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Where do amino acids get attached to tRNA and where is it synthesized?
Some very basic parts of transcription/translation seem to be left out in various literature. I can't find the answer to this anywhere:
How exactly is tRNA synthesized? I realize that mRNA is synthesized through transcription and I know a lot about that. However tRNA is supposedly synthesized the same way but every time you read about transcription they just talk about how the mRNA then gets this and that...?
Where do the amino acids get attached? Is it in the nucleus or outside the nucleus?
Thanks.

Does this answers some questions? http://en.wikipedia.org/wiki/Transfer_RNA#tRNA_biogenesis

A pre-tRNA is transcribed from tRNA genes in DNA by RNA polymerase III. Processing occurs in the nucleus, where a 5' sequence is cleaved by RNase P, the 3's CCA motif is added, and ~10% of the nucleotides are substituted. The tRNA are transported out via the pore complexes. Aminoacyl-tRNA synthetase enzymes attach amino acids in the cytoplasm in a 2-step reaction that requires ATP. You'll find there's a unique splicing mechanism in tRNA that additionally splices out an anticodon intron which is abesnt in mature tRNA's:
The wikipedia article notes RNA Pol III generally recognizes internal control elements rather than upstream control elements as in a normal gene.

Source: Qiagen

Source: Molecular Cell Biology. 4th edition.
Addendum: I said in my post that tRNA is charged in the cytoplasm, this is somewhat true. In mammalian cells, we also see that tRNA are charged in the nucleus as well, and it might aid in the export of some of these charged tRNAs. (Source)


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What is meant by nucleated in this context?
Hi I am little confused in one of my classes; because the teacher will say that " the actin is nucleated by the ARP 2/3 complex" or "microtubles are nucleated by the centrosome". Unless I am misunderstanding, I don't take this as having anything to do with the nucleus as in the nucleus inside a cell. ( or does it). so what does this really mean than?
Thank you

http://en.m.wikipedia.org/wiki/Nucleation

Cytoskeletal nucleation refers to the de novo formation of cytoskeleton filaments. If microtubules are nucleating, that means microtubules are being polymerized from lit. "From the beginning" by α/ß-tubulin dimers. So literally, and we see in the image below, Arp2/3 complexes act as progenitor sites so to say for new actin filaments by the "nucleation" of actin:

From wikipedia for Nucleation: "Nucleation is the first step in the formation of either a new thermodynamic phase or a new structure via self-assembly or self-organisation."

In this context, i feel nucleated means being a "core structure", a substrate for the organization of one or multiple polymer chains.

source: Stack Exchange

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Bolyerine Snakes maxillary bone, split?
How is the maxillary bone split in the Bolyerine Snakes described in T.H Frazzetta's "From Hopeful Monsters to Bolyerine Snakes?"
In T. H. Frazzetta, "From Hopeful Monsters to Bolyerine Snakes?" He describes boid snakes on the island of Mauritius as being unique among snakes in that they had a split jaw, connected by a joint. This was said to be an example of how continuous evolution could not be true for all cases, as what is the point of 1/2 of jaw, according to Stephen J Gould.
I dont seem to understand the pictures illustrated in the aritcle though, and how the maxillary bone is split and where it is connected to a joint. I could not find a legible picture of a  Bolyerine Snake described like this, if anyone could help with understanding it with a picture that would be appreciated.
I would provide the pictures, but I am not sure if that counts as plagiarism.
Citation:
Published by: The University of Chicago Press for The American Society of Naturalists,
Available from: http://www.jstor.org/stable/2459073

What figure(s) are you having trouble with in the paper?

@kmm              I cant find the figures pertaining to the Bolyerine Snakes that label the "split" in the maxillary bone.

If you look at Fig. 2 in the paper, the bottom jaw has the split maxillary bone. Do you see how it says "MX" with two lines, instead of "MX" with 1 line on the top skull from Fig. 2? Each of those lines go to part of the split maxilla, with the joint being where it is pinched off (between teeth 5 and 6 on the drawing). There is also a CT image of the skull somewhere online that I've run across a few times (actually saw your question while looking for that image now).
I would also amend your statement a little in that it is not "as what is the point of 1/2 of jaw", it is that you can't have 1/2 of the joint(or split bone) existing. Either the maxilla is 1 piece or it is 2, but you cannot gradually go from 1 bone to 2 (similarly, either the cartilage of the joint exists or it doesn't. There can be a gradual change in how much cartilage there is, but if it's there or not is a binary question).
I hope that helps, off to look for the CT scan!

Nice answer - welcome to Biology.SE! The second part of your answer might be better as a comment on the question, which only asks about the interpretation of the figure.

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How does the placement of it's motor domain affect the directionality of a motor protein?
I'm going over some of my notes, and I have written down that motor proteins with + cytoskeletal directionality have a reversed schematic representation relative to - directed motor proteins. Then I have this sort of image drawn. I just want to clarify it, since I don't remember this part of lecture at all.

Schematic representations

Kinesin: N terminal - |Head||Coils||Tail| - C terminal
Dynein: N terminal - |Tail||Coils||Head|| - C terminal

Does this look right?

I don't understand your question. Both schematics are the same, just written in reverse. The 5' end of an mRNA always codes for the N-terminal end of a protein. Perhaps your asking which protein domain (head or tail) occurs at the N-terminal end in each type of motor?

Sorry! It's been a long day. I fixed it to what it should've been. Now their motor domains are at the opposite termini.

"The direction in which cargo is transported is dependent in part upon the position of the motor domain, which can be located N-terminally (N-kinesins), C-terminally (C-kinesins) or internally (M-kinesins).  In general, kinesins with N-terminal motor domains move their cargo towards the plus ends of microtubules located at the cell periphery, while kinesins with C-terminal motor domains move cargo towards the minus ends of microtubules located at the nucleus." Source

@drowsy Feel free to roll back my edits if my understanding is inaccurate.

No. DNA, and RNA have a polarity in the orientation of their sugar-phosphate backbones, based on the numbering of the carbon atoms in the sugar rings. So, for example, we say that the sequence of this RNA is being read from the 5' to the 3' end, which indicates that the first nucleotide is exposing the hydroxyl at the 5’ carbon on its sugar ring.  At the other end of the linear polynucleotide the sugar is exposing the hydroxyl on its 3’ carbon of the sugar ring.
All mRNAs are translated in the 5’ to 3’ direction and all proteins are synthesized from the amino terminus to the carboxylate terminus, because the peptide bonds in the protein also have a directional polarity.
You appear to have mislabeled the N and C termini of Dynein in your diagram. Perhaps the  lecture was about the domain structure of these two motor proteins? And the point might have been that they each have three equivalent domains but in one case the part we call the head is synthesized first and in the other case the tail is synthesized first(?).

I did. Thanks for catching that. But thanks for your response. It makes sense. Basically one is translated motor first and one is translated tail first, right?

I don't know if that is true, because it has been a long time since I thought about motor proteins, but yes, that is what your diagram shows must be the case. I would go so far as to say that these two very large ATP-ases that Carry cargo along microtubules share related structural domains but since the proteins are modular you can mix and match the modules in different combinations

So, as I pointed out in comments, and requoting:
"The direction in which cargo is transported is dependent in part upon the position of the motor domain, which can be located N-terminally (N-kinesins), C-terminally (C-kinesins) or internally (M-kinesins). In general, kinesins with N-terminal motor domains move their cargo towards the plus ends of microtubules located at the cell periphery, while kinesins with C-terminal motor domains move cargo towards the minus ends of microtubules located at the nucleus."
And that was a short excerpt from Jennifer McDowall on Interpro. And then just surveying kinesins from the mouse genome,

Source: Kinesin superfamily motor proteins and intracellular transport
In terms of dyneins, however, I believe they're all (-)-directed motor proteins with the following general structure,

Source: The 2.8 Å crystal structure of the dynein motor domain
Keep in mind these representations are always expressed N-terminal (left) to C-terminal (right). So while your model for dyneins is correct, for kinesins this depends on the location of the motor domain.


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Horizontal Gene Transfer
I understand the different ways bacteria can undergo horizontal gene transfer (transformation, transduction (phages), conjugation (plasmids)).
Is there an experimental method to tell how a specific gene got into the host (during evolution)? For example if a gene A got into host X from species Y, is it possible to know how gene A was transmitted?

I don't understand your question. What exactly are you trying to determine/distinguish?
Would you mind re-wording your question into a clearer form?

@Soph - I've edited your question, to avoid closing the question. You can revert my editing, if you wish.

Very interesting question. My wild-guess is maybe yes by looking at the DNA regions around the gene. You would probably get some base pairs from the vector yet I am not sure how many and if this would be sufficient to map that back to a plasmid or a phage. Will look that up.

@cagliari2005 - I was thinking the same. Intehration to the host genome requires homology si most likely there are some remaining eytra sequeneces around the integrated gene.

If you're looking at evolutionary timescales, then the only available source of information is the target organism's genome sequence. At least some of the methods of horizontal gene transfer you mention leave a distinctive signature in the genome. For example, retrovirus particles that have become incorporated into the human genome are easily identified by their local DNA sequence.
So in terms of an experiment, you would sequence your specific gene of interest as well as the surrounding local sequence (say, 10,000 base pairs downstream and upstream of your gene). In at least some cases you would be able to say for sure "this gene arose from retroviral incorporation", whereas in others it would be more ambiguous.
References:
Belshaw, R. et al. Long-term reinfection of the human genome by endogenous retroviruses. PNAS (2004)


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What kind of experiments could you do to see which end of a microtubule is most dynamic?
I'm stuck between two ideas. Not sure which one of them would be best.

Do a FRAP on the middle of a MT. If it grows from the + end, that section will remain dark. If it grows from the - end, existing fluorescent tubulin will be pushed into the photobleached area. However, how would I be able to tell if the middle region is dynamic using a FRAP?
Introduce GFP-Tubulin into a cell. See where existing microtubules begin to fluoresce as new subunits are added.

Do either of these sound reasonable? Any better ideas?

This sure seems like a homework assignment. The methods for experiments like these were all published by the early '90's

As i remember, it has been shown that MTs are virtually indestructible in the middle. I'd say both sounds reasonable, but as soon as you start planning experiment, you get into trouble. FRAP seems most likely to succeed. Another one is FCS -- see where in the cell GPF-tubulin is most stable, e.g. closer to soma or axonal terminal (in neuron)


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What physical force attracts the anti-codon on tRNA to the codon on mRNA during translation?
What physical force attracts the anti-codon on tRNA to the codon on mRNA during translation? I know that these two bond together, but what actually makes the tRNA move through the cytoplasm to the mRNA on the ribosome?

Diffusion is the obvious answer. tRNAs bind to elongation factors which mediate the former's entry into the ribosome. I don't know if the cell possesses some mechanism to localize these molecules to sites of high protein synthesis, but it's certainly not outside the realm of possibility.

None, simply the brownian motion in action. @canadianer not impossible and I also never heard of such mechanism. Based on this paper, Figure 2D suggests cytoplasmic regions enriched in tRNAs (protein synthesis hotspots perhaps). Could also be background noise though.

As with many processes in cellular biology, nothing really moves anywhere, attracted by specific force. What that means, is that any molecule has a chance to interact with any other molecule, say, bind to it. Only force that is acted is electrical force of attraction of negative charges to positive ones.
Due to diffusion and temperature fluctuations, molecules wander around, bumping in each other. Sometimes, two complimentary molecules will bump into each other in a very desirable, energy-efficient orientation. Their atomic-scale interfaces (with tiny charges on it) will find each other as neat as hand finds glove of the right size/orientation neat and comfy. That is the way, for example, tRNA finds slot on ribosome/mRNA complex to plug into. just simple key-and-lock, or hand-and-glove model, that's all there is. And beauty is that you can try computationally calculate probability and energy of different interactions from molecular 3D structures.
Now, there are many tRNAs, but Glycine-tRNA will bind tightest to glycine-codon/ribosome complex. There is a chance that Alanine-tRNA will get in that spot, but that chance is very little compared to chance of proper interaction. Also, because interfaces of Ala-tRNA and Ala-codone don't match exactly, molecular vibration due to heat (temperature) will destroy this complex quickly. This allows specificity.

The Ef-Tu has an affinity for a factor binding site in the A-site of the large ribosomal subunit. When the anticodon of the tRNA binds tightly enough to the mRNA during translation, two adjacent adenines in the 16s rRNA of the A site crosslink (via hydrogen bonding) the grooves formed by the correctly paired tRNA, increasing the affinity for correctly paired tRNAs. I think those physical interactions are important as well. - From Molecular Biology of the Gene, 7th ED., by Watson.

I wanted to illustrate the process I explained in a comment on aandreev's answer with some images, I just copy/pasted the actual text sections, however.
From comments:
The tRNA is bound to an elongation EF-Tu (which is also bound to GTP). The Ef-Tu has an affinity for a factor binding site in the A-site of the large ribosomal subunit. You have an anticodon triplet on the tRNA, and a bend in the 3D structure of the anticodon loop gives you wobble base pairing on the last nitrogenous base. When the anticodon of the tRNA binds tightly enough to the mRNA, two adjacent adenines in the 16s rRNA of the A site crosslink (via hydrogen bonding) the minor grooves formed by the correctly paired tRNA. These adenines don't differentiate between G:C or A:T pairs, just the tightness/correctness of the tRNA binding.

In short, electrostatic forces and mechanical forces. Electrostatic forces are responsible for the classic Watson and Crick base pairing that is de facto  what brings together codons and anticodons. Mechanical forces are involved in the displacement of the pairing and the shift of the RNAs. The ribosome's subunits literally grab and move both messenger and tRNAs.


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Markers for human genetic mapping
For human genetic mapping several different types of markers are used:

RFLPs (Restriction Fragment Length Polymorphisms)
VNTRs (Variable Number of Tandem Repeats) such as mini- and microsatellites
SNPs (Single Nucleotide Polymorphisms)

What are the pro's and con's of using each type?
Do any of these markers have a specific functionality in human genetic mapping, or can they all be used for the same purposes?

RFLP is a technique not a marker., thus i deleted this from your answer, but you can revert it if you wish.

But can't one use RFLP paired with Southern Blot as a genetic marker?

RFLP is not a sequence property it's a technique to compare sequences usually over a small segment of DNA. You take your samples, digest them, and run them on a gel, and compare the patterns. Its good for allele diagnosis etc.

The restriction sites are the sequence properties. Some people will have a different amount of them. Otherwise there wouldn't be patterns (the RFLPs) to compare.  Hence you can use the RFLPs/restriction sites as genetic markers.

Yes restrictions sites are sequence properties but they are 6-8 bases long, so there are waaay too many of them. You keep using RFLP the wrong way, that is the name of the technique / phenomenon noting more. It`s not like VNTR or SNP. You can identify SNPs with RFLP.

I have rolled back the edit to the original version. There are many cases in literature of RFLPs being referred to as markers, which they are.

SNPs are much denser than RFLPs and VNTRs therefore the DNA resolution is much greater with SNPs. VNTRs were historically used for linkage mapping while SNPs allowed for association studies (e.g. GWA studies). Therefore your question goes down to what are the differences between linkage mapping and association studies.
They are both forward genetic methods which aim to identify a genetic modification provoking a trait.
The two major differences between both approaches are 1) linkage mapping requires a pedigree but can be performed using a fairly small sample size while 2) association studies can be performed at the population level but usually require a much larger sample size.
Both approaches require markers but for different reasons. For linkage mapping, markers, such as microsatellites, are used to delimit the genomic region associated with the trait and take advantage of recombination events in the genome to pin down that region. This, of course, requires both 1) recombinant individuals in the pedigree and 2) at least one marker that is co-inherited with the trait. Linkage mapping allows to find virtually any genetic modifications, such as a genomic deletion, but only in the case of a genetic modification showing high penetrance.
For association studies, markers are the actual genomic modification themselves (usually SNPs) and are used directly in statistical tests (often a logistic or linear regression) for association with the trait. This means that either 1) the causal marker is available or 2) at least one marker is highly co-inherited with the causal mutation (i.e. in linkage disequilibrium). Association studies allows to find both low- or high-penetrance mutations, given a sufficiently big sample size. Also an association study can be conducted in the presence of a non-discrete (i.e. linear) phenotype which one cannot use in linkage mapping.
Another difference is that linkage mapping does not require any a priori knowledge of the genomic modification causing the trait while association studies do (as markers are statistically associated with the phenotype).
Usually both methods will highlight, with varying resolution based on the phenotype and markers used, the genomic region causing a trait but rarely the actual causal mutation will be found with 100% certainty.


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Do you know of ways that help a plant to produce more flowers?

In Crocus sativus, or saffron crocus, the most commercially important part is the stigma of flowers. Each plant produces one flower (so there is more than one plant in this picture) and each flower has three stigmas (stigmas are red in this picture). What are the possible mechanisms to produce more stigma in a plant for commercial cultivation?

There are few hormones that may help you.

This question might be a better fit on Gardening.SE

Each species of flowering plant produces a set number of floral parts, more or less. Having three styles and three stigmas per flower is a trait that is determined genetically. Mutations can cause floral parts to be duplicated. Heirloom tomatoes have mutations in the fascicated and locule-number genes, resulting in more locules being produced per fruit. Mutations in the fascicated gene also cause increases in other floral parts, such as petals, sepals, and stamens. If you compare a regular tomato to an heirloom, you'll notice that heirlooms tend to have around 10 petals and sepals compared to a regular tomato's 5.
Now the question is, do such mutations exist for Crocus sativus? A quick Google search didn't turn up anything other than the normal three-stigma flowers, so it doesn't look like such a mutation is common, if it exists at all. My answer to your question is: there is no easy way to get a saffron flower to produce more stigmas, for if such a method existed, everyone would be using it. I don't doubt that a dedicated botanist could come up with something (crossing with a related species, perhaps), but it's not something you can likely accomplish in your home garden.
Edit:
User Sleepses found an article where a high-yielding mutant with 5 stigmas was obtained through gamma radiation mutagenesis. I'm not sure whether or not this mutant is for sale commercially, though.

What about multiple flowers per plant, as asked in the title?

Found an article documenting C.sativa with five stigma obtained with gamma ray random mutagenesis.

@Sleepses Very interesting! I'll go ahead and append that to my answer

One way getting most attention is re-deriving Crocus sativus again.
Crocus sativus (with autotriploid chromosomes) is derived from Crocus cartwrightianus (diploid). ref for this is https://www.sciencedirect.com/science/article/pii/S1055790319300879
This article talks about resynthesizing the triploid https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4549961/
You could breed crocus relatives to have abundant and tasty flower parts. Possible ways without genetic modification could be:

grow a genetically variable population of Crocus cartwrightianus, and do mass tasting to find an suitable plant.
do a genetic comparison to find the genes that are responsible for the taste, then search through the variable population for plants with that combination of the genes needed.

Ya I was going to suggest polyploidy using colchicine or something. Colchicine is a powerful poison coming from a spring-time bulb in europe. It mutates chromosomes by preventing meiosis, and results in plants with extra chromosomes, which give profusive branching and double flowers. Generally, you can be sure that very adept botanists are trying to make saffron a bigger crop, and you can write a thesis on it. Biotechnology is very difficult to engineer.

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Cholesterol's role in lipid uptake
I'm studying the digestion of fats and I understand that our dietary fats mostly consist of triglycerides. We absorb the fats and eventually they end up in a muscle/adipose cell for storage (as triglycerides) or for oxidation for energy.
However I don't understand exactly where cholesterol plays in? I read about lipids being synthesized by the liver being exported by VLDL and then taken up by cells. We're moving closer to cholesterol here but I still don't see the connection.

Can you be a bit more specific? Are you asking about the role of cholesterol in cells in general, or its function in lipoproteins, specifially in VLDL, or ... ?


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Involuntary twitches and apnoea during early phases of sleep
I assume most people either experienced or have seen people with the following phenomenon: in the early phases of sleep sometimes involuntary twitches occur that usually accompany the pause of breathing (I'm aware that there's a  chronic sleeping disorder called sleeping apnea but I think it's different because what I'm asking about now is acute). I wonder if the twitching is some sort of emergency signal, so that the person would wake up (to some level not necessarily full awake) and start breathing. Is there any data that these (the pause in breathing and the twitches) are connected or they are independent? Also I'm also interested why this acute pause of breathing occurs?
Edit:
I've researched myself on this topic and it seems that what I've described is more likely a form of Obstructive sleep apnea.

After a discussion I would like to mention that the assumption that "most people have experienced a paucity of breathing" during sleep may be unfounded. The 'sleep starts' are a very familiar phenomenon indeed. However, the paucity of breathing aspect is not & needs clarification, preferably by identifying the cause, or by naming the phenomenon instead of assuming everyone knows what you are talking about. Take this as an objective critique to draw in answers.

Jerk-like muscle contractions occurring while drifting off to sleep are normal and are referred to as "sleep starts" or sleep myoclonus (National Institute of Health - NINDS).
Sleep Education explains the symptoms:

Sleep starts usually consist of one strong jerk that affects much of the body. The arms and legs are most likely to be affected.

So sleep starts may be quite vigorous, but may consist just of small lip movements too.
The American Sleep Association mentions that:

Sleep myoclonus will rarely disturb the subject or any bed partner to the point of waking and disrupting sleep [...].

In fact, sleep starts are associated with tachypnea, i.e., an increased in breath rate (Vetrugno & Montagna, 2011)
Hence, your hypothesis that a myoclonus is a mechanism to wake a person up (for whatever reason) seems unsupported.

Reference
- Vetrugno & Montagna, Sleep Medicine 2011; 12: S11–S16

Thank you, but this is not  I was looking for. What I was talking about is the pause of breath and a twitch affecting entire limb(s) or the body. The text you've linked says that myoclonus only affects lips toes etc - small body parts.

I edited the answer.

Thanks for the edit,but it seems you keep missing the aponea part of my question. Can you link the sleep education part please?

Maybe someone else can elaborate. I have experience related to sleep EEGs and linked to epilepsy (myoclonic seizures). The apnoea part is unknown to me and unrelated to myoclonus afaik.

After researching myself I've found what I've added as edit. Since you put much effort in your answer on a not well formatted question that helped me a lot, in my research, and realize that my question already has an answer on the internet.


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Regulation of V. cholerae virulence factors
So I know that several different environmental signals, such as pH, bile, and temperature, regulate virulence gene expression in V. cholerae. Specifically, they control expression of the genes encoding the toxin co- regulated pilus (TCP) and cholera toxin (CT).
But what are the two key (main) transcriptional regulatory proteins that control TCP and CT expression, and where is each localized in the bacterial cell? Also, what does each protein do?
I know that the proteins involved are ToxR/S, ToxP/H, and ToxT, but I don't know which are the MAIN ones and why...

Virulence factors of V cholerae is regulated by a hierarchical regulatory system. The proteins you listed in your question are part of this system. In this paper it is said that the actual activation of TCP and CT is done by ToxT- thus this could be your "key" protein. I'd also like to note that just because these are two different genes does not necessarily mean that there has to be two key factors - this assumption of yours if a bit faulty.
Also because the activation of the virulence factors are regulated by a chain of events, each link is can be considered equally important, because if one of them fails the whole chain is dysfunctional.
The short description of the regulatory chain taken from the article linked above:

The ToxR regulon is a hierarchical regulatory system that activates virulence gene expression in response to environmental stimuli (2). Induction of the ToxR regulon starts with activation of tcpPH expression by AphA and AphB (4, 5). AphA and AphB are cytoplasmic regulatory proteins that cooperatively bind to the tcpPH promoter and activate its expression. Once TcpP is produced, it functions in conjunction with ToxR to activate toxT expression. TcpP and ToxR are structurally similar membrane-bound DNA binding proteins that are thought to modulate gene expression in response to external stimuli (6, 7). When stimulated, TcpP and ToxR bind to the toxT promoter and activate its expression. ToxT then directly activates the expression of the genes that encode for CT and TCP production (8).

This paper might also be helpful. Unfortunately I could only access the full text this way (through researchgate):
Regulation of virulence in Vibrio cholerae: the ToxR regulon.
Brandon Childers, Karl E Klose
Future Microbiology (Impact Factor: 4.02). 07/2007; 2(3):335-44.
DOI: 10.2217/17460913.2.3.335
This paper provides details of regulation and mechanism of ToxT.

Taken from the third linked paper. As you can see the final activator of CT (termed CTX in the picture) and TCP is indeed the ToxT, but as I wrote it earlier each link in the chain is important.


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What is the chemical composition / empirical formula of Herpes Simplex 1?
Viruses such as polio are so well documented that a search for "empirical formula polio" gives you something like
 C332,652
 H492,388
 N98,245
 O131,196
 P7,501
 S2,340

We know that the virus consists of 70% protein, 22% phospholipid, 6.5% DNA, 1.5% carbohydrate (from the book Herpes Simplex and Pseudorabies Viruses by Kaplan)
Is there any information on the actual chemical composition of HSV1 and varieties?
Thanks!

Welcome to Biology.SE. What do you mean with atomic arrangement?

Thanks!  I'm mostly curious about the chemical composition in elements like in the above.

Thanks! Arrangement sounded like you were interested in the spatial relationships between (all the) atoms

You should modify your question as people are giving misplaced answers.

I doubt that such a formula exists for HSV 1, and for good reason: It actually is one of the most massive viruses known

I'm voting to close this question as off-topic because the atomic composition of viruses has no relevance to contemporary biology.

The Herpes viruses have a unique four-layered structure: a core containing the large, double-stranded DNA genome is enclosed by an icosapentahedral capsid which is composed of capsomers. The capsid is surrounded by an amorphous protein coat called the tegument. It is encased in a glycoprotein-bearing lipid bilayer envelope 1.

You can watch an animation of infection and steps of replication here, and below the video, they say that

HSV is a nuclear replicating, icosahedral, enveloped DNA virus. The HSV envelope contains at least 8 glycoproteins. The matrix or tegument which contacts both the envelope and the capsid contains at least 15-20 proteins[2].

In this definition of the structure, they at least assigned some values to the makeup. Additionally, in wikipedia, the viral genome is listed which I would recommend you take a look at as well. It can be found here but here is the synopsis of the table
UL1 through UL56
US1 through US12
RS1, ICP0, LRP1, LRP2
RL1, LAT

Additional resources:

HSV Genome 2nd link
The use of microarrays to analyze gene expression
Structural properties of HSV promoters
Animation of the Construction of a HSV-1 DNA Microarray for Global Analysis of Transcript Abundance
Animation of the Time-dependant Changes in HSV-1 Transcript Abundance During Productive Infection
Some Genetic Functions Encoded by Herpes Simplex Virus type 1
Herpes Simplex Virus Oligonucleotide Probes used in the DNA-microarray


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What percentage of cells in the human body are infected during a non-fatal viral infection?
I understand that this would be a very rough estimate, but approximately how many cells in the human body are infected during an average non-fatal viral infection before the infection is eliminated by the immune system? It doesn't matter what virus you use as an example, I'm just looking for a general case.
Thank you,
CDB

The following isn't really an adequate answer because (1) HIV dynamics aren't typical virus dynamics and (2) this tells us how many cells are killed, not how many cells are infected. But in case it is useful, there are roughly 2*10^11 CD4 T-cells in an adult and untreated HIV eventually infects and kills the large majority of those.

Actually, that's about the answer I was looking for. Feel free to transfer it to answer form (if you want). Anyone else with information/sources pertaining to this please don't hesitate to post them, I'll take as many cases as I can get. Thanks.

Different viruses infect different cell types. You should narrow this down. Do you mean what percentage of "target" host cells? And it also depends on the viral replication dynamics

Given that Corvus' answer gives a nice and interesting global estimate worthy of an answer, I think the question should not be closed - but an edit is definitely appropriate to narrow it down a bit. -1

I was really just looking for cases/studies, I don't care which virus they use, that's totally up to the answerer. I thought that if I narrowed it down it would just decrease my chances of getting any sort of an answer. I'm still in the beginning stages of setting this project up, so it's highly adaptable. Seeing as I was looking for a broad selection of answers (thus I did not limit the acceptable answers by adding too many details/requirements), I do not believe this questions needs editing.

This is now basically answered at https://biology.stackexchange.com/questions/93782/what-fraction-of-human-cells-gets-infected-during-a-viral-infection.


text:
How is circadian rhythm of gastric acid secretion regulated?
Gastric acid secretion shows a circadian rhythm where acid production in the morning is minimal and it reaches a maximum towards the evening.
How is this process regulated?

I'd suggest reading wiki first.
Autonomic nervous system, the one that regulates breathing rate, heart rate and other physiological processes as a function of circadian time, regulates secretion of gastric acid. Vagus nerve, part of parasympathetic nervous system (the one responsible for "rest and digest" part of behavior, opposite to sympathetic "fight or flight") stimulates secretion of gastric acid and regulated through circadian mechanism.
See also here, Circadian variation in gastric vagal afferent mechanosensitivity:

Thus, gastric vagal mechanoreceptors display circadian rhythm, which may act to control food intake differentially at different times of the day.

This is another interesting review: Gut clock: implication of circadian rhythms in the gastrointestinal tract. It states that GI tract has its segments set their own circadian clocks, different for various segments. But all of them are operating and adjusted by main clock, regulated by, as I know, melatonin and orexin hormones.
Surprisingly, not much seems to be known about this connection. Pineal gland seems to be very important in this process, because it produces melatonin.

Thank you, I especially found the last reference interesting!


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Why is 5S-rRNA is different from other rRNAs in place of transcription and usage of RNA polymerase?
While transcription of rRNAs happens in nucleolus mediated by RNA Polymerase-I, we see that 5S-rRNA is transcribed elsewhere by RNA Polymerase-III. What is the cause and why?

Nice question :)

The three RNA polymerases (RNAPs) are very similar to each other, yet not identical. As described in this article, there are subunits that are specific for each type of polymerases.

In addition to providing unique substrates that polymerase-specific subunits bind to give each of the RNAPs their specific functionality, the two largest subunits also shape the active site cleft of the enzymes where the transcription reaction occurs.

The results of the linked article also claim that even though the cleft loops are conserved regions, there are significant length differences between the three polymerases.
Also rRNA gene is similar to the tRNA genes and they differ from other genes in the recruitment of the polymerases. "Traditional' promoters are located upstream the start site, while 5s rRNA gene and tRNA genes have one and two boxes respectively that recruits RNAPIII.

The 5s rRNA and tRNA genes have promoters within the coding region of the gene.

source: http://mol-biol4masters.masters.grkraj.org/html/Gene_Structure5C-Eukaryotic_Promoter_Structure_for_RNA_Polymerase_III.htm
Here are two images form the linked page:

Edit:
In this article it is described that 5s RNA genes have translocated severeal times throughout evolution, and on of the mechanisms for this could be analogous of the second class of SINE elements, that contain internal RNAP III promoters, and are derived form tRNA (this could also indicate the similar structure to tRNA genes).
From this good review Evolution of multisubunit RNA polymerases in the three domains of life
 I'd like to take one short quote that might help:

...The structure and function of some of these factors are conserved across the three domains, whereas some non-homologous factors show an intriguing level of structural and functional similarity, suggesting that convergent evolution has led to alternative means of facilitating the same process.

Though you have mentioned how a certain polymerase identifies its target genes (by promoter architecture), you can add some more details on why certain RNAs require a separate polymerase. This is especially required in the case of Pol-I and Pol-II since both transcribe non-coding housekeeping RNAs. The OP is actually interested in knowing why all rRNAs are not transcribed by the same polymerase: possible evolutionary reasons (perhaps).

I re-read the question and realized that I answered the cause part of the question only and missed the why part. I'm sorry for that, I'll look into it. Thank you for pointing this out!

This article suggests RNA Pol III formed early in eukaryote evolution, and while there's a lot of conservation, the enzyme-specific subunits result from divergent evolution. Another article suggests the actual increase of subunits, however, is a result of the permanent recruitment of transcription factors to the core RNAP by studying homology of subunits to existing TF's. So if you were to ask why another polymerase? The article suggests gene duplication events. There are homologs for every RNAPII subunit in archaea, and and the subunits unique to RNAPI and III are homologous to transcription factors for RNAPII (TF's denoted TFII...). They further conclude that,

The first RNAP duplication event(s) likely resulted in
  two RNAPs: RNAPI and the ancestral RNAPII/RNAPIII. This
  is supported by the existence of three homologous proteins
  that are found in the RNAPII and RNAPIII transcriptional
  systems but with no homologs in RNAPI. The first two proteins
  are TFIIE a and b that are found in RNAPII and that
  are homologous to RPC82 and RPC34 in RNAPIII, respectively.
  In contrast, RNAPI lacks a homolog of either subunit
  of TFIIE, indicating a loss of TFE in this RNAP. Thus, the
  ancestral TFE was likely lost along the RNAPI lineage
  but maintained in both RNAPII and RNAPIII following
  duplication of the RNAPII/RNAPIII ancestor. The third
  such protein is the archaeal TFB, which is common to both
  RNAPII (where it is named TFIIB) and RNAPIII (where it is
  named TFIIIB-BRF) but absent from RNAPI (fig. 4). These
  recruitment events resulted in the expansion of the number
  of RNAP subunits from 12 in the ancestral eukaryotic
  RNAP to 14 in RNAPI (Kuhn et al. 2007) and 16 in RNAPIII
  (17 if we include the unikont- and plant-specific RPC31
  protein; Proshkina et al. 2006).

So in speculation, if you had to ask why a different polymerase, the evolution of the two lineages of RNAP's dictated a different binding/initiation motif for what are perhaps (retro)viral or (retro)transposable elements [the tRNA and 5s rRNA genes]. This is still under investigation, however.


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NADH shuttles - Why cytosol?
Why is the malate-aspartate and the glycerol-3-phosphate shuttles located in the cytosol and intermembrane space?
The krebs cycle happens in the matrix so why wouldn't they push electrons from the matrix and into the intermembrane complex for oxidative phosphorylation??

The electrons for shuttling are mainly generated in the cytosol from glycolysis. NADH can easily pass the outer membrane, but must be shuttled over the inner membrane. It is important to consider that the electrons must be fed to oxidative phosphorylation from the matrix of the mitochondrion, and not the intermembrane space.

I believe more NADH is generated during the citric acid cycle rather than the glycolysis? You say that the electrons are mainly generated in glycolysis?
Also is this shuttling mechanism only used for the electrons generated by glycolysis and NOT the ones made in krebs cycle (as they are already situated in the matrix)?


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What is the difference between sinew and tendon?
I wonder what the difference between sinew and tendon is. I searched for it but didn't get any clear answer:
https://www.quora.com/Whats-the-difference-between-sinew-and-tendon:

They are often used interchangably but to be technical, a tendon
  connects a muscle to a bone. The term sinew also seems to include
  ligaments which connect bones to bones. It is however, not a medical
  term.

https://answers.yahoo.com/question/index?qid=20070410182936AA2Kcnk

Sinew is another word for muscle which is the functional unit of
  movement.
Tendons connect bone to muscle to make movement possible: The muscle
  contracts and pulls the bone that it's connected to Source(s)

http://the-difference-between.com/tendon/sinew :

Sinew is a synonym of tendon. As nouns the difference between sinew
  and tendon is that sinew is (anatomy) a cord or tendon of the body
  while tendon is (anatomy) a tough band of inelastic fibrous tissue
  that connects a muscle with its bony attachment.

http://www.thefreedictionary.com/sinew

sinew = tendon

https://en.wikipedia.org/wiki/Tendon

A tendon (or sinew) is a [...]

Is sinew a synonym for tendon, and if not what is the difference?

They get used somewhat interchangeably, which blurs the lines on the definitions.
When I had my anatomy classes, sinews were regarded as an inclusive class, which included both ligaments and tendons.
For the breakdown:

Tendon: Fibrous tissue that connects muscle to bone.
Ligament: Fibrous tissue that connects bone to bone.
Sinew: Includes both of the above.

A tendon is a fibrous connective tissue which attaches muscle to bone. Tendons may also attach muscles to structures such as the eyeball. A tendon serves to move the bone or structure. A ligament is a fibrous connective tissue which attaches bone to bone, and usually serves to hold structures together and keep them stable. So sinew = tendon. Sinew is a bit more general and somewhat ambiguous. It is mostly used today synonymously with tendon, but historically it has been used to mean either tendons or ligaments, or even to mean muscle.

Please provide a citation or link to supporting evidence. Thanks!


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What is the purpose of gluconeogenesis?
The gluconeogenesis pathway seems quite pointless to me. I don't understand why an organism would want to spend energy to create a molecule that can then be metabolized again for less energy? The pathway seems only to serve as a complete waste of energy?
Can someone explain why we have gluconeogenesis and when it is used?

Gluconeogenesis is not the reversal of the glycolysis, but the generation of glucose from non-carbohydrate precursors (like odd chain fatty acids and proteins). The reason why we have this process is because some organs and tissues can only use glucose as their energy source. These include the brain (although ketone bodies can be used here as well), erythrocytes, testes and the kidney medulla.
Usually the glucose for the supply of these tissues comes directly from carbohydrates in food or storage carbohydrates as glycogen or starch, but when these are not available, the body has another way to get around this problem and to avoid the starvation of these tissues. See for example here and here.

fatty acids are not a substrate for gluconeogenesis.

@AliceD Fatty acids are no direct source for gluconeogenesis, but where does the necessary Acetyl-CoA come from? For example from the beta-oxidation of fatty acids.

I thought the backbone of the glucose as the end product is not structurally related to fatty acids, but to the substrate of GNG such as amino acids. As the answer is formulated it reads like fatty acids are converted to glucose, which is not the case. I thought an essential feature of metabolism in general was that sugars can be converted to fatty acids, but not the reverse. Hence the problems people have to reduce bodily fat. GNG doesn't take fatty acids in as a substrate. Correct me if I am wrong.

I will make the answer clearer later today.

@AliceD In a way, we are both right. Odd chain fatty acids can be oxidized to propionyl-CoA which is then converted into succinyl-CoA and further into pyruvate, which can enter the glucneogenesis pathway. Even chain fatty acids are oxidized to Acetyl-CoA which enters the TCA cycle but cannot be used for making glucose. It's good to have the thick biochemistry books at hand :-)

Before discussing gluconeogenesis it is necessary to be clear on the following:

What organism you are considering
Under what physiological circumstances gluconeogenesis is occurring
What is the substrate for gluconeogenesis

and, if one is considering mammals:

Which tissue is performing the gluconeogenesis
Which tissue(s) will consume the glucose produced

because these latter two are never the same,
or in other organisms:

What is the glucose produced actually used for

MAMMALS
Gluconeogenesis is performed almost exclusively by the liver, which is able to provide the NADH and ATP for this process from its oxidative metabolism. (The kidney also has a small capacity for gluconeogenesis, but the reason for this is another question). The tissues consuming the glucose are predominantly erythrocytes, brain and nervous tissue and muscle, depending on the circumstances.
Resting post-absorptive ‘lactate recycling’
Erythrocytes have no mitochondria so can only respire by anaerobic glycolysis, reducing the pyruvate to lactate (in order to regenerate NAD+). The lactate goes into the blood, and is taken up by the liver and oxidized to pyruvate. Gluconeogenesis converts the pyruvate to glucose which passes back into the bloodstream, restoring that used by the erythrocytes. (The brain also uses glucose here but I’ll deal with it below.)
‘Lactate recycling’ in exercise
Muscle has a certain aerobic capacity depending on type. However in vigorous exercise the skeletal muscle becomes anaerobic and obtains ATP for muscle contraction from aerobic glycolysis, again producing lactate. The liver glycolysis recycles this lactate to maintain the blood glucose, as in the previous section. (This overall co-ordination between tissues is often called ‘Cori Cycle’ in text books. However the name can be misleading, as it is not a chemical cycle like the tricarboxylic acid cycle or the urea cycle.)
Starvation
In starvation the net supplies of energy will fall. However the one tissue that must be kept supplied with a glucose is the brain (even though it can obtain part of its energy requirements from other sources). Liver gluconeogenesis provides this, but substrates other than lactate are need to restore the glucose lost by net consumption after the liver glycogen reserves have been depleted. The main gluconeogenic precursors are a subset of amino acids from protein breakdown (the so-called glucogenic amino acids) which feed in at different parts of the pathway. Glycerol from the breakdown of triglycerides can also be used, but fatty acids themselves cannot, because they are converted to acetyl CoA, which condenses with oxaloacetate to feed into the tricarboxylic acid cycle, and produces no net carbon skeleton that could be used for glycolysis.
PLANTS
I am not a plant biochemist, so I am happy to be corrected if wrong, but I understand that gluconeogenesis is important after seed germination for production of hexoses for use in cell wall polysaccharides during growth. Seeds contain reserves of fat, which on germination is oxidized to acetyl CoA which passes into the tricarboxylic acid cycle. However plants (and some bacteria) are able to convert this to pyruvate by means of a pathway mammals lack — the glyoxylate cycle (http://www.ncbi.nlm.nih.gov/books/NBK22383/). So in plants the glucose produced is not being used to provide energy by oxidation, but as a biosynthetic precursor.
BACTERIA
Gluconeogenesis is present in certain bacteria, where the pathway presumably arose (rather than in mammals). So it is of interest to consider its role there. Again, I am no bacteriologist, but the glyoxylate cycle is also present in bacteria, and it is likely that one function of gluconeogenesis would be to allow growth on fatty acids, with the glucose produced being required for synthesis of cell-wall polysaccharides.

Gluconeogenesis occurs during prolonged starvation or overnight fasting, mostly in liver and kidney to provide glucose to brain and RBCs. As brain and red blood cells require continuous glucose for their activity, this process comes in handy. The steps involved in gluconeogenesis are different from that of glycolysis, it is not the reverse of it. You can get more details 1 and 2.

Could you expand on the linked articles please? I also don't think this answers the question


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How are ketone bodies used?
While searching for literature on ketone bodies, I can only seem to find how they are synthesized, but not how they are broken down.
I'm looking for the series of events with enzyme names and intermediates. Does anyone have this?

First, there are three ketone bodies: Acetone (top), acetoacetic acid (middle), and beta-hydroxybutyric acid (bottom), see the illustration from the Wikipedia:

The second and the third are taken up by heart and brain cells and then converted into Acetyl-CoA which is fed into the citric acid cycle where it is further metabolized. Acetone is mostly excreted. See here for some more information.
Aceto acetic acid is either converted into acetone and removed from the body or enzymatically converted into beta-hydroxybutyric acid by the beta-hydroxybutyrate dehydrogenase.
The third possibility is that it is converted into Acetyl-CoA. See the figure for the scheme:

For a more detailed explanation of this process (both, the generation and the metabolization of the ketone bodies) see here.

You say the second and third are taken up by heart and brain cells. Aren't they also used by muscle cells during starvation?

During starvation/fasting*

@Paze - muscle cells predominately continue to oxidize fatty acids in the fasting/starvation state


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Time required for RNA precipitation in ethanol
I precipitated bacterial RNA during 1 hour at -80ºC after depleting rRNA with Ribo-Zero kit.
Does more time lead to better results?

I typically leave my mRNA in isopropanol at -70C overnight, but that's because I usually get to that step at the end of the day and I'm lazy. I would also like to know the optimal precipitation time in case I'm hurting my yield. Note that I'm not using ethanol, and different solvents may have different optimal times.

With isopropanol even keeping for 15-20 min at room temperature is sufficient. With ethanol you can keep at -20⁰C for 1-1.5-hours. Keeping at -80⁰C is not required.

You should also consider what is occurring during this precipitation step. The monovalent cations are performing two functions: (1) they are shielding the negative charges from the phosphate on the nucleic acid backbone, those negative charges would ordinarily repel each other. (2) they are decreasing the chemical potential of the water molecules in the solvent (by ordering them), so this is a dehydration effect. The alcohol also has a dehydrating effect. So if the RNA is in solution and the water is the solvent, then by dehydrating the RNA it will precipitate. When it's complete its done

As far as I know this has never been thoroughly analyzed for RNA, but there is an excellent paper on the precipitation of DNA and the usual conditions in BRL Focus by Zeugin (see below for the paper). Since DNA and RNA are pretty much the same (except for one OH-Group) and the conditions used for precipitation are also similar, I think we can use this for a very close estimate.
Interestingly neither the time nor the temperature of a precipitation have a great influence on the outcome - they change the yield only by a few percent. If you look on figure 2 from the paper mentioned, you see the following:

This subfigure shows that the recovery is almost not influenced by the temperature, but only by the conconcentration of the DNA (or RNA). Depending on how much RNA you expect (how much cells did you use for the isolation) I would add a co-precipitation agent when you have only very small amounts on RNA. Glycogen works very well here. Otherwise I wouldn't worry.

This figure shows that the incubation time has only an influence on the percentage of the recovery when then time is too short. If you incubate for an hour, you are on the safe side.
Reference:

Ethanol Precipitation of DNA.

Since I usually get 100ug of mRNA from an in vitro transcription, I probably don't have to worry about time or temperature too much then? Unless isopropanol is totally different ethanol, but I doubt it.

I wouldn't worry about this. Follow your protocol and you should have plenty of yield.

As many kits suggest, RNA concentration has the most profound influence on precipitation efficiency / recovery fraction. Time, temperature and precipitation agent concentration has lesser effect. See for example instruction by Life Technologies on LiCl precipitation:
The Use of LiCl Precipitation for RNA Purification

N.B. Precipitation of RNA by 4 M LiCl does not include any type of alcohol (as I recall), will not work on DNA (as I recall), and is usually performed when there is still tons of rRNA present (i.e., not just mRNA)


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Why doesn't the body optimize how many fatty acids it burns?
Ketone bodies are produced due to an excess of fatty acids being burned (accumulation of acetyl-CoA) so my question is: Why doesn't the body simply regulate how many fats it burns so it doesn't have to produce ketone bodies?

Under which conditions does the body burn preferrably fats? What makes you think that this process is not optimized (in fact, most biochemical processes are)?

At about 65% VO2 in a trained individual or during fasting.
I still don't understand your point, but I assume that it is optimized it just doesn't seem so to me.

When there is not enough fast disposable energy like carbohydrates around. He does this to maintain the support of certain critical tissues, while producing more energy by breaking down fatty acids. If he had glucose (or other sugars) available, this wouldn't happen. Fatty acids cannot be used directly but need to go through beta-oxidation to make the energy available.

I understand that. But I've read that Ketone bodies are supposedly the end-product of beta oxidation, which is not true if I look at the exact process of beta oxidation. Ketone bodies seem to synthesize because an excess of Acetyl-CoA accumulates when fats are burned, so ketone bodies seem to be an unwanted side-effect of too much fat being burned. I'm asking why the body burns so much fat that it gets an excess of acetyl-coa instead of regulating it.

Can you provide a reference for you statement that ketone bodies results from "excess" fatty oxidiation? In my view, ketone bodies are not an unwanted side product, they are deliberately synthesized (mainly by the liver) to support other tissues like the brain when glucose is scarce, as Chris mentioned. Also, I don't think it likely that acetyl-Coa accumulates to high concentrations, since this is limited by the amount of CoA available.


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Why use creatine phosphate?
We use creatine phosphate as an energy storage to resupply ADP with a phosphate group as our muscle cells only contain about 2-5 mM ATP. But why doesn't the muscle cells just keep 20-30 mM ATP instead of 20-30 mM creatine phosphate?

Because all available ATP will likely be quickly spent by various cellular machinery.
If there was 20-30mM of ATP, what would stop muscle from contraction and how could you keep ATP level constant at rest, be ready for rapid movement? By blocking all myosin? This creates enormous regulatory problems for the cell.
Phosphocreatine buffers energy for a period of time when it will be actually needed. Having buffer allows for more robust control of energy spending, for example via regulation creatine kinases and other enzymes. Just by activating single enzyme you then start rapid conversion of ADT into ATP via phosphocreatine.


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Phylogenetic method to detect shift in mean of continuous variable
I am currently working on a project where I study the change of a continuous morphological variable with body size (measured as body weight) across diverse taxa (insects, spiders, lizards, frogs). In order to account for the non-independence of the data, I built an approximate tree based on published phylogenies. I have a reasonable branching pattern down to family or genus level for most taxa, but lack statistically supported branch length.
I find a strong change of the scaling coefficient when using phylogenetic least squares (with a covariance matrix based on my tree) vs a non-corrected least-squares approach, suggesting that most of the change observed in my continuous variable is explained by evolutionary history, rather than by body mass as such. I would now like to investigate how early on in the tree these shifts occur.
Intuitively, I could start collapsing my tree into polytomies down to arbitrary taxonomic levels, eg genus, family, order etc, and re-do my phylogenetic least squares. I would expect a stepwise approximation of the pgls to the uncorrected result (in the extreme case, I would end up with a star phylogeny, which should give an identical result to my uncorrected regression). Such an approach may allow to say something about whether most of the change occurs between genera, families etc, but it requires the use of somewhat arbitrary (and controversial) taxonomic levels. I would be grateful if someone would have an alternative suggestions on how to perform such an analysis, with arbitrary branch length and non-ultrametric trees.
Thanks
Thriceguy

Quick question - do you have fossils for your trait and group?

I have no fossils. The non-contemptuous tree tips (I assume your question relates to them?) arise because different parts of the tree are resolved to different levels, and I set all branch length to 1 in my analysis. I suppose I should be able to ultrametrize the tree, however, if this would be helpful/better/required.

In case anyone encounters a similar problem, this blog entry: http://blog.phytools.org/2012/11/code-for-contmap-new-minor-phytools.html, and, in more detail, this paper http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12066/full may provide a solution. In short, one can estimate ancestral states of continuous or discrete variables and plot them on an existing tree. In case of scaling studies, phylogenetic residuals from a regression of the trait against mass may be the most meaningful parameter, clearly visualising the contribution of common history independent of size.

Do you want to test this formally or just evaluate whether the variance seems to lie closer to the root of the tips of the tree? To me, your basic idea to test "how early on in the tree these shifts occur" seems to imply a model with different rates of evolution (e.g. stasis-shift-stasis). If that is the case, I think you need to fit evolutionary models with different assumptions (bursts, brownian motions etc) to your dataset, to see which one fits best. See e.g. Uyeda et al (2011) for inspiration. Or am I misunderstanding you?


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Reasons for the HIV-1 epidemic
So, the HIV-1 jump to humans occurred as early as the 1920s, but the AIDS epidemic didn't start until the early 1980s.
Some things I don't understand about this:

Why the delay?
What is needed for a successful zoonosis transmission in the first place?
If Bushmeat practices (eating meat from non-domesticated animals, in this case HIV-infected fruit bats) have been the same for centuries, why has HIV only really spread in THIS century?

There is probably a decent answer, and aandreev may have touched on some the reasons, but I don't have time to write one right now. I have heard about blood samples taken in the Congo in like 1914 that tested positive for HIV. The advent of european colonialism, easier travel with trains, etc probably allowed HIV to get from remote villages to larger cities. Also, the virus probably had to mutate to grow in humans instead of only chimpanzees. So it probably took both the mutant virus getting into a human at the same time as travel became easy.

As usual, Wikipedia has a long article on this topic. Did you read it?

if Bushmeat practices (eating meat from non-domesticated animals, in this case HIV-infected fruit bats) have been the same for centuries, why has HIV only really spread in THIS century?

We can't really rule out the existence of similar epidemics in the more distant past. In fact, almost certainly they were transmission events from bushmeat (not necessarily of the same virus). The thing that made 20th century different, as the other commenter rightly says, is the mobility. Previously, such transmissions would have lead to local epidemics which would have run their course - leaving super-controllers or individuals with immunity and killing everyone else. And since most of the African cultures haven't left a written record we wouldn't know about such isolated local epidemics. Not to mention that in the unlikely event of such records existing they would hardly be scientific - the disease would be most likely attributed to "evil spirits" or some other supernatural cause.
So, it is really the mobility, the public policies (mass vaccinations by colonial authorities that used the same syringes repeatedly) and the fact that we can retain information in a much better way which make the HIV epidemic different than the ones that almost certainly have happened in the more distant past.


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Question about cytoskeleton coordination
I am trying to study for a biology and I am having some confusion over the following topic. Can anyone help explain/ shed some light on the concepts of Rho family GTPases. Is it true that we have Rho activates forimins to relieve  auto inhibition of actin filaments while Rac promotes lamellopodia and Cdc42 works on the leading edge and fillipodia?
Secondly, how are the microtubules involved in cytoskeleton coordination? Do they simply affect Rho and Rac concentrations. How else is the concentrations of these spread throughout the cell as to maintain distinct concentration gradients?
Thank you all for any help!

The dynamics of Rho GTPase activities are highly complex.. Try to read this article.. it could help you understand or it could make your confusion worst :P


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Why is Pilobolus phototropic?
Pilobolus is a fungal genus whose fruiting bodies consist of a stalk ending in a spore mass that is launched via turgor pressure to disperse the spores.  The fruiting bodies grow towards light, which ultimately influences the direction in which the spores are launched.
It seems that gravity-directed growth would be sufficient to ensure an upward trajectory, so I'm wondering what the value is of phototropism.  Has this been studied at all?

Most of the "why" questions have no scientific answers. Reasonable questions I can imagine in this context would be: "how does it work?" (pathways involved), "how did it evolve?" (evolutionary history of individual components of the system and of the system as a whole) and "what kind of biological role does it play?" (if we knock out some key components of the phototropic system: would it break/diminish spore dispersion?).

@har-wradim I'm most interested in the third question - i.e. what adaptive benefit does the phototropism confer?

My thoughts - pilobolus is only 1 cm tall. Its spores need to be ingested by an animal to complete its life cycle. Suppose some detritus like a dead leaf landed on or near it. If it only responded to gravity, the spore mass would be ejected into the leaf and back onto the dung on which it grew, and will not likely be eaten until the dung is thoroughly decomposed and the area re-grown with vegetation for host animal to feed upon (herbivores give a wide berth to feces when feeding). By growing toward the light, the spore mass misses the dead leaf and travels over a meter away, onto vegetation th


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Can we use the HIV antibody test to detect HIV in newborns?
Adults and elder children can use HIV rapid test to test HIV infection. Can we use the HIV antibody test to detect HIV in newborns too?

It is a prerequisite here on Biology.se to do some research yourself and not only dump in one sentence questions. Additionally your question is rather broad. So please edit your question and add the information you found yourself and ask about what's unclear.

The question itself holds potential, please elaborate to avoid closure.

I found the question fine the way it is. This is how you chase away new members. It's also a prerequisite to assume the question hasn't been answered somewhere else and write an answer here for posterity rather than linking to a uniform resource location that may or may not exist in the future.

The rapid screen usually tests the oral mucosa by swabing the inside of the cheek and checking for the presence of anti-HIV envelope antibodies. Although the precise target of these antibodies seems to be kept propriatary, my guess would be the detection of either p24 antibodies or envelope antibodies that bind the V3 region.
Regardless, the point is they test for the presence of antibodies, which a child does not start making until they are born. See this post for a great explanation
Since a child has mostly maternal antibodies, the presence of anti-HIV antibodies would only mean that the mother has started producing antibodies to HIV (Seroconversion). This means that although the child has been exposed, they may themselves not be infected.
The mucosa, particularly in the oral region has a very low titer of anti-HIV antibodies, so I think this test would probably be best to direct the physician to conduct additional tests that are more indicative of HIV infection like p24 western blot.


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What pattern can be learned from the data of RNA seq counts and HiC matrix?
I now have some data on the RNA seq counts and related Hi-C matrix of gene segment on a chromosome. My concern is, basically, what can we do with these data so as to establish the connection between the two types of data such as the level of expression of gene segment and the interaction of the gene segment, since it seems that they are correlated. Thanks

Maybe start with some tutorials? This one looks interesting: http://www.jove.com/video/1869/hi-c-a-method-to-study-the-three-dimensional-architecture-of-genomes Also, you haven't done any background work for your question, so don't expect substantial answer

You need to be more clear than this. There are many things that you can do with the data. An experiment is performed to test some kind of hypothesis. With just the data and no underlying question you can calculate any thing. It can be even comparison of sequencing fidelities between two kinds of methods. The main point is what are you interested in finding?

This seems to me to be two independent pieces of data. mRNA seq allows one (in case of linear amplification) to quantify message RNA transcripts of genes of interest. that is, how many copies of mRNA for given gene are in the cell at the moment. It is ultimately, how active this gene is. In neurons different genes will be more active, than in epithelial cells, and vice versa. Genetic expression pattern provides identity of the cell.
Hi-C method, closely related to chromosome conformation capture answers question: what genes are physically interact in the nucleus via stabilizing proteins (e.g. enhcancers). There is more in the video, but general idea is that it allows you to see how genes positioned inside intricate chromatin. Since many genetic elements might physically interact via, for example, enhancers, 3C/Hi-C allows detection of such interactions. Or, at least, quantification of correlation between physical positions of two genes.
Now, the only direct connection between mRNA seq and Hi-C that I can draw is following logic: actively transcribed genes are located in expanded, less tense regions of chromatin. Hence, it will be hard to crosslink genes in such regions and correlation going to be low. Silent genes, if they are located closely in nucleus will be cross-linked with high probability, because chromatin is denser around non-transcribed genes.

HiC and 3C (chromosome conformation capture) do not idenify which genes are located nearby in chromosome. These techniques capture long range DNA-DNA interactions such as that between enhancers and promoters. Basically it captures stable DNA loops.

would it be fair to say that such techniques detect physical proximity in chromatin? I understand, that they are not about position along the chromosome

yes they do. In fact trans-DNA regulation has also been studied but these interactions have to be stabilized by some factor which is usually a protein

RNA-Seq lets you measure the steady-state levels of a transcript in a cell or tissue at a specific time-point (averaged over all of the cells that were harvested and lysed).


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Hardy-Weinberg Color-blind
In a city, 4% of male population have color blindness. How many of the female are (a) color blind carrier, (b) color blind? Suppose the city holds Hardy Weinberg equilibrium.
My progress: 4% of male have color blind => $p=F(cb~allele)=0.04$ and therefore $q=F(not~cb)=0.96$. Since HW equilibrium stand, we get the allele frequency among female is the same as among male. Then (a) $2pq=2*0.04*0.96=0.0768=7.68\%$ and (b) $q^2=0.9216=92.16\%$.
Am I correct?

http://en.wikipedia.org/wiki/Hardy%E2%80%93Weinberg_principle#Sex_linkage

Are you given any other data, total population, sex population, genotype of colorblind allele ?

@Macedon93 you don't need more data... HWE assumes organisms are diploid, only sexual reproduction occurs, generations are non overlapping, random mating, infinite population size, allele frequencies are equal in the sexes and there is no migration, mutation or selection. Color blindness is a trait known to be X-linked and recessive.

A: wild-type allele / a: color blind allele
Because color blindness is recessive and X-linked your assumption $p=F(a)=4\%$ is correct as men do only have one copy of the allele. Subsequently $F(A)=q=1-p=0.96$ is also correct. Therefore:
a) $F(Aa)=2pq=7.68\%$ is correct and b) is wrong, a is the color blind allele and $F(a)=0.04$ therefore it's $p^2=0.04^2=0.0016=0.16\%$.
92% color blind among females seems a bit high :).

Thanks @cagliari2005 haha, it totally slipped my mind :)


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Are genotypes with the same two alleles equivalent even if the alleles come from different parents?
I am looking at the following question

If $m$ alleles may occur at a given locus, how many distinct diploid genotypes are possible at that locus?

The obvious answer is that there their is $m$ possible paternal alleles and $m$ possible maternal alleles so the solution is $m^2$. However this considers inheriting allele $a$ maternally and allele $A$ paternally as the same as inheriting $a$ paternally and $A$ maternally.
If they are considered distinct we have double counted all matchings apart from matchings where the same allele is inherited maternally and paternally so I think the answer to the question if $Aa$ is the same as $aA$ would be $\frac{m(m-1)}{2}+m$
My question is which if any of my interpretations is correct?
Thanks in advance

1 allele (a) means one possible genotype (aa), 2 (a,b) means four possible combinations, but three distinct genotypes (aa, ab, ba, bb... I say three distinct genotypes becuase ab and ba would not be distinct when looking at the offspring unless you can determine parent of origin)... that would be my interpretation at least. What is the source of the question?

Okay @GriffinEvo, so if we have 3 alleles then we have 9 genotypes, 6 of which are distinct? If we had two loci one with 2 alleles and another with 3 alleles would the number of distinct genotypes be $3 \times 6 = 18$ (just to check I understand)

(a,b,c) = (aa, ab, ac, bb, bc, cc) so according to my logic, yes, but I don't know whether the question is looking for my logic.

My instinct is inline with your logic but we'll see what others have to say if you aren't 100%. Thanks

If you have genomic imprinting then $k^n=m^2$ (with k=m and n=2 because of diploidy) is correct as inheriting a from the father and b from the mother (i.e. ab) is not equivalent to inheriting b from the father and a from the mother (i.e. ba). For 3 alleles (a,b,c) you have 9 possible genotypes (aa,ab,ac,ba,bb,bc,ca,cb,cc).
Under no genomic imprinting, ab and ba are equivalent. This is equivalent of calculating the number of elements of a triangular matrix which is $\frac{(m+1)*m}{2}$. So for m=3, you have 6 possible genotypes (aa,ab,ac,bb,bc,cc), for m=4 you have 10 possibilities (aa,ab,ac,ad,bb,bc,bd,cc,cd,dd) etc...
I hope this helps. Your formula is actually equivalent.


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Is the motor cortex identical to the sensorimotor cortex?
As far as I understand, the primary motor cortex (M1) and primary sensorimotor (SM1) are notations for the same cortical area in the brain. Am I right that there is no dedicated motor cortex, and that M1 actually processes both sensation and movement functions?

I edited the question wording to improve clarity. Feel free to roll back.

@AliceD tnx for the edit

The primary somatosensory and primary motor cortices are distinct cortical areas. According to the structural classification of Brodmann, the primary somatosensory cortex is referred to as Brodmann's areas 1,2 and 3 (BA1, BA2 and BA3). The primary motor cortex is referred to as Brodmann's area 4 (BA4). The primary sensory cortex is sometimes denoted by S1, and primary motor cortex by M1.

Source: My Brain Notes
The primary somatosensory cortex is concerned with the processing of somatosensory input, such as tactile stimuli coming from the skin. The motor cortex is concerned with executing movements and hence with motor output. As such, there is a functional as well as structural distinction between the two areas.
Within the primary somatosensory cortex, basic processing of somatosensory information takes place in BA3, while more advanced processing takes place in BA1 and 2. Neurons in the somatosensory cortex project to adjacent regions, including the motor cortex (Kendal et al., 2000).
Because the primary sensory and motor cortices are four strips of cortex closely situated together, and because they are functionally coupled at the physiological level, they are sometimes collectively referred to as the sensorimotor cortex.
Reference
Kendal et al. 2000. Principles of Neural Science


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Why do four spermatids have different genomes?
It's been a while since my last class in genetics, so I've forgot most of it. However, I found myself studying human reproduction and I've the following doubt concerning spermatogenesis:
the process begins with a spermatogonium, a diploid cell (i.e. it contains 23 chromosomes and the corresponding homologous), which, through mitosis, generates the primary spermatocytes. The latter undergoes meiosis generating the two secondary spermatocytes; these are haploid, one of them contains 23 chromosomes and the other the corresponding homologous.
Since a chromosome A and its homologous B contain the same genes but with (generally) different alleles, the two secondary spermatocites have different genomes. Now, each of them splits into two equal cells (spermatids), through mitosis. My textbook says that the four spermatids have all different genomes, but shouldn't there be only two genomes?

You're forgetting about homologous recombination during meiosis.

Look at this post. I explained what could be the result of homologous recombination in mitosis and this is similar to what would happen in meiosis.

Spermatogonia contain 46 chromosomes (not 23) Spermatogonia increase their number by mitosis and one of Spermatogonia grow by increasing it's size to form primary spermatocyte. Primary spermatocyte undergo meiosis to produce spermatid. In 1st meiotic division secondary spermatocyte is formed following it in 2nd meiosis spermatids are formed. Both primary and secondary spermatocyte have 23 chromosomes.

Welcome to SE Biology. Your answer sounds, and may well be, correct, but as this is not my area, how am I to know? And that is the basic reason why we require answers supported by external authoritative sources (when it’s not just a question of logic). You just need to reference a Wikipedia article or book excerpt available on the internet, or quote from a printed edition. Have a look at the Help on answering questions. We look forward to your amended answer and future contributions.


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Beta oxidation of saturated fats
In my text book there is an example of a 18 carbon long fat and it says that it can run 8 laps of oxidation. I don't understand why it doesn't run 9? 2 are removed each cycle?
Thanks.

I believe your textbook is referring to the fact that you only perform the complete beta oxidation eight times.  Because there's a carboxylic acid at the terminus of a fatty acid chain, the cell takes a slightly different route and reacts it with ATP, which generates a fatty acyl adenylate and pyrophosphate (PPi).  This AMP can subsequently be displaced in an attack by CoASH, at which point the beta oxidation process can proceed in full to begin cleaving off acetyl-CoA.
Here's a visual representation of this activation process, too.


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What produces the strong odor of decaying dead animals?
Are there specific chemicals responsible for producing the strong, putrid odor that is present after an animal deceases? Also, how long does this odor last?

Mostly putrescine and cadaverine. The list of chemicals emitted during decomposition is avalailable here starting from page 59.

Two compounds are specifically associated with the smell of decaying cadavers (Hoffman et al., 2009), namely:

1,5-pentanediamine (cadaverine), and
1,4-butanediamine (putrescine)

Cadaverine is produced by breakdown of lysin and putrescine by the breakdown of ornithine (Science ME). Both are nitrogen-rich compounds and particularly pungent-smelling.

Source: Science ME
Both compounds are also responsible, in part, for the smell of bodily fluids such as urine and semen, smell of rancid butter, bad breath and stinky cheeses (Science ME).
Forensic Science Central UK mentions that after death, the body begins to decay after about 5-11 days (after an initial phase of bloating). The putrid smells subside mostly after 10-24 days, although a rancid cheesy smell might persist due to butyric acid. Note that many factors will affect decomposition rates and will affect this time course. Moreover, trained police dogs may be able to sniff out minute amounts of putrescine and cadaverine long after humans cannot detect it anymore.
Note that, given the complex composition of animals and the complexity of the decomposition process, a host of volatile organic components are released during decomposition besides putrescine and cadaverine.
Reference
- Hoffman et al. Forensic Science International 2009; 186: 6-13

addition: semen contains related molecules spermine and spermidine


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Genetic Imprinting and Cell differentiation
It does not seem possible that these two processes can coexist:
1) Genetic imprinting is the phenomenon where genes are expressed differently depending on the parent of origin:
1a. Methylated stretches of DNA are not transcribed.
1b. If the gene copy originating with mom is methylated but dad's copy is not, then only dad's copy will be expressed (e.g. Prader Willi syndrome).
1c. Methylation is preserved during cell divisions.
1d. Methylation is wiped at gametogenesis, when females will erase dad's imprints and re-imprint according to maternal imprint before meiosis.
But now I'm reading about the role of epigenetics in cell differentiation, and I discover:
2) Cell differentiation occurs with lineage-specific patterns of methylation.
2a. Immediately after fertilization (prior to the first cell division), the paternal genome undergoes demethylation.
2b. The maternal genome undergoes demethylation during the first few cell divisions.
2c. Cell differentiation is accompanied and perhaps even accomplished by progressive re-methylation following these "wipes."
Source for 2): http://labs.genetics.ucla.edu/fan/papers/HuangK_RM2010.pdf
"DNA methylation in cell differentiation and reprogramming: an emerging systematic view" Huang & Fan (2010). Regen Med. 5(4):531-44.
I suspect that there is no conflict and I merely misunderstand one, the other, or both. Otherwise, how can a pattern of methylation be wiped both during gametogenesis and early embryonic stages and still be inherited?

What if imprinted regions are immune to being wiped? Also, you may be confusing DNA methylation, and histone methylation (?). Classical biochemistry posits that DNA methylation states can be transmitted from a dividing mother cell to both daughter cells because after DNA replication the two daughter chromosomes will each be hemi-methylated, and a DNA methylase that finds a hemi-methylated site will methylate the other strand (like a corrective editing mechanism).
The third thing to consider in your question is that parental imprinting is established in the germ line. In terms of wiping other epigenetic marks during early embryogenesis, the only ones present would be the ones involved in gametogenesis.  In other words, as far as we know, genes activated in muscle development are never expressed after fertilization in the zygotic cells that will give rise to the primordial germ cells, so those muscle-specific epigenetic marks don't need to be wiped off in the embryo. Neither the sperm nor the egg ever expressed muscle myosin, etc.

Probably, there are narrow and wide definitions for imprinting. I am guessing the history of researches about imprinting would be like the followings.
Initially, maternal or paternal phenotype transmissions were recognized and some of such phenotype seemed because the maternal or paternal responsible gene does not work. As you know this is clearly imprinting.
Then, DNA methylation was discovered and turned out to be responsible for inactivation of imprinting genes defined above. However DNA methylation and repression of the expression by methylation occur to other genes, too. ES cells have distinct a DNA methylation pattern, which can probably explain the distinct gene expression pattern at least partially, I think. In addition, suppression of some tumor suppressor genes by methylation occurs during the course of carcinogenesis. It looks like DNA methylation regulates gene expressions as well as imprinting defined above. I know people call all gene regulations by DNA methylation imprinting. This is the wide definition.


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How to define drug-resistant or -sensitive cell line when knowing the IC50 values?
I have got the IC50 data for a drug on different cell lines. How to define if the cell line is sensitive or resistant towards this drug?
Could anyone tell me how to define this?

A low IC50 marks a sensitive cell line, a high a resistant.

From this post.
The IC50 is the concentration of inhibitor required to reduce the activity of a molecule/protein by one-half. It is the inverse of EC50. Usually inhibition curves looks sigmoidal so the IC50 is the middle point of the S curve. Here an example. (Note that the Y-axis can be pretty much anything, like enzyme activity and the X-axis is the concentration in a logarithmic scale).

Now for your actual question. The IC50 you got is by plotting a measure of the cell death rate vs the concentration of the drug. IC50 is expressed as a concentration so the higher the concentration of drug needed to kill the cell line the more resistant that cell line is. If the IC50 is very low then the concentration (or amount) of drug needed to kill the cell line is also very low which means the cell line is more sensitive.


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Blood as newtonian flow and Poiseuille law
For a prep exam:
A healtly pacient has a carotid with the following characteristics:
intern ratio: = 2.8 mm,
2 = 89 ,
1 = 90 ,
 blood = 3.5 cp,
=10.0 cm.
Using the following equations calculate:
$$V(r)=\frac{P_1 - P_2}{4 \mu L}R^2 [1-(\frac{r}{R})^2]$$
$$V_{max}= V(r=0)$$
$$\overline{V} = \frac{Q}{A}=\frac{1}{2}V_{max}$$
$$Q=\frac{\pi(P_1 - P_2)}{8 \mu L}R^4$$
where P_1 and P_2 are the mean pressure to in and out the vase, R is ve vase radius, L is the length of the vase segment and $\mu$ is the viscosity of the fluid.
A healthy patient has a carotid withe the following characteristics: intern radius R = 2.8 mm, $P_2$ = 89 mmHg, $P_1$ = 90 mmHg, $\mu_{blood}$=3.5cp, L = 10cm.
Using the previous equations calculate:
a) Mean velocity on the carotid artery Rta: 0.372 m/s
b) Maximum velocity Rta: 0.744 m/s
c) caudal on the carotid artery Rta: $9.16x10^{-6} m^{-6}$
I have tried to solve this problem but when i try to replace changing the units to the adecuate I have not the correct answer

could you please elaborate on how you went about solving it

I'm voting to close this question as off-topic because it is better suited for physics.SE.


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Identifying an insect looking like a crumle
Recently a little insect crawled over the carpet. First I did not notice, as its appearance is quite similar to the coloring of the carpet. Then I understood that it is not a rolling crumble, as the window and the door were closed.
I took it on an ordinary sheet of DIN A4 paper, but have not the slightest idea, what kind of insect it is. It makes the impression to have taken a shower of water and dust in a row.
What's that insect called?
The second photo gives an idea of the size, as it shows a drinking glass turned upside down.
Note: The place this insect was encountered is in eastern Germany

Where do you live?

South-eastern Germany. Approximately at 50.993479, 13.649035

looks really nice btw

Looks like the nymph of a masked hunter.
They carmouflage in dust and sand.

if it really is what i belive it is, it can hurt you

I checked the article and to me it seems likely that your assumption is correct. However, this one appears to be really young and therefore not terrifying at all. But if its parents or older friends are around it could be a concern.

I thought the original image looked like an assassin bug covered in dirt, so this sounds right to me.


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What Goes on in Photosystems at the Molecular/Atomic Level?
In light-harvesting complexes, how is the energy of a photon transferred from one pigment molecule to another? And in reaction-center complexes, how does the primary electron acceptor capture an electron from the chlorophyll a? It’d be best if any of you could explain this to me in terms of what’s happening at the molecular or atomic level, say with electrons.

The energy transfer is achieved by a process called "resonance energy transfer". It needs the positioning of the donor and the acceptor in very close proximity to each other - the light harvesting complexes are optimized for this. This allows the collection of small amounts of light energy and still enables photosynthesis. The figure shows how this works schematically:

The figure is from this webpage, which gives a good introduction.


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Do The Traces Genetic Diseases Remain in families?
I know that there are certain diseases that are predominant on genes. But, is there any sort of surety that if parents are suffering from a disorder then their offspring has to suffer from the same. Like my dad is schizophrenic so will I become the victim of the same mental disorder?

just like any genetically affected traits (e.g. height), there is on average greater resemblance between parents and offspring than between two randomly chosen people. If a parent has a genetically controlled disease there is an increased likelihood of it developing in the children but it is by no means a guarantee (even for dominant mendelian traits if mutation occurs). Few things are entirely genetically determined.

In the case of schizophrenia, it has always been evident that there is a genetic factor. However it has not been identified. More recent hypotheses suggest epigenetic mechanisms. Meaning the trait can be inherited, but is very sensitive to short-term environmental changes.

Welcome to Biology.SE. Your question reveals that you probably don't know the concepts of Mendelian segregation/dominance/additivity/pleiotropy and epistasis. You should check out those terms on wikipedia. Also You will probably want to increase your understanding of heritability. Here is an answer that link to 4 other posts that talk about heritability.


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Closing a Plasmid by Ligation
I have been having trouble with what should be a fairly simple ligation. I had a plasmid that I needed to cut part out of, so I designed a couple PCR primers to do that. The plasmid already had a BamHI site on 1 side of the region I wanted to remove, so I made the other PCR primer with a BamHI site on its 5' end with 3 extra Cs so the restriction enzyme would bind better. Here is a crude diagram of what I tried to do:

So I did the PCR and BamHI digest, it looked good on gel, so I purified it from the gel, got the concentration on the Nanodrop, and set up a ligation.
However, I keep getting zero colonies. I have tried a 24 hour reaction at 4 degrees, and 10 minute reaction at room temp. I am currently trying a reaction where I supplement the buffer with fresh ATP, because the buffers are a little old. If that works, problem solved, if not, I am asking how to troubleshoot this.
This seems like it should be relatively simple, because I have no insert, just trying to close an empty vector, which seems to happen on its own when I don't want it to and dephosphorylate the vector.
UPDATE:
The reaction with extra ATP did not produce colonies. I will keep trying. One idea I had was to do the PCR and then try blunt end ligation, since the Pfu polymerase should make blunt ends. Also got a new sample of ligase.

Can you heat inhibit your restriction enzyme and go straight to ligation without the purification step? I am asking because gel purification (or column purification) sometimes trim a bit the end and interfere with the ligation. This is quite rare but might have happen to you.

@cagliari2005 According the NEB poster on my wall, BamHI probably can't be heat denatured.

How do you know the BamHI enzyme is working? 2. How do you know the ligase is working? 3. How do you know the cells are actually competent? 4. What is the selectable marker--is that the same drug in your plates?

@mdperry The removed sections are too small to tell if the digest worked, but the same BamHI batch works for other plasmids with visible fragments. The same batches of cells produced colonies when transformed with intact plasmid. The plasmid has an ampicillin resistance gene, and ampicillin is in the plates, the plates are less than a week old and have been stored in the fridge. Only thing I'm not sure about is the ligase or its buffer.

How far from the end of your PCR product are the restriction sites located?

@Chris The short end is only three nucleotides, which concerns me a little because other sources I've read suggest I should use 6, but I've gotten away with 3 before, but those used other restriction enzymes, maybe BamHI is a little more sensitive.

Hmm. According to NEB this should be ok.

Could it be due to low transformation efficiency? Have you tried higher competency cells?

@MarchHo No, just standard subcloning DH5 Alpha E. coli so far. Might see if I can borrow a tube of better cells from another lab, our on campus store makes me buy a whole box of the better cells, but I can get the subcloning cells 1 tube at a time for less money.

One more question, have you checked your primer's BamHI site directionality? If the sticky ends produced are in the wrong orientation, it can explain the poor ligation.

@MarchHo That might be it, I just looked at the primer sequences and tried to draw what the overhangs would look like and I think I got one of the sites flipped. Primer 1 is 5' GGATCC 3' and primer 2 is also 5' GGATCC 3'. I think if I get another primer with the CCTAGG orientation this might work better. Alternatively I could trim the overhangs down with klenow and try blunt end ligation.

@MarchHo After thinking about it a little more and writing the sequences on strips of paper, cutting the ends and wrapping them in a circle, I'm not so sure I was wrong the first time. Either way, I already ordered the new primer, will give it a try.

The recognition sequences of type II restriction enzymes are palindromic, so if you always read the sequence of each strand from 5' to 3' prime it will always be the same sequence. If, reading from 5' to 3' you specified the sequence CCTAGG then after PCR there would be absolutely no overhanging sticky ends on that end of the fragment. It would be completely blunt. BamHI cannot recognize or cut CCTAGG.


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Why differentiated cells can't "undifferentiate" (under normal conditions)?
In a process called differentiation, the cells of the developing organism undergo huge changes, which result in cells, functioning "completely" differently. Two cells are considered to be of different types if they are having different sets of template-competent genes, though most of the genes in the human genome are common even in highly differentiated cells. Being able to produce specific proteins from the same genome is achieved by something called open chromatin state of the DNA. What I would like to ask is why can't this specific conformation of the DNA be reversed as this would likely answer the title of this question? I would also like to have some tips on further reading in the topic of DNA conformations and about DNA generally.

I used Gabor Forgacs's and Stuart A. Newman's book called Biological Physics of the Developing Embryo

This "undifferentiation" is actually possible and it is known as induced pluripotent stem cell (iPSC). The first "undifferentiation" cells i.e. iPSCs were mouse fibroblasts created in 2006 by researchers in Shina Yamanaka's lab who got the Nobel prize in 2012 for this work.
You can find further reading on this topic on the according Wikipedia-Page or more scientific details on the according nature.com topic.


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ratio between heat transfer coefficient and thermal conductivity
Consider the Robin boundary condition for the diffusion/heat equation $\mathrm{u_t=a(t)u_{xx}+f(x,t)}$:
$$\mathrm{-k(t)u_x(0,t)=h(t)u(0,t)}$$
or
$$\mathrm{u_x(0,t)+\frac{h(t)}{k(t)}u(0,t)=0}$$
where $\mathrm{k(t)}$ thermal conductivity and $\mathrm{h(t)}$ heat tranfer coefficient.
My Question: Is it possible that the ratio $\mathrm{h(t)/k(t)}$ to be constant? Could anyone please help me? I have really no idea.

This is probably better suited to chemistry stack exchange as it smells like physical chemistry.

I'm voting to close this question as off-topic because it is more suited for physics

Most likely, you can't assume that $h/k$ might be constant. Reason is that those parameters are characteristics of two very separate systems.
Thermal conductivity shows how fast heat can be propagated through material. That is, it answers question: if block of metal has $T_0$ temperature on its surface A, and you apply temperature $T_1$ (higher) to opposite surface B, how long it will take for whole block to get to temperature $T_1$.
Heat transfer coefficient is a characteristic of a system. For example, when you have coolant on one side of metal plate, and heated air on the other. Question is how efficiently heat will be transferred from one side to the other. For more you can check this link. As you can see, transfer coefficient $U$ is a function of conductivity of the metal plate $k$. Hence, generally, relationship is non-linear.


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How can human infants express chymosin with only a pseudogene at their disposal?
I read on the Wikipedia article about Chymosin http://en.m.wikipedia.org/wiki/Chymosin
It stated that chymosin is produced by gastric chief cell in human infants.
But it also stated that human only has a pseudogene for chymosin that does not actually encode the enzyme. On the other hand, another article show that gastric chief cell only secret chymosin in ruminant http://en.m.wikipedia.org/wiki/Gastric_chief_cell
How can infants express chymosin without a functional gene?

TL;DR: Chymosin is similar to pepsin and I couldn't find any evidence of functional/expressed chymosin gene in human genome.
It seems like a common misconception that chymosin is functional in humans. Already in 1940s it has been shown that rennin (aka chymosin) is absent from "gastric juice" in adult humans.
Genetically there is only pseudo-gene for chymosin, as wiki and other sources state. At the same link that leads to chymosin gene page you can find some literature on cloning and structural analysis of chymosin pseudo-gene.
If you use BLAST for finding homologous proteins to chymosin from, say Bos  mutus (aka yak), you can find that in humans closes sequence can be attributed to pepsinogen and similar proteins. Which very much might mean that what is called chymosin in other animals is pepsin in humans, or there is some convergence/divergence which eliminated chymosin in humans. But this is only a speculation.
You can try to scan Google scholar for more sources.
NB link to BLAST search will expire in ~24 hrs.