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Does any animal species have two sexes and more genders?
Are there any animal species that have two sexes and a kind of different internal diversification in two genders or more? I don't mean something like different-task-based diversity, but something biological?
For example let's imagine a species with:

2 sexes (male and female)
2 gender (A and B)

and individuals can match iff they are not only of different sex but also of different gender.
So you can only have Ma-Fb, Mb-Fa.

What sort of other classification are you thinking of? There are lots of different classifications, e.g. both male and female humans can have any of the four blood groups. Another example could be dogs (or a lot of other animal species) where another classification is race - each race has male and female dogs.

I would exclude those features because they don't determine directly the matching process (dogs don't match iff they are of different races, human beings don't if they are of different blood group). I've in mind some kind of upper-level biological feature, like sex is (different apparatus), that can influence sexual-selection.

You might find some things of interest with the search term 'alternative reproductive tactics'.

Your definition isn't very good. For instance, a monolingual German speaker and a monolingual French speaker are extremely unlikely to "mate" in a conventional reality (in fact, there is even evidence somewhat supporting this). Obviously it's preposterous to call them "different genders", however.

related: http://biology.stackexchange.com/questions/2738/why-do-only-only-two-sexes-exist-for-animals

The question is interesting but I think there is an issue of definition. Different sex necessarily imply different gender (the opposite is not true though).  Strictly speaking, any standard sexual species would fit your description. A woman can only mate with a man if they are of different gender (because they necessarily are of different gender given that they are of different sex). What you meant is rather something like: 2 sex and 4 genders (including the sexes).

I find this very unclear. Are you talking about specifically about gender (which can be hard to apply for non-human animals) or any kind of trait that can affect mating success and work as some sort of "mating type"?

@Remi.b That depends on you definition of gender. A fairly common definition is to see gender as a social construct (gender identity), which means that different sexes doesn't necessarily imply different genders.

@fileunderwater You're right!

Many organisms have multiple sexes. For instance, here is one which apparently has 7 (and each sex, or "mating type" can only mate with the others). The "gotcha" is that, mostly, they're unicellular organisms where mating in itself is weird to begin with. I haven't ever heard of a metazoan which truly has more than one sex (there may be variation within the males or females, but I think the sperms or eggs are always interchangeable).
Gender, I think, is more of a social term relevant to human behavior. Especially nowadays, so much of the literature and understanding of what is referred to as "gender" is closely linked to things such as gender identity, sexuality, gender roles and personality that is difficult to see how you could meaningfully speak about the "gender" of (non-human) animals.
It's analogous to the idea of "animal language" - certainly some animals may be said to behave in stereotypical ways which influence their mating behavior. Does that mean that what is written about human gender applies? I suspect precious little of it would. I would be quite skeptical of someone discussing gender (in the modern sense) for even uncivilized humans, let alone non-human animals.

Yes, it is called Alternative Mating Strategies and is well known. As an example High-backed pygmy swordtail (a fish) are known for having two types of males, one that is large and aggressive and another that is small and looks like a female to avoid aggression from other males.

There are hermaphrodites and gender changing (M->F, F->M) fish.  Also occasionally, there are also individuals who are neither male nor female, which may or may not count here.
However, I haven't seen 3+ separate genders except for fungi, which might occasionally be multicellular, but probably not what you are thinking of. Fungal genders are so many because they define combinations where mating is compatible.  This news story has a decent summary of why as far as gametes goes, larger animals are known to have only 2 gametic genders, while fungi can have thousands.  You might say that bacteria have gender when they want it (when they have a pili-containing plasmid) and otherwise they have none - any individual may transfer DNA to another under the right conditions (like death).
I know this isn't what you are asking about, but this is the closest I can find. Digging around, biologist Joan Roughgarden has written a book "Evolution's Rainbow" about cases where there may be more than one social role in a given species for biologically male or females - dominance, display, homosexuality and behaviors like this.  Social gender roles has been a way of talking about the biological nature of human social roles since the 1970s - see also Sarah Hrdy.

You're right when you say that social gender is the closest notion to what I might be looking for. A question: can a social gender of a certain individual change over time? If yes, I would exclude it from my research because I'm looking of something can't change naturally over time, as sex does.

I really believe the social gender can change over time - I think if you look around you will find lots of human examples.  Its harder to decide for animals but I'd be surprised there were no supporting cases to be found.  Animals including humans have this wonderful but slippery quality when it comes to their personality/identity - they can learn and change.  Large changes in social environment can usually change us all a lot. For people you should look at the Big Five personality tests - might give you some ideas?

Are there any computational model of sexual reproduction?

too many to count.  from cell division to population models.  ask a question, but maybe think about what sort of model you'd like.  pop = pop * 3.5 - deaths; is a population model.

I'm not sure what you mean by "gender" in the context of non-human organisms.  Gender is usually defined as the intersection between biologically determined sex, and the surrounding culture.
Maybe you could argue that in social insects like, say, ants, the fertile queen and the infertile female workers diverge so much in behavior and gene expression that they aren't the same "sex", or that they could be considered different "genders", but I  think that is really stretching the usual definitions of those terms.

The closest thing you will find to what you're looking for, I think, are animals with multiple different mating strategies where one sex (usually the male) can have multiple distinct phenotypes. Some examples include:
Patas monkeys, where some males are large and have harems of females while others are dubbed "sneak maters" and instead of having their own harem they sneak in and mate with females in another male's harem
Scarab beetles, where males either have a horn or lack one. Horned males defend their females at their tunnel entrances while hornless males sneak into tunnels to mate with females

(I also remember reading about this one species of waterfowl that had three distinct male phenotypes, but I can't remember the name off the top of my head, so if anyone else knows what I'm thinking of go ahead and comment)

Tetrahymena thermophila is an organism with 7 different "fuzzy" genders, not only male and female. Its seven sexes are rather prosaically named I, II, III, IV, V, VI and VII. An individual of a given sex can mate with individuals of any except its own, so there are 21 possible orientations. Here is the link: Zoologger: The hairy beast with seven fuzzy sexes

The white-throated sparrow has two sexes (male or female), but also has an addition "gender" (tan or stripe).
So male will only mate with female. AND Tan will only mate with Stripe
This behavior is probably due to a massive chromosome inversion of 1100 genes on chromosome 2. It is starting to cause the birds to act as if it were a second sex chromosome.
http://www.nature.com/news/the-sparrow-with-four-sexes-1.21018

The males of some Lake Tanganika cichlid species such as Lamprologus callipterus exhibit extreme dimorphism of behaviour and size (see e.g. https://www.jstor.org/stable/40407772). These represent alternative reproductive strategies for mating with the same female population though; the big aggressive 'nest males' attempt to guard a 'harem', while the small 'dwarf males' attempt to sneak in, exploiting the fact that they look similar to females and can sometimes deceive the nest males.
I'm not sure this is completely answers your question though. The assortative "Ma-Fb, Mb-Fa" example you give almost certainly does not occur (at least for long) since that would result in two reproductively isolated populations which would speciate rapidly.


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Do miRNA and antisense RNA do essentially the same thing?
Don't they both just disrupt RNA so it can't make a protein? If so, then what is the difference between the 2?

Antisense simply means that a sequence is the complement of another. miRNAs are naturally occurring antisense RNAs yes. The "difference" is that antisense RNA is often used for sequences developed in the lab and used for processes such as RNAi.
miRNAs, on the other hand, are encoded by the genome and are used by the cell for regulating gene expression. They do this through the RISC complex, just like artificial antisense RNAs such as siRNAs.
Basically, antisense is the general term, and can be applied to any sequence whose complement exists in the genome. miRNAs are a particular class of antisense RNAs.

@guest you're very welcome. If this answer solves your issue please take a minute and check the check mark under the vote count to the left, this will signify to everyone that your issue's been resolved.

Antisense RNA is any RNA that is complementary to another RNA. Therefore, miRNA is a type of antisense RNA. Antisense RNA can inhibit translation of mRNA by hybridizing and preventing ribosomal binding/translocation. Antisense RNA in this context could be any length and bind anywhere between the RBS and end of the CDS. miRNA also prevents translation but it does so through the RNAi pathway by facilitating binding of the RISC complex to mRNA (often in the 3'-UTR, which is after the CDS). miRNA are around 22 nts long (but it is species dependent).

Strictly speaking, it does not need to be complementary to mRNA. It can be complementary to any RNA moiety.

Thanks! I've updated it. If I had seen your answer I wouldn't have posted but I got sidetracked in the middle of typing mine and it got delayed.

No reason not to post! The more the merrier :)

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

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In the endomembrane system, after a protein leaves the rough ER, where does it go?
It can either go to the smooth ER then to the Golgi or it can go directly to the Golgi, right? Also, the smooth ER gets all of its material to synthesize things from the rough ER, right? Sorry, I looked around but couldn't really find a direct answer to my question. Thanks!

I'm no expert at this but will do my best to answer your question based on the title. It depends on the protein! proteins can either be cytoplasmic, nuclear, transmembrane or secretory. Cytoplasmic proteins (as far as I know) get released to the cytoplasm after they have been folded correctly (through chaperones) and gone through the quality control mechanism. Nuclear proteins get transported through the nuclear pores, across the nuclear envelope through chaperones. Now for the transmembrane or secretory proteins, the fate of these proteins and where they go is decided by the ER (but obviously the information is there in the protein sequence). Transmembrane proteins have a signalling peptide and a transmembrane domain signal anchor sequence which ER recognises and through fancy looping and elongation across the ER membrane, the proteins is further translated by the ribosomes and eventually gets translocated to the cell membrane. There is very very nice nature review paper (Rapoport, 2007) about this and if you look at Figure 5, you will get a good ideas as to what goes on. For the secretory protein again its the interaction of the protein sequence with the ER membrane, helped with the ribosomes (in fact the groves in the ribosomes are key for making these fancy looping happen as the protein residues in ribosomes interact with peptide residues (amino acids) that are being produced on the fly), that processes it and sends it for secretion (Rapoport, 2007) and trans-golgi network is also important in the secretion process (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1424219/).
Hopefully these information would provide you with some hints.

there are also scads of poorly or uncharacterized lipid compartments within the cell.  I'm not sure we can even name them all, but the proteosome is an example, as are the vescicles that recycle receptors like insulin receptor within the cell.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


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Getting xyz co-ordinates from a .map file (CCP4 format) in VMD
I have a .map file which contains x-ray crystallography data of a bacteriophage. The format of the file is CCP4. I can open the file using VMD. However, I am unable to get the xyz co-ordinates. It shows the following error when I click on the option of saving data in xyz format:
`No timesteps selected; trajectory file will not be written.'
It is a big file of 64MB.
The file I am referring to may be downloaded at:
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1086/map/emd_1086.map.gz
Can't we save xyz co-ordinates for CCP4 files? Or is it possible to extract any other form of data?
I am new to VMD and these formats.
Any help would be appreciated.

It's an electron density map. What xyz coordinates do you want to extract?

Just Download and Install: CCP4: Software for Macromolecular Crystallography

CCP4 is a suite of 200+ programs, just installing it won't solve any problem.


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Role of Calcium and Magnesium in capacitation/acrosome reaction
During the acrosome reaction, the activation enzyme present in the sperm dissolves the corona radiata and zona pellucida enabling the sperm to reach the plasma membrane of the egg.
Also calcium and magnesium ions play an important role in acrosome reaction [ref].
What I fail to understand is how exactly do calcium and magnesium ions play a key role in acrosome reaction?

The process is not clearly understood. Calcium helps in capacitation: During capacitation calcium enters the spermatozoa through ion channels; blocking these channels inhibits the acrosome reaction but what calcium does inside the spermatozoa is not very clear. This paper says that calcium activates a certain tyrosine kinase in the spermatozoa which in turn activates a protein called p32. This they say occurs "concomitantly with capacitation". Other papers cited by this article talk about involvement of calcium dependent adenylate cyclase.
This article also says that protein tyrosine phosphorylations are important for capacitation but doesn't describe how.
I could not find a more precise information on this topic. I shall update the answer if I find one.


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Why does the affinity of haemoglobin for oxygen increase at higher elevations?
Why does the affinity of haemoglobin for oxygen increase if an organism lives at a higher elevation where the oxygen pressure is lower?
Wouldn’t its affinity for oxygen decrease because the acidity of the body would increase with the lack of oxygen? The textbook said otherwise though and I don't understand.

There is a subsequent related question with answers here.

Possible duplicate of Why does the affinity of haemoglobin's for oxygen decrease at high altitudes?

@tchrist — The problem is that this is the earlier questio, and has an answer with votes. Could it be merged with the later one? I only flagged the link to the later question because I am trying to tidy up the questions on oxygen binding curves (there was another recently) so that anyone asking about this or searching is shown links to them all. (I had to add the haemoglobin tag to some of them.) It seems to me there are three types of question so far — Bohr effect, high altitude/2,3-BPG, and the interaction of the two. (No question about foetal haemoglobin yet.)

The question seems to be based on the idea that there would be physiological adaptation to low oxygen, possibly through the Bohr effect. In fact the usual mechanism of adaptation is through genetic change.
There are a lot of examples of animals which live (or fly) at high altitude and which have a haemoglobin with a higher oxygen affinity. Examples which spring to mind are the bar-headed goose and the camelids of South America (llamas, alpacas etc.)
Haemoglobin has evolved as an efficient oxygen-delivery protein by having a variable affinity for oxygen: low affinity at low oxygen concentration, high affinity at high oxygen concentration. This is achieved through co-operative binding (allostery), and it ensures that the protein loads up with oxygen in the pulmonary circulation but releases oxygen in the peripheral tissues.
At high altitude, where the partial pressure of oxygen is lower, the haemoglobin of humans, for example, will not be fully saturated, impairing the delivery of oxygen to the body. Haemoglobin variants with an increase in the overall affinity for oxygen can achieve full loading at the expense of slightly less release in the tissues - overall a better oxygen delivery function. This is what happens in the camelids, but there is no such adaptation in humans living at high altitudes.

Instead humans have more red blood cells when living in higher altitudes. This is why athletes train at high altitudes.

@Chris, in fact this isn't the case. It is true that if a sea-level dweller goes to high altitude the red blood cell count goes up (ertythrocytosis), and this is exploited by athletes. However this increases the blood's viscosity and can lead to unwanted complications. Tibetans have an adaptation which prevents this increase taking place in the first place.

Interesting. There are limits for a maximum hematocrit for athletes, if they go over it (this is mostly due to EPO doping) then they are not allowed to participate.


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How is the nasal secretion system of local immunity coupled with lymphatic circulation?
I started a thread about Nasal chronic Inflammation after influenza virus here.
However, I do not understand enough well the structure of the nose to answer the questions there.
I know that the lysed DNA (proteins) of small bronchial tree are circulated on the nasal epithelium.
I am not sure how this happens but my intuition is

first through lymphatic circulation
then on posterior nasalis membrane upward progression on the nasal membrane in the nares.

Picture about the nasal membrane.

Better pictures about the linkage of lymphatic circulation from the small bronchial trees into posterior nasal membrane are wanted.
However, I am not completely sure how this organisation occurs.
How is the nasal secretion system of local immunity (IgA) coupled with the lymphatic circulation around the back of the nose?

I know that the lysed DNA (proteins) of small bronchial tree are circulated on the nasal epithelium: Do you have a reference for this ?

@WYSIWYG Thank you for your question! This sentence was introduced by one leading researcher in the field last year in London. I contacted him about your question. I hope I can provide it to you.


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Advantages of bisexual reproduction over asexual one toward species promotion?
Are there any advantages of bisexual reproduction over asexual one towards species conservation and promotion? Do animals that have two or more sexes have more chances to reproduce?
Does anybody had a quantitative account of this fact?

Those are very good questions. Unfortunately answers are not easy and ask for writing a lot! But maybe someone else will give it a try and make it better than I can. Note that the evolution of recombination and of sexual reproduction are not quite the same thing. Also, evolution of sexual reproduction is not the same than evolution from various reproductive system. Finally there are also questions concerning the evolution of sexual determination system. You might have more chance to get useful answers  by splitting up your question and to ask for evolution between different reproductive system. Hermaphroditism vs Bisexual reproduction. Asexual vs sexual. And finally on another post you may add the "conservation" part of your question.
What do you mean "animals that have two or more sexes"? Do you mean hermaphrodites?
You may have a look to other posts on this sites that discuss the question. I don't think there is one post yet that really goes in depth though.
I think that would be great if someone could post an easy-to-read source of information on the subject. Here is one but it is in french only. This presentation by Sally Otto will probably interests you.
Some hints in very short: One issue with hermaphroditism is selfing and its associated concept inbreeding depression. For conservation purposes, note that if one beneficial mutation occurs (at any locus) before another beneficial mutation had time to reach fixation, then  the frequency of one of the two beneficial mutations will necessarily goes to zero. You may be interested in the two-fold cost of sex. Müller's ratchet is also a concept you may want to learn about. There are several very interesting quantitative models on the subject and it is still an ongoing debate. You may be interested in the work of S. Otto and B.& D. Charlesworth. You may be interested in E. Charnov's book although it is a bit old now.


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In genome research, what is the problem in Mapping that may be caused by reads being too short?
In the following scenario: You were given short sequence reads of plant RNA obtained from a next-generation sequencing machine (fragments of 20–30 nucleotides in length). You attempt to map them back to the genome, but a significant proportion of them do not align.
The question is: give some obvious explanations why the alignment of short sequences can fail, apart from possible contamination or technical difficulties during the preparation of the RNA.
I would answer it as because reads are short, and because of introns(since it is RNA)
Another scenario: There are some indications that the problematic sequences come from an uncharacterised plant RNA virus. What would you do next? What are the specific caveats with short sequence reads?
I got the above questions, I am a computer science student doing bioinformatics, any biologist could answer it will be well appreciated

Welcome to StackBiology! Your question very looks like a homework question. You should have a look to the homework's questions policy. Because you haven't really showed attempts to answer the question, it is likely that nobody will answer it. Also, you should always try to limit your posts to one question only.

@Remi.b It is not a homework question, it is a past exam questions. I have attempted several answers. Thank you

There is no correlation of fragment size with its likelihood to arise from an exon-exon junction.
Some reads may arise from the adapters. They are generally filtered out.

You may also be interested to look at RNA editing in plants. Again, this doesn't connect to the small reads issue.

Being a bioinformatician as well, I am not really what you asked for, but I work with plant genetics so I'll try and answer anyway.
What you are mapping is RNA. So, as you already figured out, splicing events will be a problem for end-to-end mapping of the reads. There are tools managing that, though, so let's assume you used one of them and still a lot of your reads do not map. To put in WYSIWIG's good point: Another event that can mess up with your alignments is RNA editing, although this is not too likely to cause a high proportion of reads to not align at all.
Some aligners might filter out "too short" queries, so make sure you are not using one of them.
Then, have you preprocessed your reads? If you have not, there might be adaptor sequences left. Or may reads have very poor quality, thus are also aligned with poor quality, thus might be counted as unaligned.
And then check what you are aligning to. Many published plant genomes are also of minor quality, including lots of unassigned bases. So, there could be large proportions of your reference genome that count in the genome length, but are only Ns and nothing will align there.
Last but not least, your thought about a virus could also be right. Depending on the experiment, there might be pathogenic RNA in your sample, so check against a suitable database.
If the problem is only that the reads are "too short" for whatever reason, try doing transcriptome assembly before comparing to your reference.

Dear @skymninge, the question is indeed a exam question, I am not actually doing the experiment but trying to answer them.

Well then all of those are possibilities and the exam question as such is fairly broad. To get an example answer, you will have to ask the person that held the lecture and graded the exam.

I don't think it's possible to answer part 1 without more information.  Specifically, are you using a splice aware mapper, like Tophat?  Are you using a predetermined gtf with putative exon coordinates?  If so, is it for an extremely well studied plant, like Arabidopsis, or something brand new?  Your answer isn't right, introns would align to the genome fine.  The aligner doesn't know or care that those sequence shouldn't be in the sample, that won't affect mapping.  Personally, I don't think there is a very good answer to the question.  Short reads aren't more likely to fail than longer reads.  They are more likely to map to the wrong place, but that's not failure to map.


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Elevated position effect on recovery times from upper respiratory infections at rest?
In nursing school, they advice for people with upper respiratory infections to be in a slightly elevated position at the head region when sleeping.
My intuition of the reason is that the lymphatic drainage to the venous arch works better; gravity helps to drain the lymph to the venous system; not only the heart.
Bacterial infection of the pharynx occurs in a prolonged exposure of the concentrated lymph.
I got today exact information about exact positions to relieve the body most when sleeping:

5-10 % angle to relieve body most, while gravity helping to suck the lymph from the throat; can be helped with the hormone motilium (domperidone)
more than 10 % is for other conditions

Is there any studies about the effect of elevated sleeping position on the recovery time from the upper respiratory infection?

Physiology
My conjecture.
The slightly elevated position causes greater venous return (work against gravity by smooth musculature and thoracic pump).
Why this is happening this way is partially based on my question here about Fast standing and the heart's insufficient accommodation of the increased venous return.

where the venous return reacts first the change in the position from supine by shifting the VR1 to VR2.
The stroke volume increases initially to SV1 to SV2, while the end diastolic volume from EDV1 to EDV2.
The increased stroke volume cannot be maintained long time so the cardiac output shifts to the right from CO1 to CO2.
So the initial stroke volume SV1 is the same as SV3 (not in the picture).
However, the EDV has increased (EDV3 >> EDV1) which increases much the lymphatic drainage.
Lymphatic drainage is not dependent on the stroke volume.
Increased lymphatic drainage then again increases the circulation of lymph.
This then again supports the recovery from the upper respiratory infection where the fine regulation between

the thoracic pump,
respiratory pump, and
smooth musculature

determine the final effect of the body position on the recovery times.
The size of the thoracic cavity puts some limitations, for instance.
Cardiology
In some cases, the upper respiratory infection can cause myocarditis.
This will decrease the functioning of the heart and cause possible

premature atrial contraction, and/or
premature ventricular contraction.

Elevated position helps small arterioles of left ventricle supply preload.
Otherwise, ectopic beat can be heard or also called "epics beat" which is sign of the two previous conditions.
The nurse is educated to listen to the patient and ask for possible jolts and flips in the chest.
Elevating position in such a case can help because of better supply for preload in the left ventricle.
Pathophysiology
Upper respiratory infection is often acute respiratory infection (acute respiratory distress syndrome).
There is an increased permeability of the vessels.
The fluids and plasma proteins are going through alveoli.
Acute hyaline membranes are formed.
Cytokines play a big role in this process.
To maintain lymph retention, the result of increased venous return compensates.
These patients can breath normally in the sitting position.
There are also other reasons for the infection:

overweight - the greater intra-abdominal pressure $\to$ more liquid diffused into the lungs OR other organs are suppressed.
Big chest suppresses lungs such that the architecture can change.

Pharmacology
There are different drugs which effect is dependent on posture and position of the body.
Hypertension is a common disease which amount increases during ageing in population.
Let's take hypertensive drugs as a case study.
Peripherally acting sympathoplegic drugs are generally dependent on posture more than centrally acting ones.
In hypertension treatment, the peripheral acting sympatholegic drugs are used often in combination with diuretics.
Blood pressure can be under control when blood volume is 95% of normal, but much too high when blood volume is 105% of normal.
So this study should be considered with no hypertension and hypertension.
Sources

For Pharmacology, Basic and Clinical Pharmacology, 11th edition, Katzung et all.


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Exocytosis of mast cell secretory granules
I've been doing a bit of reading about mast cell degranulation and have become thoroughly lost while trying to understand how the secretory granules are actually secreted.
I understand that there are many ways in which mast cells can be stimulated to degranulate, but I have been focusing on the example of IgE bound to FcεRI receptors. I believe I'm right in saying that antigen binding causes cross-linking of FcεRI receptors (since the antigen epitopes bind with the IgE paratopes and the IgE antibodies are themselves bound to the FcεRI receptors.) This recruits Lyn which phosphorylates ITAM motifs on the β and γ chains of the FcεRI receptors. This recruits Syk which is phosphorylated and activates LAT. This phosphorylates PLCγ which catalyzes the breakdown of PIP2 into IP3 and DAG.
All of this leads to the activation of PKC. I understand that PKC is (at least in part) responsible for the exoctyosis of SG but my question is by what means? Wikipedia, KEGG and this handy resource are all very cursory, whereas the academic papers which google turns up are way over my head.
So, if I might, what is it that PKC does and, in general, how are the secretory granules transferred from within the cell to the plasma membrane and out into the environment around the cell?

SG = secretory granule(s). I'm sure you already knew that if the above made sense to you, but I think it's good to be clear

I would say a complete answer warrants a literture review on the topic and you're not likely to get all the details here.

You might be right about that, that was certainly not my intention in asking the question, really, though; I don't know very much about cell biology and don't particularly want to, I'm writing about immunology. I just didn't want to simply finish my paragraph with ...which leads to degranulation, I was hoping for merely a 'bare-bones' description of what PKC then does, whatever it reacts with and a simple description of how exocytosis happens

Mast cells contain a number of large, granular structures that are regarded as “secretory lysosomes,” yet they share several features in common with large dense-core vesicles, particularly with respect to the mechanisms of exocytosis. Upon activation, mast cells "degranulate" and exotcytose the contents of granules.
SNARE-dependent mechanism mediates exocytosis of neurotransmitters, hormones, and cytokines. Exocytosis of MCG is also SNARE-dependent. SNARE proteins are a family of evolutionarily conserved proteins that facilitate docking of apposing membranes and facilitate the fusion of membranes to accomplish exocytosis. The characteristic feature is a SNARE motif, a stretch of 60-70 amino acids, arranged in heptad repeat. This feature allows SNARE motifs of the individual SNARE proteins (from opposing membranes)  to zipper together, forming a core complex of a four helix bundle. The major SNARE proteins involved in mast cell degranulation include VAMP-8 (integrated in mast cell membrane), SNAP-23 and syntaxin-4 (both plasma membrane bound). There are other layers of regulation of course. The SNARE accessory proteins synaptotagmin 2 (a calcium sensor), Munc13-1/2, Munc18-2 and complexin-2, exert negative or positive modulatory effects on mast cell granule exocytosis (Woska & Gillespie 2012).
EDIT: I don't know about PKC's involvement, but I can speculate that it's part of the signalling pathway after activation of the Fc receptor and upstream of events that initiate mobilization of intracellular calcium, which would then immediately trigger exocytosis. As for movement, if they're like dense-core vesicles, move along actin filaments using a myosin motor (Va or Vb, for example), and in association with Rab-3. This is speculation though, and I'd suggest looking into the literature for more detailed analyses as you are asking for a broad literature review.

Okay, thanks very much :) So where does PKC (Protein kinase C) come into it, do you know? Also, how do te secretory lysosomes actually move, as in, under what impetus to they travel to the membrane?

I've updated my response above.

You've already learned much more than I know about cellular cascades in mast cells, but I wanted to be sure you knew about this handy resource - a free, searchable "Molecular Biology of the Cell" textbook: http://www.ncbi.nlm.nih.gov/books/NBK21054/
For general explanations about cell biology, it's thorough and readable. For instance:

Transport from the Trans Golgi Network to the Cell Exterior: Exocytosis
B Cells and Antibodies

Carry on learning.

Here is a paper reviewing PKC action in exocytosis. Although it dates from several years ago it should be a good start for accessing the literature on this topic since it has been cited 90 times.

Morgan A. et al. (2005) Regulation of exocytosis by protein kinase C. Biochem Soc Trans. 33:1341-4.
PKC (protein kinase C) has been known for many years to modulate regulated exocytosis in a wide variety of cell types. In neurons and neuroendocrine cells, PKC regulates several different stages of the exocytotic process, suggesting that these multiple actions of PKC are mediated by phosphorylation of distinct protein targets. In recent years, a variety of exocytotic proteins have been identified as PKC substrates, the best characterized of which are SNAP-25 (25 kDa synaptosome-associated protein) and Munc18. In the present study, we review recent evidence suggesting that site-specific phosphorylation of SNAP-25 and Munc18 by PKC regulates distinct stages of exocytosis.

Having returned to this topic, I found this very handy journal article:
http://journal.frontiersin.org/Journal/10.3389/fimmu.2012.00130/full
Much of it, I'm afraid, is very difficult for me to follow, but I still managed to take a lot from it and I hope others may find it useful. I would summarise what I have found thus:
PKC and the increased levels of Ca2+ combine to direct the reorganising of the cytoskeleton through various intermediaries. The cytoskeleton is like the skeleton of the cell and it also provides the structure along which the secretory granules move to the cell membrane. The vesicle will bind with the cell wall and disperses its contents.
I have read suggestions that PKC may be involved in the process of the secretory granules fusing with the cell membrane. Wikipedia suggests that PKC is involved in severing the links between the surface of the secretory granules and the exoskeleton, allowing it to merge with the cell membrane.
Any corrections are obviously welcome.


text:
How does a Na+/H+ antiporter drive osmosis in this "osmotic motor"?
This recent paper in Cell describes a cancer cell using osmotic pressure to move in confined spaces. The cell preferentially inserts Na+/H+ antiporters in the leading membrane. I want someone to double-check my osmosis before I make students reason it out:

The normal Na+/K+ pumps cause an increase in Na+ ions outside the cell, but little change in osmotic pressure across the membrane.
Increased Na+/H+ antiporters will allow Na+ in while pushing H+ out at the "front" end of the traveling cell.
While this causes little net solute change, it increases water flow into the cell via aquaporins (?? this part I find mysterious)
Na+ continues to be pumped out of the cell by the Na+/K+ pump at the "back" end of the cell
Water follows the Na+ through aquaporins out the "back" of the cell, moving the cell forward

I don't feel convinced that moving ions around like this is causing osmotic gradients. Can anyone convince me?

Why don't you think that moving ions builds up osmotic gradients?

Because the same number of ions cross in and out - Na+ in, H+, out.

This means you are not building up apotential across the membrane (which would happen if you only transport ions in one direction), but you build up osmotic gradients. This is the reason why glucose is phosphorylated when it has been taken up by cells to remove it from the glucose gradient.

Sorry, I still don't understand how water flow can be triggered if there is not a net change in solute molecule number across the membrane... can you tell me more?

But how does an antiporter exchanging 1 solute for another build up an osmotic gradient Chris?

Since posting, I did some more research using background refs from the intro (who knew?).
The trick seems to be that when protons are pumped out, the cell regenerates them from water in order to maintain pH. So the solute concentration DOES increase inside the cell with more Na/H transport.

Thanks for the clarification, I was expecting something along the lines of that, but I had no idea about the specifics.

@Adrienne Can you make your comment into an answer (it is perfectly ok to anwer your own questions)?

Sure.
Typing more until this counts as a comment.....

Since posting, I did some more research using background refs from the intro (who knew?). The trick seems to be that when protons are pumped out, the cell regenerates them from water in order to maintain pH. So the solute concentration DOES increase inside the cell with more Na/H transport.


text:
Comparing Shine Dalgarno scores, creating a distribution
I am in the process of creating a poster for the phage that I recently annotated. The phage is an A4 and the portion of the poster I am working on is analyzing the data that we have collected. I have an excel sheet that has all the Shine Dalgarno scores for each gene that we annotated and decided was the best. Using mathematica I tallied all the data into a table and this is what I got (The x value of the list shows the score, the y value shows the amount of genes that had this score):
How can I create a distribution from this data? Would I need to use a Histogram, a plot, or some other graphic to represent the data?
Biologically speaking, can we make any observations about the genome from these scores?

you can use histogram to plot this data but I am not sure what your scores mean. In the end your figure should convey some relevant information..

me either - this print out is highly idiomatic to the software you are using...

Please give us the data in text form so we can work with it. It would be relatively simple to produce a histogram using R for example but I'm not about to copy it by hand.

{{441., 6}, {168., 1}, {378., 3}, {483., 8}, {462., 4}, {336.,
4}, {143., 1}, {587., 1}, {504., 4}, {819., 1}, {468., 1}, {567.,
5}, {351., 1}, {294., 3}, {399., 2}, {438., 1}, {588., 2}, {299.,
2}, {525., 3}, {426., 1}, {390., 1}, {609., 4}, {225., 1}, {693.,
2}, {420., 5}, {357., 2}, {672., 2}, {231., 1}, {315., 2}, {455.,
1}, {252., 1}, {273., 1}, {364., 1}, {300., 2}, {546., 1}}

I know what Shine-Dalgarno sequences are, but what are Shine-Dalgarno scores and how did you determine them?

I would expect to see if every gene has a strong SDS, and that every strong SDS is in a gene (and if not, an explanation of why).
Mathematically, that can be calculated using Fisher's Exact Test (since I don't see any p-values for your scores).
You should also provide a diagram of the genome showing coding sequences or genes, and mark each SDS on it.


text:
To diagnose osteomyelitis of vertebral column in chronic kidney failure
Assume you suspect amyloidosis because of the history of the patient: problem with vertebral column and "purulent" (serous, fibrous, or hemorrhagic) inflammation when patient very young.
Now, the patient has a chronic renal failure.
Is there any other method to diagnose the fracture of some bone than röntgen?
Assume you do not know where the fracture is exactly.

Osteomyelitis can be diagnosed with the following imaging techniques [1]:

first of all: radiography to view the anatomy of the bone
the sonography can be used to diagnose fluid collections, periosteal involvement. It is also the most useful procedure for kidney assessment [2].
CT is also useful to detect early osseous erosion, but is less sensitive when it comes to bone infection
MRI is the most sensitive and specific for osteomyelitis
Nuclear imaging can be used to identify multifocal osseous involvement.

References:

Carlos Pineda et al., Radiographic Imaging in Osteomyelitis: The Role of Plain Radiography, Computed Tomography, Ultrasonography, Magnetic Resonance Imaging, and Scintigraphy
American College of Radiology, Renal failure

Is there any techninques in Propedeutics to limit the area of the research. Assume you have no idea where the fracture is, not about side and how big fracture is.

You can look for the basic signs and symptoms of fracture http://www.webmd.com/a-to-z-guides/understanding-fractures-symptoms


text:
Can an insect poison itself with food?
Is it possible that an insect poisons itself while eating "wrong" plants/fruits/... and have symptoms like pain (may hard to measure or detect) or orientation disorder?
Background:
I observed a physically apparently healthy caterpillar moving in circles (or rather changing its direction constantly and end up at the same point again) on the street and falling over in middle of moving or standing. My first and a bit naive thought was, that it may have eaten something wrong...

this sounds like a parasite.  http://en.wikipedia.org/wiki/Behavior-altering_parasites_and_parasitoids

Indeed, many plants produce molecules which are poisonous to things that eat that plant (insect, mammal, bird) in the "hopes" of preventing that animal from eating them. In this sense, even eating the "right" fruit may be dangerous (if that individual plant happens to be an exceptionally vigorous producer of the poison, or because the eater is weakened for some other reason, or simply ate too much). I doubt insects would eat the wrong fruit that much, because evolution favors insects that can precisely recognize correct prey plants, at least in indigenous surroundings.
Indeed, many plant "flavors" that we humans enjoy (such as garlic and peppers) are likely such herbivore poisons that we happen to be immune to. In fact, almost every plant is actually poisonous - the question is, poisonous to which species?
Plant defense is a very actively researched topic these days, since it relates to things like agricultural efficiency and global food shortages (and besides, it's a very interesting phenomenon). Here is a review discussing what you ask about in more detail: http://www.plantphysiology.org/content/121/2/325.full
An addendum upon reading this question many months later: While evolution has perfected the ability of insects to recognize correct food, this has not been the case for man-made pesticides. I would guess that the caterpillar you saw is more likely to have eaten an artificial chemical (either pesticide or pollutant) than a "wrong fruit".

The article is really interesting, but explains more the plants point of view. I was a bit more interested on the actual affect of poison on insects.

@Zwie Here's another one: http://www.ncbi.nlm.nih.gov/pubmed/12179963

Caffeine is also one such toxin. A neurotoxin in insects...


text:
What information do microarray image convey?
OK I have read that a cell generates 4 kinds of digital (to be precise discrete) data namely DNA, RNA, Protein (sequences that can be encoded as string sequences of nucleotides/ amino acids) and micro array image. I am not a biologist, but my interest is in the statistics and information theory of these data. I would like to know what information do DNA micro array image convey? For example after processing it with the aid of a suitable software, what sort of information we do obtain?
Sample micro array image:

In the general case the color simply indicates how much of a specific RNA or DNA is in your sample. What you get out of this depends heavily on the exact experiment you're performing.

Where can I get more information? What is the relation of micro array image with gene expression?

http://en.m.wikipedia.org/wiki/DNA_microarray In the context of an expression level experiment, each spot represents a unique oligonucleotide probe. The relative colour intensity of each spot tells you the relative abundance of RNA in the cell that hybridizes to that probe.

The color is because of a fluorescent tag (Cy3/Cy5) attached to the DNA that you hybridize to the array.

Each spot overlaps with an oligonucleotide probe, that is designed to identify a specific nucleic acid sequence. Gene expression arrays have probes which are complementary to sequences derived from the exons; therefore they will hybridize with these sequences.
Before hybridization the cDNA (in this case) is labeled with a fluorescent molecule such as Cy3 or Cy5 (two dyes can be used to differentiate treated and control). Note that each spot will have many probe molecules.
Fluorescent intensity is proportional to number of hybridized DNA strands, which in turn is proportional to its expression in the sample.
Extensive amount of texts are available on microarray data analysis which you can find quite easily.


text:
Membrane potential after exposure to glutamate

Neurons were kept in a physiological solution. During the resting
  phase, the membrane potential in the axoplasm of neurons was negative
  compared to the extracellular space and a potential difference of -70
  mV was observed in this phase. Neurons were then treated in two
  different experiments with either gamma-amino butyric acid (GABA; an
  inhibitory neurotransmitter) or glutamate (an excitatory
  neurotransmitter) and the membrane potentials were recorded. Choose
  the correct statement/s:
(A) The resting membrane potential of -70 mV would not change with
  either GABA or glutamate treatments.
(B) The membrane potential would be even more negative than resting
  phase with GABA treatment.
(C) The membrane potential would be positive when the neuron was
  exposed to glutamate.
(D) The membrane potential would be more negative than resting
  potential after glutamate treatment.

I feel, since, glutamate is excitatory, so resting potential should decrease when exposed to glutamate and increase when exposed to GABA. So (A)&(D) automatically gets eliminated and (B) is correct answer. I am confused at (C)

This is a homework question, right? If so, please provide what you think about it, otherwise this will be marked off-topic.

@Chris Yes, this is a homework question. However, I am not being able approach the question. What do I do then?

No thoughts about it?

I feel, since, glutamate is excitatory, so resting potential should decrease when exposed to glutamate and increase when exposed to GABA. So (A)&(D) automatically gets eliminated and (B) is correct answer. I am confused at (C)

I dont think this should be closed please leave it open

positive membrane potential cannot be maintained...

It is more correct to call it "resting potential difference" (like your question), because electrical potential is relative, not absolute.
That phrasing exposes a crucial point: The difference of what? Cell cytoplasms are negatively charged (to remember this, it helps to remember that protons are usually pumped out of the cytosol either into the periplasm, vesicles, mitochondrial intermemberane space, or outside of the cell). If you subtract the potential of the outside from the inside, you'll get +70. If you do it the other way around, you'll get -70. By convention, the (+) probe of the voltmeter is stuck inside the cell, and the (-) is stuck outside, so we end up with the "official" figure of -70 mV.
Nature obviously does not like this potential difference, and wants to neutralize it by pushing current across the membrane. Luckily the membrane is not very conductive, and the cell can expend energy to undo the effects of any leaking and prevent the potential [difference] from drifting toward 0 (it would actually drift toward a number above 0 because potential difference isn't the only factor, there is also the concentration difference).
So the cell is like a battery that keeps itself charged. It also has a threshold, and it will only empty itself if it has discharged at least to a certain point. That point depends on the cell, but a typical value is -55 mV (so closer to equilibrium point than the resting -70 mV).
What will an inhibitory chemical like GABA do? It will pull the cell further away from the threshold, so it's harder to overcome it. Bringing -70 mV to -90 mV would be lowering it (because the number goes down).
What will an excitatory chemical like glutamate do? It will bring the cell closer to the threshold, so it's easier to overcome it. Bringing -70 mV to -55 mV would be raising it (because the number goes up).
The question, unfortunately, does not specify whether the action potential fires. Typically, the peak of the AP is +40 mV. In theory, you could have a threshold say, at +20 mV, and then perhaps the potential could go positive (eg. +10 mv) and stay there. But I really, really doubt you could find a cell with a threshold above 0. If the threshold is below zero, then the cell will reach a positive potential difference (if you use enough glutamate to elicit the AP), but it will only stay there momentarily before collapsing back to -80 mV (the refractory state).

Contrary to your answer, GABA does not necessarily move a cell further from threshold for an action potential or even necessarily change the resting membrane potential at all.  GABAa receptors, e.g. have a reversal potential around -70 mV.  See my answer.

@Chelonian To be honest I'm not an expert on neuroscience and I was not aware of this. My undergraduate neuroscience classes have always said GABA is inhibitory and hyperpolarizing, without emphasizing whether it is GABA-A or GABA-B. I assume that in such simplified discussions about ways of manipulating the membrane potential, when one says "GABA" without specifying subtype, it is to be understood that the more interesting GABA-B is meant.

@Chelonian Furthermore, even with GABA-A the potential would still go down if the cell's resting potential was above -70 to begin with, am I wrong?

I wouldn't say GABAb is necessarily "more interesting" (though I could see why one might feel that way). Given how important GABAa are, I would want to include both in any discussion. In fact, most initial undergrad treatments of GABA receptors start by making it seem like it is only GABAa (because GABAb is a metabotropic receptor and that's a more complex story to explain). And yes, if the neuron were sitting more negative than -70 mV, then even GABAa receptors would bring the membrane potential down to closer to -70 mV.

I believe C is also correct. The excitatory neurotransmitters open $\ce{Na}$ channels which makes the cell membrane more permeable to sodium as compared to potasium and therefore the equilibrium membrane potential would be much closer to the nernst potential for sodium. Now, since the concentration of sodium outside is much greater than inside, the nernst potential for sodium is positive with respect to the inside of the membrane. This makes the overall potential also positive.
If you want further clarifications regarding the calculation of the equilibrium and the nernst potential across the membrane, feel free to ask.
ADDENDUM
The approximate concentrations of sodium and potassium inside and outside a cell are :-
$$\ce {Na+_{in}}=10 \text{mmoll}^{-1}$$
$$\ce {K+_{in}}=105 \text{mmoll}^{-1}$$
$$\ce {Na+_{out}}=140 \text{mmoll}^{-1}$$
$$\ce {K+_{out}}=5 \text{mmoll}^{-1}$$
The Nernst potential is given by $E=-\frac{RT}{nF}\ln\frac{\text{in}}{\text{out}}$
Which for the given concentrations comes out to be $+67.7mV$ for sodium and $-78.1mV$ for potassium. During a sufficiently strong action potential, the relative permeability of sodium with respect to potassium becomes $10$. Using the GHK equation(ignoring the contribution of chlorine) gives us a net potential of $+47.5mV$.
The graph of the action potential clearly indicates that at the peak of the AP, the membrane potential is positive. Source : Graph of action potential

It would be helpful if you could add calculation of nernst potential.

@Rudstar Added in the answer.

peak is positive, but it won't be positive for a long time. the question is ambiguous in that aspect...

"excitatory neurotransmitters open Na channels":  Glutamate generally opens a mixed cation conductance of Na+, K+, and Ca++.  The equilibrium potentials for all three ions comprise the overall reversal potential, which is around 0 mV., not really near Na+'s equilibrium potential of +67.7 mV. (Also, it's chloride, not chlorine.)

I don't think any of the answers here are quite right, so I'll give a try:
(A) The resting membrane potential of -70 mV would not change with either GABA or glutamate treatments.
The answer here is:  "It depends".
For glutamate, if the neuron only had NMDA receptors that were not "open" at -70 mV, there would be no change in resting membrane potential. If there were at least some AMPA receptors, though, the membrane potential would change to more positive.
For GABA, if the cell has only GABAa receptors, then the resting membrane potential wouldn't change, because the reversal potential for GABAa is right there at -70 mV.  But if the cell had at least some GABAb receptors, their reversal potential is around -100 mV, and so would cause a change in the resting membrane potential to something more negative than -70 mV.
(B) The membrane potential would be even more negative than resting phase with GABA treatment.
Again, if GABAa receptors only, then no, it would be no more negative and would in fact stay the same at -70 mV.  If there are GABAb receptors, then yes, the resting membrane potential would be even more negative.
(C) The membrane potential would be positive when the neuron was exposed to glutamate.
Maybe--it depends on whether the neuron is allowed to have an action potential. Glutamate receptors generally reverse around 0 mV.  0 mV is neither positive nor negative. If there were no action potential in this neuron, we should therefore not say the membrane would be "positive" (though this is splitting hairs, I suppose). However it could be said to be "more positive than -70 mV". However, if the cell were allowed to have an action potential, then yes, the membrane potential would shoot up to about +20 mV, so could be said to be positive.
(D) The membrane potential would be more negative than resting potential after glutamate treatment.
No. Again, glutamate receptors' reversal potential is about 0 mV, so it would only move the membrane potential to more positive values, close to or right at 0 mV.

I suspect that you are over-thinking this likely undergraduate-level question: 3 of your answers are "maybe" and one is "none"; you are unable to execute the prompt of the question ("choose the correct one" whilst there is not a single statement that you think is correct). I'm not saying the exceptions you point out are not valid or important, but I think the question was meant to be definitely answerable, not open-ended.

@Superbest Sure I'm over-thinking it!  For fun. The point is, neuroscience is so darn complex that you can have fun with even the professor's questions which, in this case I think (and I may be wrong) actually doesn't have an air-tight only-one-correct-answer. In fact, I guarantee someone can come along and improve my answer because I left out some other corner cases (like the fact that there are some excitatory GABAa receptors in certain cases, and probably stuff I am not even remotely aware of). Along the way, I felt it was roughly still in the spirit of answering the question.


text:
Question regarding 2 constructs of tobacco plant
Six independent transformation experiments of tobacco leaf explants were carried out using
two different constructs - (1) construct I containing only a Hygromycin-resistance gene
$(HYG^R)$ as a selection marker and (2) construct II with the $(HYG^R)$ gene as a selection
marker and a passenger gene encoding a dephosphorylase enzyme $(DEP)$ that inhibits
phosphorylation in cells in which it is expressed. The marker as well as passenger genes
were placed under transcriptional control of a constitutive promoter $(CaMV35S)$, which
expresses in all cells/tissues. The results obtained are tabulated below.

Explain how The $HYG^R$ gene used in construct II lost its functionality probably due to
mutation(s) either in the gene or in the promoter.
My approach: There is a probability that Expression of the $DEP$ gene is lethal to the transformed cells.

Having a toxic product for the cell in an expression vector is a not uncommon problem when overexpressing proteins.
The other possibility is that the selection marker itself is the problem. Here you can have mutations either in the promoter of the gene as well as in the gene itself resulting in a protein which is not capable of protecting the cells from the selection. Both possibilities (no expression and mutated protein) leave to the death of the transfected cells, since there is no protection of them by the resistance protein.


text:
Is there a hormone combination that makes humans grumpy?
Imagine a typical situation that is likely to give rise to a bad temper within an individual: a person is awoken very early in the morning by a sound of a lawn being mowed next door.
Unlike expected awakening by an alarm clock, such unexpected awakening by a lawn mower is likely to leave the person in a bad temper, feeling grumpy or sulky.
I'm interested if there's a specific hormone or process that makes a person experience the feeling of grumpiness? Is it related to adrenaline and fight or flight instinct?
In other words, can experience of grumpiness be induced under laboratory conditions by using some combination of hormones/drugs?

I don't think morning grumpiness is related to adrenaline or fight/flight. It's more a matter of being irritated by the discomfort of abrupt awakening (at an inappropriate phase of sleep). "Grumpiness" per se is also poorly defined; for anger I am sure adrenaline and (if male) testosterone is often high, but I doubt just these hormones by themselves can induce anger (although they could make someone more prone to fits of anger).

I've seen anecdotal evidence suggesting that "low dopamine" contributes to irritability

I live in an apartment complex of 20 buildings. They used to send a huge loud truck around to empty the giant trash dumpsters, every Thursday at 4 am. It sounded like a war for about 20 minutes. I finally complained and they moved to 8 am. They still come around early once in a while though. I usually felt "grumpy" due to that! Who wouldn't? A completely stupid policy.

This is a hard question to respond to.
Many things might make someone grumpy.  There are also individual temperaments, making grumpy hard to quantify - a Grumpy to one person might barely be a blip on another individual's scale.  Hormones like cortisol reflect stress, and can make people in general irritable, but I doubt any one combination of hormones would always cause grumpiness.
But I thought I'd venture an answer since I did see this paper today:  "Low glucose relates to greater aggression in married couples" doi: 10.1073/pnas.1400619111
Being hungry will do this for lots of people, so maybe a bit of an answer for you. There are lots of different kinds of signals that mediate hunger though, so still a tough call.
Update: here's an additional article that specifically talks about parts of the brain involved in aggression and grumpiness as response to a drop in glucose.


text:
Can dish soap really be used to kill ticks and fleas?
An answer at Pets suggested using dawn dish soap to kill fleas. I did a little looking around, and found several references supporting the idea.  Most of what I found was in 'selfhelp' and 'save a dime' type books and web sites. So while it seems to be a popular idea, I am unsure if it is an effective idea.
Is there any reliable science supporting the use of dish soap to kill fleas and/or ticks? If so what points in the life cycle would it be effective?  If it does work, how often would I need to use it to be relatively sure all the fleas/ticks have been through the appropriate life cycle and are dead?

I think completely submerging a flea in water, whether with dish soap or not (probably the soap could reduce air pockets in thick fur) would drown it, much like most terrestrial animals. However, fleas may be able to survive it for a protracted period (like cockroaches) so you may have to keep your pet in a bath for quite some time. I don't think eggs would drown, but the soap could disrupt their casing, poison them, or simply stop the adhesion and make them fall off hairs.

First part of the answer - Yes fleas (Siphonaptera) can be drowned. But not as easily as the internet would lead you to believe.
There are many claims on the internet (and printed works) expounding on how simple it is to drown fleas.  The best science I found so far on the topic is in Forensic Entomology: An Introduction By Dorothy Gennard; John Wiley & Sons, Apr 30, 2013; section 4.3 which reflects a 1985 work by Simpson K. (Journal of the New York Entomological Society 76: 253-265, not finding this online). Gennard is using the fleas present on a human body at death to determine how long the body had been submerged.  Findings -

A flea submerged for up to 12 hours will appear to dead, but can revive in about 60 minutes after being removed from the water
A flea submerged for 18 - 20 hours will appear to dead, but can revive in  4- 5 hours after being removed from the water
It takes 24 hours of full submersion to fatally drown a flea

Side note; lice (Phthiraptera) can be fatally drowned in about 12 hours.

Second part of the answer - Yes soap can facilitate the death of fleas in bathing
So far the best I have is Medical and Veterinary Entomology by Gary R. Mullen, Lance A. Durden Academic Press, Apr 22, 2009

This work suggests the process of washing the flea (and the pet) removes integumental waxes on the fleas body and they die from desiccation (dehydration).

More Research
I have been unable to find solid research specific to fleas (Siphonaptera) and soap (surfactants), so I had to reach in to the general insect works for answers.  There are a number of pesticides which include surfactants in their make up to increase effectiveness but these seem to be to an aid in the delivery of the pesticide not because the surfactant has any additional killing power.

a surfactant may affect the efficacy of an insecticide by its influence on wetting, spreading and run-off rather than by its influence on cuticular penetration

The Physiology of Insecta, Volume 6 edited by Morris Rockstein
There is some science suggesting soaps can help break down cell membranes but they seem to be most effective on soft bodied insects (which fleas are not)

Soaps... kill insects by disrupting the exoskeleton and breaking down cell membranes.  Soaps generally work best against small soft bodied insects such as aphids, scale crawlers, meatybugs, and young caterpillars as well as spider mites.

Destructive Turfgrass Insects: Biology, Diagnosis, and Control By Daniel A. Potter
Summary
There are multiple online reports of "drowning fleas" and killing them with soapy water.  After looking for the science there does not seem to be much support for these fatal claims. There is little doubt that giving your pet a soapy bath in the tub will help remove the fleas, they may even appear dead.  But in all likelihood these fleas are just waiting to dry out and be revived, hopefully in the city sewer.  If you bath your pet in the yard, and than let the dry pet in the yard again the next day the clean pet and clean revived fleas will likely reunite. Soapy water is more likely to facilitate removal of the comatose flea from the pet and carry it down the drain. So it is reasonable to have noticeable decrease in the flea population after a bath.  But excessive bathing has it's own risks and given the life cycle of a flea soapy baths alone are unlikely to be a final solution.

Though it's not important to the point you made, we can't forget the additional effects of some chemicals used in certain soaps.

You have to use Lemon Dawn specifically because they have Limonene and Linalool from Lemon essential oil. There are actually registered patents on these compounds for use in killing and repelling fleas and other insects.

Limonene: http://www.google.com/patents/US4379168
Linalool: https://www.google.com/patents/US4933371

Lemon oil paralyses and can kill the fleas. After the bath you have to comb the dog with a flea comb to remove the fleas, eggs and larva. Do this once a week and your dog should be flea free. Lemon also repels fleas, so it prevents re-infestation.

D-limonene, a citrus peel extract, is toxic to adult fleas; products with D-limonene plus linalool control both adults and larvae. DO NOT USE THESE PRODUCTS ON CATS, AS SOME CATS HAVE ADVERSE REACTIONS. Only use products on pets that are labeled for use on the animal
source(idl.entomology.cornell.edu)

I have added a reference that supports this claim.  Note that some reference suggest that there is more research required, and that if Limonene and Linalool are not used in combination, they are known to be ineffective.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Base Substitution Probabilities Derivation
In Felsenstein's 1981 Paper Evolutionary Trees from DNA Sequences: A Maximum Likelihood Approach, he describes (in equations (6) and (7)) a derivation of the equation of the probability of a particular base substitution.  I am having trouble making the connection between equations 6 and 7.  That is, going from
$$P_{ij}(dt) = (1- u\  dt)\ \delta_{ij} + u\ dt \ \pi_j \quad\quad [6]$$
to
$$P_{ij}(t) = e^{-ut}\ \delta_{ij} + (1- e^{-ut}) \pi_j \quad\quad [7]$$
where $u$ is the rate of base substitution per unit time, $\pi_j$ is the probabiltiy of observing a particular base and $\delta_{ij}$ is the Kronecker delta function (1 if i=j, 0 if i != j).
In the paragraph that follows these equations there is an explanation as to why the exponential term makes sense (if you already know thats what it is), but I'm not understanding how to get from the first equation to the second. Any insights?
In case anyone is ever interested (or perhaps if I eventually forget), it appears that Felsenstein is using a Poisson Process approximation for equation [7], although even with this new information I still do no see the connection between equations [6] and [7].
Page 9 of this thesis had a pretty good explanation of this.

(1) There are two cases. For the first equation (6), the case $i \neq j,$
$$(1) \hspace{13mm} P_{ij}(dt) = u~dt ~\pi_j $$ if we have a transition from one base to another (for example G to C). In the case $i = j,$
$$(2)\hspace{10mm} P_{jj}(dt) = (1 - u~dt) + u~dt~\pi_j $$ holds for a same-base transition (G to G) or a non-transition (say, G and no change). Intuitively, we expect that, all things being equal, the probability of a base to same-base situation is slightly higher: it is the sum of probability that the base changes to itself plus the probability the base sits and does nothing in time $dt$ (with the same net result).

(2) Now we look at the equation(s) (7). Again there are two cases.
$$(1a) \hspace{10mm} P_{ij}(t) = (1 - e^{-ut})\pi_j $$
For case 2 (base to same base transition, $i = j$):
$$(2a)\hspace{13mm} P_{jj}(t) = e^{-ut} + (1 - e^{-ut})\pi_j. $$

(3) The author uses  $P(dt),$ $P$ at a very small (infinitesimal) quantity $dt.$ He tells us the leap from (1) to (1a) follows "almost immediately" when we see that $e^{-ut}$ is the probability that no base transition occurs. Well, then $(1 - e^{-ut})$ is the probability that a transition occurs.
Now $e^{-ut} \approx (1 - ut) $ (a truncated Taylor series) or $ut\approx (1 - e^{ut}).$ So for short times $dt$ we have $u~dt \approx (1 - e^{-u dt})$ and this explains his first equality $P(dt) = u~dt~\pi_j.$
So we have to recognize when he tells us about $e^{-ut}$ that $u t$ is the [truncated] Taylor series representation of $(1-e^{-ut})$ for $t$ very near 0. That is how he gets from 1 to 1a and (6) to (7).

(4) $(1 - u)$ is the probability that no transition from one base to another occurs in some short time $t_i.$ The probability that this happens over n consecutive time intervals is $(1 - u)^{(nt_i)}.$ Let $nt_i = T.$
Note that  $u \ll 1.$ We can write $(1 - u)^T = (1 - \frac{uT}{T})^T $ and
$$\lim_{T \to \infty} (1 - \frac{uT}{T})^T= e^{-uT}.  $$ This reasoning comes directly from that used to derive the Poisson distribution which is used to study rare events. See, for example, Deonier, Computational Genome Analysis, p.74.

It seems that you are giving a description of why equation [7] refers to the same probability in equation [6].  But this is only possible because you are given equation [7] already.  How would one arrive at equation [7] given only equation [6].  Is there a mathematical trick short of reversing the process you showed at the end of your post?

@fermats_last_nerve: The bottom line is that he only includes (6) because he begins with the probability $u$ and the statement of (6) is an intuitive re-statement of the English. He (or Kaplan before him) already modeled the substitution as a rare event, so he is just trying to justify (7) in the simplest way possible. The power series for $e^{-ut}$ is $1 - ut + \frac{(ut)^2}{2!}-\frac{(ut)^3}{3!}+...$ Someone working in this setting is probably expecting this trick. When I see $dt$ I think integration but his hint is generous enough.


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What is a suicide plasmid?
What is a suicide plasmid?
Example: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2737453/ mentions a "suicide vector". See also http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/plasmids/allele-exchange.html which also mentions them.

While the answer to this is quite straightforward (see mine below), finding a source is less so. I will accept an answer which provides an appropriate reference for the definition.

Check out this page - it has a long discussion of suicide vectors, and from the note at the bottom it was adapted from a published source.

As can be inferred from the Shanks et al. paper linked in the question: In molecular biology, "suicide plasmid" is a term that refers to a plasmid which is replication incompetent.*
Plasmids normally bear a sequence called "origin of replication" Ori which marks the plasmid for replication by the host cell. Plasmids that lack this Ori will not be replicated during cell division, and will become diluted away and/or degraded after a few generations. Hence the name: The plasmid will "commit suicide" by promptly becoming eliminated from the population of DNA molecules inside each cell.
Note that because not all Oris are universal, the same exact plasmid may be a normal vector in one species (eg. E. coli) and a suicide vector in another species (eg. P. aeruginosa) - which is logical: If a vector can't replicate in any species at all, how do you produce this vector in the first place? (there are ways, but they are laborious)

*: I am unable to find an authoritative source for this definition. The other two paragraphs are common knowledge.


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Transverse diffusion of lipids in red blood cells
The membrane of a human erythrocyte has polarity:

Phosphatidylethanolamine and phosphatidylserine are predominantly on the inner side.
Phosphatidylcholine and sphingomyelin are predominantly on the outer side.

Although these can diffuse in the lipid bilayer, they stay on only one side of it. How is this sidedness preserved?

Looks like a homework question. I would start by looking up flippases.

I need answer to this Question urgently Kindly plz help me..

flippases, and polarity is in many cell types, not just erythrocytes.

There are two reasons for the asymmetry for the lipid composition of membranes in cells usually.
The first which was mentioned by @Superbest is proteins which are called 'flippases' which describes three broad categories of proteins which facilitate the translocation of the lipids through the membrane, despite the fact that they all have polar or even charged head groups.
This is not really an answer to your question here though - they will have little to do with asymmetry of lipids in erythrocytes I think because the these proteins will only allow lipid diffusion to equilibrium on either side of the membrane.  To force an energetically unfavorable mixture of lipids they would require the use of energy.  While some lipid translocases can force the composition to change against the equilibrium, these seem to require ATP and human erythrocytes do not have mitochondria.
The second, probably better answer is that the lipid composition of a membrane at equilibrium is dictated by of the curvature of the membrane.  The outside of a membrane takes lipids with larger head groups and shorter or fewer chains, the interior will compose more of lipids with smaller head groups and longer and more aliphatic chains.
This capacity of a lipid to take up a greater volume in its head group vs its non-polar end is called its 'intrinsic curvature'.
Erythrocytes have some cytoskeletal structures such as ankyrins which give the cell its characteristic curvy 'dented lozenge' shape, which must also drive some of the lipid composition in some parts of the cell.

Erythrocytes still perform glycolysis for ATP generation.


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The use of proteins in memory creation
I have very limited knowledge of how the human memory works as I think, at this time, most people do. However, I have been reading and some articles which say, and I quote the article just linked

Memories are made by messenger RNA (mRNA) that encode β-actin protein.

Now, correct me if I'm wrong but proteins of any sort have mass. So, why following this rule of proteins being used to create the memory does our brain not grow in mass with each memory we create/ encode. And also, if our memories are encoded using proteins, why can neurodegenerative  (E.g. Alzheimer's) cannot be cured by artificial proteins in the same way we use insulin. I quote again,

memories were merely out of reach

full article
Surely this means that, it is possible to, by using artificial proteins or possibly electrical stimuli we could recover memories. Or have I wandered off on a wrong track here? Am I correct? Or are my concepts of memory slightly wrong?

Read about synapses; you'll be clear ..

I think its important to mention that the particulars of memory storage in the brain are still being worked out.  I think what we do know about it is that memory storage depends a lot on the physical configuration of the neurons in the brain.  They move about and make new connections as they process information (and probably also when they are not processing information!).  Different regions of the brain store short vs long term memory and different sorts of memories.  They neurons themselves have a lot of internal cell physiology that can change as well - there are many different neuroreceptors that constitute the synaptic junctions.
All these things may not be a comprehensive list.  But at the basis of all these processes, the cell expresses new proteins in mRNA and these proteins are doing all this work.  beta-actin and histone de-acetylase, as mentioned in your link, are responsible for the cell rearranging itself in the cell shape and in terms of its internal transport processes and in the nucleus respectively.
I'm pretty sure that exactly what is happening here is not really well understood.  monitoring the interior of the cell is difficult.  The work where histone deacetylase is inhibited is a fresh new thought, showing that the arrangement of the chromosomes in the nucleus is involved in hiding memories.  Its still the equivalent to getting a stopped watch to start again by shaking it - there are parts there that fell into place and started ticking again, but we don't really know what the parts are doing in any detail yet.
This hints that if you were to disrupt the cells in some ways you might be able to free up memory, but its a long way from guaranteeing that any given approach will work.  I'd be surprised even if Dr Tsai's cell treatment worked even 70% of the time in her experiment.  Hypnosis or a focused meditation session might still be just as effective.  I think that its a bit too much to expect that Alzheimer's memories are completely preserved and recoverable.  In some cases probably, but categorical statements rarely hold in bioscience.
Like a lot of neuroscience, this work is suggestive, but still just progress towards a clearer understanding of these processes.


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Gene perturbation, what is it used for, explain to computer scientists?
I am trying to build a gene regulation network, and I need some basic knowledge of it.
So, in gene research, we perturb genes. Such as knock down them?
Can people tell 2 or 3 experiment methods to perturb genes?
And 3 or more observations (phenotypes) after perturbation?
If it could be explained in the context of Microarray, it will be well appreciated.
The question is not that organised, if you can tell a whole story before the computational work started, I will thank you so much.

I'm afraid this is really a bit too broad. Perturbation can mean very many things from changing the expression level, to switching genes on or off, to altering the protein produced. The phenotypes will depend both on the particular perturbation applied and on the specific gene perturbed.

@terdon Thanks for your comments, What I am asking is how to perturb genes ? How to do experiments to perturb genes ? and what are the possible phenotypes/outcomes after perturbing ?

I'm not sure how you can explain it by microarray, since a microarray only gives a readout at a transcript level, and genetic purturbations can be applied down-stream at a protein level (say by expressing a mutant protein). Also, perturbation studies in vitro are quite diverse as terdon already mentioned. I would suggest reading literature for the types of questions you wish to answer, and see how they were addressed experimentally to better focus your question.

This questions doesn't fit the SE format too well. While there are several ideas that could be good questions on their own ("how can genes be perturbed?", "what phenotypes result from gene perturbation?", "how is gene perturbation used for microarrays?"), it seems like this question wants someone to write a report tailored to this person's research needs (how many future visitors will benefit from such an answer?).

@GeekCat, currently your question is too broad and actually includes several sub-questions. You are more likely to get a good answer if you break it down into distinct separate questions. For a start, I would recommend that you ask "What does gene perturbation mean in the context of gene regulatory networks and how is it achieved practically?" as this will help you to understand what else you need to ask.

Here are 3:
1) gene knockout.  Just delete the gene from the genome.  The function is gone - useful for demonstrating a direct involvement of the gene in the phenotype.  As a phenotype, the microarray will register all sorts of reactions to the loss of the gene in addition to the RNA in question being gone.
2) use selection to find mutants for the gene.  Expose the organism to a mutagen or high amounts of UV radiation.  Useful mutants vary by what the function of the genes are.  Temperature sensitivity - the gene doesn't function above 30 deg C is an example of a phenotype for a mutant that has been used classically.  In this case the functioning of the gene itself is a phenotype.  This is an example of a weaker perturbation.  Can be used when knockouts are fatal or when the system is too sensitive for a knockout.
3) change the environmental conditions. increase the concentration of a substrate or lower the availability of nutrients.  Phenotypes can be rate of growth/division, production of a given metabolite from the cells, but it goes on and on.
The affect on whole genome microarray data can be quite complex in such perturbation experiments because the coupling of many genes, even in bacteria can be broad and significant.

Thanks, @shigeta, could you please give 3 possible phenotype outcome of it ?

well the microarray itself is often the phenotype itself - RNA production.   That's why its so popular as a technique.  Mutant studies have a measurable phenotype such as a the amounts of a chemical that is produced in the cell, or the rate of growth.  Phenotypes are a very broad topic - they are essentially ANY observable w.r.t. a cell or an organism.  that's a very large list if you include observations by instrumentation.  Its akin to asking a mathematician to list all the properties of numbers.

Perturbation is when you either introduce a gene or gene product or inhibit it using a variety of approaches to see what other genes show changes in expression or other epigenetic modifications, which can be measured using a microarray.
If genes A,B,C,D,E are expressed more due to the activity of Gene X while F,G,H are unaffected, when you compare microarray data from samples where X has been turned off to those where it hasn't, you will see decreased expression of A,B,C,D and E - you can represent this as a graph with Gene X being the hub.
Hope this helps,
Ankur.


text:
Why do our eyes close when we sleep?
Why do our eyes close when we sleep? Is it to relax our eye muscles? How can it be explained from an evolutionary point of view?

The human optic nerve connecting an eye to the brain has about 1,000,000 or 10^6 fibres, each with a response time of about 1/100th of a second. In computer terms that accommodates a bandwidth of about 100 Megabits per second. We are awake in general for about 16 hours per day which is 57,600 seconds, so the brain receives from the eyes about 10 trillion or 10^13 informations bits per day. Under extreme conditions the the human brain can stay awake for longer than this, but its performance degrades significantly and becomes unusable at a week (168 hours) of wakefulness. During a week of wakefu

Our eyelids close when we sleep probably for the obvious reason that it prevents the sclera and cornea from drying out, becoming accidentally scratched (such as blowing dust) and allowing oxygen diffusion from the inside of the eyelid (to the sclera and cornea). Fragile corneas are a requirement for our vision. Thick corneas are much less fragile but then attenuates more light.
From terdon:
1) blinking requires muscle movement which sort of defeats the purpose of resting
2) closed eyelids offer much better protection than periodic blinking
3) if you can blink, you have eyelids.

@speedoheck 1) blinking requires muscle movement which sort of defeats the purpose of resting 2) closed eyelids offer much better protection than periodic blinking 3) if you can blink, you have eyelids. Why bother flapping the garage door up and down every few seconds when you could just close it and be done with it?

@speedoheck Because you need to be able to see of course! Take the car out if you like. In sleep, there is no such necessity. Also, we get a lot of visual cues from light and that affects the concentrations of certain hormones. I would guess that is also an important reason why our eyes need to be closed.

@terdon. if evolution gave us the protection of eyelids during sleep, why did it give us fragile corneas

Fragile corneas are a requirement for our vision. Thick corneas are much less fragile but then attenuates more light.

Perhaps all these comments should be added to the answer.

Can you explain that? The points I've raised are matters of physics and physiology.

Protection and relaxation can be answered by a first-grader. I was wanting to know if there was more

Why should there be more? Sleeping causes a state of paralysis, so it's better if the eyelids remain closed than open. Not to mention enviromemtal light directly modulates sleep/wake cycles, arguing again for closed being the preferred state for sleeping.

There's definitely something to the fact that eyes work better when they are closed periodically and don't work well when they are open constantly, but there is another angle to this topic.
I think its worth adding that not all animals sleep with their eyes closed.
This is because some animals sleep with only half of their brain at once.  Ducks, some birds, aquatic mammals like whales dolphis and seals engage Unihemispheric sleep.  In Unihemispheric sleep, half the brain is asleep and the other is awake.  Not necessarily fully awake, but enough that one eye is open and watching for predators or other threats.
One might ask - didn't we all have predators and threats?  Why don't we all sleep half the brain at a time?  The answer is not clear, but it appears that unihemispheric sleep is not a trait that is maintained easily.  Very few animals really have the ability.  As such there must be some advantages physiologically to closing both eyes at once and experiencing total sleep.  Once the threat is not so great from being sleeping prey, animals start to close both eyes pretty quickly.

is it necessarily the case that full sleep confers an advantage? Couldn't it also be true that unihemispheric sleep is advantageous but the requires very complex adaptations that have simple only happened in a few species? Or is the likelihood/difficulty of a mutation taken into account when biologists use the term "advantage?"

Great comment.  I think its the case the unihemispheric sleep is definitely an advantage!  Keeping one eye open must be very helpful.  You have hit the nail on the head.  the advantage of an adaptation must be large enough to eliminate the mutants that don't have it efficiently.  that is pretty much how I understand 'advantage': 'advantage' means an adaptation will stay around...

Through psychology, It shows that proper sleep aids in memory retention and learning. It could be possible that evolution led some animals/organisms to better retain information by allowing for full sleep compared to unihemispheric sleep. Just food for thought.

Tears contain an important hormone that kills bacteria. Closing eyelids during sleep allows a prolonged contact between the cornea and tears killing resistant bacteria in the process. The action of the tears during blinking is not sufficient to completely get rid of the foreign bodies in the eyes. Closing eyelids gives the tears a capacity to accumulate forming a film of moisture above the cornea and acqeous humour. This has many important uses. It allows dust particles to dissolve and be eradicated when the tears flow out of the eyelids. This partially explains the residue that is seen on the cheeks when people wake up in the morning in addition, of course, to the sodium and potassium salts in the tears. The other importance of the film of tears accumulated on the eye is to help keep the acqeous humour moist. This has a great effect on how the lens receive light and also on the overall refractive index  of the eye as system.

Any references to add to allow for background reading?

"an important hormone that kills bacteria" ... which is?

@AliceD One reputable source is: "Antimicrobial Compounds in Tears" (Jul 20 2013), by Alison McDermott, published on the US National Library of Medicine website. There are similar articles about lysozyme elsewhere.

@Rob - in that source I've searched for hormone and it's not mentioned anywhere in the paper. Please adapt answer and include the reference in the answer and not in the comments

I agree that hormone isn't there (or in relevant information elsewhere). Pride Chigs only used the word once in their answer. Whether they found something that I wasn't able to, confused hormone with enzyme, or confused the types of tears their properties and function, is unknown to me and will have to await a reply from the OP. I'm reluctant to make edits where the meaning (premise) of the question or answer is altered as reviewers are keen to reject such edits, and then I must successfully appeal (increasing the effort). So I suggested an improvemnt


text:
Color van der waals bonds in swiss PdbViewer
I'm trying to color certain amino acid's van der waals bonds as in the following picture:

can anybody please describe the steps to accomplish that?

Use Photoshop? Please clarify, I assume you want to do this using the same program that produced the image, so tell us what you're using!

If I'm right in assuming you are trying to get colouring like the purple AA VDW bonds then I can only specifically colour VDW bonds in solid 3D view (under display, Render in solid 3D) in SPDBV but not when solid 3D view is not activated, as in the example in your picture. One option is to use POV-Ray but I haven't worked with it.

@Bez thank you, so I guess it's possible only via 3d mode, please consider writing your comment as an answer so I could mark it as the right one

If I'm right in assuming you are trying to get colouring like the purple AA VDW bonds then I can only specifically colour VDW bonds in solid 3D view (under display, Render in solid 3D) in SPDBV but not when solid 3D view is not activated, as in the example in your picture. One option is to use POV-Ray but I haven't worked with it.
If the purple colouring is not photoshoped by the authors of the paper you got the picture from, then the chances are they have written a custom script for it in the software, which allows them to do this. So I would just contact the corresponding author and ask them how they managed it and if they have done it through a script or some other software. Most of the time people are happy to share their methodology once they have published it!
Also have you tried the Jalview software? Although it's designed primarily as an alignment tool but it has a nice 3D Jmol view. You can load up your sequence and the associated PDB file and you can play around with it. The graphics output are quite publication friendly. I'm not an expert at it and I've only been playing around with it for a bit but when you get the hang of it, it's quite nice graphically. Although the VDW view is still space fill 3D but it's a bit nicer as it has opacity etc etc. Just download it and as soon as you open it up, you are presented with an example alignment and Jmol view. Just play around with the alignment section and the Jmol view and see if you like the aesthetics. The only tricky part in the software is getting the residues you want selected but once you manage that, you can get the program to display VDW only for the selected residues.
Hope this helps.

You might also want to look at which version of SPDBV was used to generate that image. It's not uncommon that certain features of applications get disabled in new versions for whatever reason.


text:
What's the difference between Ki and IC50?
I have just read this post at researchgate: "How to calculate experimental binding free energy from the IC50 value"
I am not be very sure about what the difference is between Ki and IC50. Could anybody explain?

In biochemistry the Ki is the dissociation constant of a complex and molecules bound to it. It is a measure for the  functional strength of the inhibitor. This can for example be an enzyme and its substrate, the Ki defines the stability of the complex.
The IC50 on the other hand is the halfmaximal inhibitory concentration of a substance on a biochemical process. This can be an inhibitor of an enzyme.
See this figure (from the Wikipedia article on the IC50):

The Ki plays an important role in the calculation of the IC50, as it defines the strength of the enzyme-inhibitor complex.

I don't know if I'd call the Ki a measure of functional strength, I think it measures binding. It might be possible for a ligand to bind a protein tightly, giving it a low Ki, but not inhibit it, giving it a high IC50. But this situation probably only exists with allosteric binding sites, where a ligand can bind in a location separate from the active site.


text:
Drosophila grey / yellow
I am studying biology by myself via distance-learning. I have been trying to solve the following problem for a while now and hoped you could help me. As this is "homework" I would appreciate hints rather than solutions.

Drosophila has a gene "yellow body", $y$, on the X chromosome. The other, dominant, allele is "grey body", $y^+$.
When crossing female grey bodies  with male grey bodies we get 50% grey females, 22% grey males and 28% yellow males.
What is the genotype of the parents?

My work so far:
The genotype must be $Xy^+X?$ for the female and $Xy^+Y$ for the male.
There are two cases to consider: $?=y^+$ or $?=y$.
In the former we get $\frac{3}{8}$ grey females and $\frac{1}{8}$ yellow females and $\frac{2}{8}$ grey and yellow males each; that seems correct except for the yellow females.
In the latter, we get twice as many yellow females.
Perhaps the XXyy (yellow females) genotype is lethal but this doesn't help in determining the parents' genotypes.
If $? = y$ then cross-over from $Xy^+\mathbf{Xy} \; x \; \mathbf{Xy^+}Y$ would not eliminate yellow females.
I don't know of other effects to take into account, so I am stuck.
$ $
If you'd like to suggest resources (websites, textbooks $\ldots$) pertaining to this subject or on biology at this level in general, I would very much appreciate it.
Thank you.

Edit: I'd like to add an image for anyone having a similar problem.

Since Drosophila have the same system of sex chromosomes as human beings, (XY males and XX females).  Its clear that the sex determination is important - no females have yellow bodies. This is the key observation.
Amongst the males you have about 50%/50% Y/y phenotype.  This appears to be a classic sex chromosome related trait.  Does this help?  I can go further, but this should get you there.

Thank you for your answer, it did help. I made the problem more complicated than it is, the answer seems obvious now.

great to hear!  it takes some practice to get into this stuff !

@user34914 Although for your question, you can use the same system of sex chromosomes as human beings' , it actually is  more complicated. It also depends on autosomes. See this wikipedia article.

@user34914 Genetics - by Ursula Goodenough is an excellent book for studying classic genetics.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
What is the close and related genome used for in Gene models?
all
I am a little bit confused about using the related genome or reference genome.
When we have a reference genome, we can do alignment. Also we can do the assembly.
Can you give some more reason why a related genome can help to improve gene model ?
And if we do use a related genome, what kind of problems or caveats may occur there ?

can you please be more specific, like what species you have in mind and if you are talking about RNA or DNA?

Why a related genome helps:
1) Alignment of the reads first and assemble next.
 2) The gene-space is already predefined ( the genes and their co-ordinates are already known), so if your assembly is fragmented or missing a portion of the gene information, that can be accomodated with reference genome.
Limitations: Rather than assembling your own genome, you are forcing the reference genome to be part of your genome assembly. If at all, any differences are there, they are washed out, when you do a reference assembly.