!

@AlanBoyd why are those beads a good idea? I understand that they can spread liquid around very nicely but you then need to pick the things out one by one (there were 9 in that video) which means extra work, I would guess it takes more time to pick them out than to manually spread in the first place. It also means more time with the dish uncovered which increases the chances of contamination. Is the uniformity of the spread so much better as to justify their use?

I agree with the "plate lid facing down" comments below. Contamination falls, so keeping the inside surface of the lid away from the air column is always a good idea. I work with mammalian cell/tissue culture most of the time, and so always do all of my work inside a laminar flow biosafety cabinet, but when I'm doing cloning and whatnot with bacteria the lid is always off for as little time as possible, always faces down, and I always try to work in an area with as little air flow as possible.

@terdon You don't have to pick out the beads. Once you have "spread" you invert the plate as usual and they fall into the lid. After incubation,as you check the plates you can tip the beads out for reuse. I put beads onto plates before adding the liquid - the lid is opened slightly for a second or two. (I autoclave beads in glass tubes and tip a few on to each plate). The main advantage of the method (apart from no alcohol, no disposable plastic) is in plating a whole stack of plates: add beads, pipette samples and then swirl the stack all at once. Really, I recommend that you try it out.

@AlanBoyd Ah, that makes perfect sense, thanks. The video you had linked to showed the beads being removed one by one which seemed tedious. What you describe sounds much easier.

@terdon I admit, I didn't watch it till the end   - I just wanted a quick link to illustrate the idea.

DISCLAIMER: I am a computational biologist and haven't touched a Petri dish since I was an undergraduate biology student.
I would expect that the best thing to do would be to place the lid face down.
When placed so on the bench, it is only the tip of the lid that comes into contact with your (presumably sterile-ish) bench. If you place it face up, the interior of the lid will come into contact with the air of the lab. Despite the presence of the bunsen, I would expect that to gather more contamination.
Since the lid is larger than the dish itself, the lip of the lid never touches the dish. Therefore, if the lip of the lid touches the bench and becomes contaminated that is not a big problem since that contamination should be blocked from spreading to the actual culture. If, on the other hand, the lid were placed face up, the interior of the lid (which hangs just above your culture when closed) will have come into contact with possibly contaminated air and could then cause contaminants to drop onto your culture.

@LanceLafontaine I asked a grad student I know in the microbio department and she says the same thing as terdon.

Working with petri plates both microbially and in tissue culture, there is one rule of thumb to follow. Contamination falls. Your main enemy is time, how long the medium is exposed (bar actually touching the surfaces). Ethanol DOES NOT sterilize the working surface. Think of it as a convenient scrubbant which evaporates quickly. The flame DOES NOT work to sterilize the air (except in the heated column above it, where you can't work). The flame creates an updraft near your workspace (see the rule of thumb), reducing falling contamination.
Placing the lid on a "clean" working surface is a common and reasonable practice. If you are coordinated, holding the lid in the non-dominant hand can also be done. If you are using a 'hockey stick' spreader (dip in alcohol, then flame, then spread a dispensed drop after cooling), there may be a better way.
Get a good petri plate turntable (might have to lubricate it with dry graphite).
Dry your petri plates for a while until no free moisture is visible in the dish.
Obtain some small volume glass pipettes (say 1 ml), with smooth tips, and sterilize them.
When you are ready to plate your suspension, place your petri dish on the turntable, remove the lid and give a good spin.  Dispense 0.2-1 ml of your suspension onto the medium directly, working the tip on the medium surface from the center to the edge, keeping a wet edge (surface tension). If you press too hard or hold the pipette too vertical, it digs in. Quick to learn this though. Replace the lid, and rest the plate a little while on the bench. A perfect spread (slight spiral) every time. Okay, a little practice helps. No flame, no alcohol, more free time for beer. Moisture content in the media is the only issue, but drying the plates inverted in a standard microbial incubator is easy enough.
I've used this method for years, with no major contamination issues.

In my experience, I have always used some kind of selection marker (typically antibiotics). In this case, it doesn't matter at all because any miniscule amount of foreign contamination would not be expected to carry an antiobitic resistance gene.
Alternatively, when following sterile bench technique by wiping the benchtop with ethanol and working near a flame, then it also does not matter. The ethanol will take care of surface contaminants, and the flame keeps the air around it from being contaminated.  Also, when working with selection markers, the flame is usually unnecessary if the rest of your technique is aseptic.

Depends what exactly you are doing - fungal contamination can also be a problem, especially when working with yeast.

I agree, which is why, from my view, the orientation doesn't matter. However, I can see when it might.


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Growth Hormone and diabetes
Growth hormone and insulin like growth factors are diabetogenic, so I assume that people with high growth hormone (say due to pituitary tumor) may be at high risk for diabetes.  Has any correlation been established between these two? I know that diabetes is a multifactorial disorder and so only a correlation may be established.

Which type of diabetes mellitus are you interested in? Or both?

@leonardo I think this should not affect diabetes type 1 as dt1 is a mostly autoimmune disorder. So if some papers are available on this, I think, they would mostly be on type 2.

Yes:

That GH has an effect on glycaemic control is most evident from the abnormal glucose tolerance seen in acromegalics...

acromegaly is defined as abnormal growth of the hands, feet, and face, caused by overproduction of growth hormone by the pituitary gland.
Such an effect has been known for decades, which makes sense given how interrelated the axes are.  Although I think the best evidence is the fact that the side effects of growth hormone therapy says that Some patients have developed diabetes mellitus...


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Giving diuretics to insipidus patient
I read in Tortora and Derrickson that giving diuretics to diabetes insipidus patients may in fact alleviate the symptoms of the disease.  How is this possible?

Wikipedia has your answer:

It seems paradoxical to treat an extreme diuresis with a diuretic, but the thiazide diuretics will decrease distal convoluted tubule reabsorption of sodium and water, thereby causing diuresis. This decreases plasma volume, thus lowering GFR [glomerular filtration rate] and enhancing the absorption of sodium and water in the proximal nephron. Less fluid reaches the distal nephron, so overall fluid conservation is obtained.

The source for that is an editorial from 2004 that has some good other sources, including what appears to be the 1959 original paper finding this seemingly-paradoxical result.

Thiazide diuretics inhibit the NaCl co-transporter (NCC/TSC) in the renal distal convoluted tubule (DCT). The DCT is water impermeable and considered to be part of the diluting segment. Therefore, the water-preserving effect of thiazides is unlikely related to a direct effect on the DCT. In fact, the most widely accepted hypothesis suggests that the antidiuretic action of thiazides is secondary to increased renal sodium excretion. The renal sodium loss causes extracellular volume contraction leading to lowered GFR and increased proximal tubular sodium and water reabsorption. Hence, less water and solutes are delivered to the distal tubule and collecting duct and are lost as urine.


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Euthyrodism and goitre
I read in Tortora and Derrickson that goitre is associated with euthyrodism.
How is that possible?

I don't know the answer, but here is a fairly recent and highly-cited review that may be a good place to start: Krohn et al. (2005) Molecular pathogenesis of euthyroid and toxic multinodular goiter. Endocrine Reviews 26: 504-524

In this context, euthyroidism refers to the amount of hormone present.
What is a goiter:

The term “goiter” simply refers to the abnormal enlargement of the thyroid gland. It is important to know that the presence of a goiter does not necessarily mean that the thyroid gland is malfunctioning. A goiter can occur in a gland that is producing too much hormone (hyperthyroidism), too little hormone (hypothyroidism), or the correct amount of hormone (euthyroidism). A goiter indicates there is a condition present which is causing the thyroid to grow abnormally.

See also here and here for more of the same info.
ETA: According to this:

Chronic lymphocytic thyroiditis (CLT), also known as Hashimoto thyroiditis, is an autoimmune, inflammatory process that causes up to 55% to 65% of all euthyroid goitres...

Although, as the link I already gave above state, regular ol' iodine deficiency can still cause euthyroid goiter.

What condition can cause an increase in size of thyroid gland but still produce normal amount of thyroxine ? (I specifically want to know this.)