Are freshwater jellyfishes really jellyfishes? Articles from the aquaticcommunity.com and the Nature Conservancy suggest that freshwater jellyfish, Craspedacusta sowerbyi, are more closely related to the Genus Hydra. From the Nature Conservancy article:

  It should be known that though Craspedacusta sowerbii is touted as a
  jellyfish, some argue it is more   related to the family Hydra than a
  "true" jellyfish. Many researchers still call it as such, but others
  may simply refer Craspedacusta as a jelly. The main difference between
  Craspedacusta swerbii and "true" jellyfish is the presence of a velum.
  Its velum is a thin, circular membrane around the cap that helps
  propel, or move, the jelly forward.

An articles from the US Geological Survey (USGS) states that Craspedacusta sowerbyi is a hydrozoan that can take the form of a jellyfish. From the USGS:

  Craspedacusta sowerbyi is a hydrozoan (Phylum Cnidaria, Class
  Hydrozoa), which is most easily identified when it takes the form of a
  small, bell-shaped jellyfish, known as a hydromedusa.

The Merriam-Webster dictionary defines a jellyfish as follows:

  a free-swimming marine coelenterate that is the sexually reproducing
  form of a hydrozoan or scyphozoan and has a nearly transparent
  saucer-shaped body and extensible marginal tentacles studded with
  stinging cells

This definition, to me, seems to suggest that Craspedacusta sowerbyi is a jellyfish, however there must be some other reasoning that I'm missing that makes others believe that they aren't. Any clarification would be greatly appreciated.

The issue here is simply the meaning of the term "jellyfish" and the term "medusa". The first has no taxonomic value and, as such, can be used the way the book/zoologist/layman/journalist wants, unfortunately. Let's see it:

Cnidarians (Phylum Cnidaria) have two basic morphological types: medusa, or medusoid form, which is free-swimming, and polyp, or polypoid form, which is sessile:

There are Cnidarian species that display only polypoid forms and there are species that display both medusoid and polypoid forms in their life cycles.

Regarding the taxonomy of the most common Classes of Cnidarians, Hydrozoa displays both the polypoid and medusoid forms; Scyphozoa displays both the polypoid and medusoid forms; and finally Anthozoa displays only polypoid forms.

So, we can clearly see that Craspedacusta (an hydrozoan) is a medusa, or, in other words, that it displays the medusoid form in some point of its life cycle. There is no doubt regarding this:

The problem comes when we try to use the term jellyfish.

Again, jellyfish has absolutely no taxonomic value. For instance, my teachers used to call an hydrozoan medusa as a "jellyfish". Some time later, when I started teaching zoology, I used to say to my students that an hydrozoan medusa is a jellyfish... that's not a big deal.

However, some zoologists apply the term jellyfish only to the scyphozoan medusae... in that case, jellyfish does have a taxonomic value. And, because of that, since Craspedacusta belongs to the Class Hydrozoa, its medusoid form cannot be called a jellyfish (again, if we accept the definition of those zoologists).

So, in conclusion, it depends on the book/zoologist: some say that that both Hydrozoan and Schyphozoan medusae can be called jellyfish, while some say that jellyfishes are only the medusoid forms from the Class Schyphozoa. That's the definition used by both the aquaticcommunity.com and the Nature Conservancy articles.

PS: Hydra is a Genus, not a Family. I edited your question just to realize that the mistake is from the original article, not yours.


High pressure cryonics In this link, it is suggested to use high-pressure cryonics to freeze living cells, tissues or small organism as opposed to various and potentially toxic anti-freeze agent. The core idea is that over a certain pressure, ice is anamorphic and will not form ice crystals. Thus, organic manner will not be destroyed by said crystals.

Detailed information about the proposal can be found at this link:

https://www.benbest.com/cryonics/pressure.html

I have considering self-financing the experiment. Could anyone chip in with some advice? Do you see any red flags, design tips, etc.?

One premise of the full proposal is that the freezing process should avoid the formation water crystals which prevent structural damage of membranes and proteins and keep the integrity of the life organism being frozen under high-pressure cryonics.

I have not seen a discussion on the thawing process which I always thought was a problem for example when thawing cells for in vitro cell culture.

For the design I would try small with for example mammalian cells like HeLa. Maybe full organisms like worms or flies for "tissues" and "full organisms".


Is the covid-19 vaccine-induced copy of the protein spike also damaging cells? In recent scientific articles, it has been discovered how the spike protein not only is a respiratory disease but also damages blood vessels cells directly, and is connected with higher risk of trombosis.
So, does the Spike Protein produced by the covid-19 vaccine also bring the same risks and damage?
How many spike proteins the immune systems produces after being instructed by the vaccine, and how do they behave afterwards ?
Thank you
EDIT: adding some references
-1) https://www.salk.edu/news-release/the-novel-coronavirus-spike-protein-plays-additional-key-role-in-illness/
-2) https://scitechdaily.com/covid-19-is-a-vascular-disease-coronavirus-spike-protein-attacks-vascular-system-on-a-cellular-level/
-3) here it says how the "creation" of the spike protein happens-> Can spike protein induced cell fusion be triggered by the mRNA vaccine?
EDIT2: Someone in the comments pointed out how articles 1 and 2 reference the same paper, and one paper doesn't constitute discovery.
But how the spike protein which are "created" after the vaccine, behave? Are they the same as the one from Covid-19?
Are they harmful? if not, why ?

The spike proteins expressed by cells that take up mRNA or ChAdOx vaccines are modified so they cannot induce membrane fusion. However, the research article you refer to indicates that circulating spike protein damages endothelial cells simply by binding ACE2, which suggests vaccine derived spike protein could still cause this kind of damage if it enters the bloodstream somehow:

we show that S protein alone can damage vascular endothelial cells (ECs) by downregulating ACE2 and consequently inhibiting mitochondrial function.

Spike protein is necessarily attached to a membrane, so for it to damage cells by binding ACE2, bits of membrane containing the spike would need to be exported from the cells. The SARS-CoV-2 genes that allow it to do this in a real infection are not present in the vaccines, of course. The only other route I know of by which S protein could theoretically enter the blood is in exosomes. This article analyzed circulating exosomes from COVID patients and did not detect any viral proteins:

We did not identify viral proteins via the purification of exosomes; thus, we can conclude that viral particles were not purified together with exosomes

Research creating hybrid S-protein that can make spike-coated exosomes indicates the natural spike protein does not get into exosomes:

the S protein could not be detected in the sample from pSwt-transfected cells. In contrast, the SGTM protein could be detected in the pelleted supernatant of pSGTM-transfected cells.

I was not able to find any studies looking for spike protein in exosomes of vaccinated people, but it should be less likely than for the actual virus.


Why do mitochondria fuse together? Contrary to all of the textbook images of mitochondria that I have seen over the years, I had just learned that the mitochondria within a cell form a dynamic branching network along microtubule scaffolding by fusing with each other.

Why would they need to fuse together?

When they fuse, would this involve only the outer mitochondrial membrane?

Would it not behoove a mitochondrion to remain distinct from others both physically and genetically?

Mitochondria produce a large quantity of reactive oxygen species (ROS) that damage the mitochondrial genetic material. These cell organelles do have a  DNA repair mechanism similar to that of the nucleus to some extent 3 which is not entirely understood however they have multiple copies and so the fusion and fission of mitochondria work together to maintain as many viable/healthy mitochondria as possible.

When two mitochondria fuse, their genetic material can recombine and thus exchange their damaged DNA. In this way, one of them repairs its DNA at the expense of the other accumulating more damaged DNA. Mitochondria that accumulate too much damaged DNA will 'die' - get eliminated, but they can be replaced by fission of healthy ones. Take a look at this wiki page, it has useful info.

Edit: This article may also be useful. (Mitochondrial fusion and division: regulation and role in cell viability
Giovanni BENARD and Mariusz KARBOWSKI, Semin Cell Dev Biol. 2009 May;20(3):365-74.)


Evolution of Upside Down Catfish (Synodontis nigriventris) My Biology teacher asked us to write 3 texts, explaining the evolution of the Upside Down Catfish Synodontis nigriventris, each one according to Lamarckism, Darwinism and Neodawrinism theories. She asked the same thing for other species but I'm having trouble with this one, since the other ones are simple to explain (like giraffes' necks or flamingo's legs).

She gave us a sheet in which there is some information:
They swim upside down, and their colors are inverted, because their backs are light and their bellies are dark (unlike the general fish). Their predators usually swim below them and it is harder for predators to find fish if their belly is light, because of the sun rays.

Well, all of this suggests that this fish swims upside down so that he can avoid predators, but how could he do this according to Lamarckism and Darwinism?
Also, how does he have inverted colors, and did he get them because of evolution?
I believe that the things which cause the evolution are the predators and the environment, but which characteristic is the first one and which is the one who appears because of the evolution? Also, both of them could be a product of evolution, right?

So how can I really explain this according to the theories of evolution?

Well, I haven't managed to find many studies that explores this but I suspect that their coloring was a result of their upside down swimming rather than the other way around.
They evolved from benthic (bottom-living) creatures that ate off the ground and would have had mouthparts evolved for that. So in order to feed at the surface they would have to turn themselves around. The areas that they lived in may have changed to have poorer benthic food quality making surface feeding more advantageous. They also do this for aquatic surface respiration in hypoxic (low oxygen) waters.

Check out "Chapman, L. J., Kaufman, L. and Chapman, C. A. (1994). Why swim upside down? A comparative study of two mochokid catfishes. Copeia" for more information.


Could all mammalian receptors be described as allosteric? Allosteric regulation in enzymes is where a molecule binds at a site other than the active site and thus changes the tertiary structure of the active site, hence altering the binding of substrate and formation of enzyme-substrate complexes.

As I understand it, if this is extended to receptors, for example G protein-coupled receptors, which effectively causes a conformation change which is transmitted across the membrane and 'activates' a G protein which is associated with the receptor. The Gα subunit swaps a GDP for a GTP which causes the dissociation of the alpha from the beta-gamma coupled subunits and from the receptor. The dissociated Gα and Gβγ subunits then take part in a cascade process interacting with other molecules.

However, photoreceptors such as rods/cones in the eye respond to light. These photons tend to cause changes in the structure of the rhodopsin/iodopsin pigments and not the actual 'receptors' themselves. G proteins do seem to be involved in this process too.

Therefore, are photoreceptors allosteric? And if not, are they an anomaly in mammalian receptors, or are there many other examples of receptors that do not rely on allostery?

"Allosteric" refers to an alternate site of action, but it is not limited to a discussion of enzymes. For a protein that is a receptor, allosteric modulation refers to modulation of that receptor away from the binding site or "active site" of the endogenous ligand.

Although it is true that the receptor may have enzymatic activity when a ligand is bound, it would be non-standard to use the term "allosteric" to refer to the normal ligand binding site, even if this terminology is technically correct with respect to the enzymatic activity.

There are many receptors which are not enzymes at all: a great example would be ligand-gated ion channels - all of the activity of these proteins is due to their conformational changes, and not due to any catalyzed reaction.


Do humans produce rennin? At school, we've been taught that human infants produce rennin/chymosin (which aids in the digestion of milk). More specifically, it is the peptic cells in the stomach which secrete prorennin, the inactive form of rennin (in addition to pepsinogen, the pepsin proenzyme).

User @another'homosapien's answer here also seems to concur with this (excellent answer by the way, I enjoyed reading it).

However

According to Mod. @AliceD's answer here (yet another excellent answer):

  ...in humans there is only a chymosin pseudogene present...

Which (probably?) implies that humans (infant or otherwise) do not produce rennin.

I managed to get my hands on the Textbook of Medical Physiology (Guyton and Hall, South-Asian edition), and according to the book (Chapter Gastric secretions, page 406) peptic cells produce a large quantity of pepsinogen. There is, however, no mention of prorennin. I even flipped over to the Appendix at the back to look up "Rennin", but it turns out there is absolutely no mention of rennin in the book.

My questions,

Some sources claim that rennin is produced in human (infants). Is this true?
Other sources claim that rennin is not produced in humans ( we have a pseudogene for it though). Is this correct (I mean the "rennin-is-not-produced" bit, not the "pseudogene" bit)?
If rennin is produced in humans only during infancy, what stops it from being produced as we mature? (I'm asking this because every source I've seen that claims that rennin is produced in humans, explicitly states that is done so during infancy...which would suggest that rennin is not produced in adults)

Scanning various reviews it seems that everyone who mentions the possibility of a human chymosin refers to a single paper. So for example this 2014 review has a single reference to a human chymosin:

  Henschel et al. detected a
  protease in the gastric aspirates of newborn infants within 6–10 h postpartum that was not
  pepsin [62]. The electrophoretic mobility and immunoreactivity are similar to that of calf
  chymosin, a protease that cleaves κ-casein and causes casein curdling. This protease is
  unique in that it disappears from gastric fluid at 10 days postpartum and is not found in adult gastric fluid.

I don't have access to the Henschel et al. paper (from 1987) but here is the abstract:

  The electrophoretic mobilities of proteases present in gastric juice taken within 10 h of birth from 5 healthy, premature infants were compared with calf chymosin, pig pepsin A and human adult gastric juice. The juice from 2 infants contained predominantly a chymosin-like enzyme, another had almost exclusively pepsins similar to those of the adult juice, while the other two contained a mixture of both. The pepsins consisted of two elements, probably pepsin A (EC 3.4.23.1), and pepsin C (EC 3.4.23.3). Single radial immunodiffusion gave a definite reaction to calf anti-chymosin serum in five samples taken from a further 17 infants. These results indicate that some human infants secrete chymosin. The reaction in the immunodiffusion assay indicated a much lower enzyme activity than that implied from electrophoretic separations. It is suggested that species differences resulted in poor cross-reactivity of the antiserum.

Now, obviously, without seeing the data it isn't possible to be conclusively critical, but the quality of the evidence seems to be rather weak, being based upon similar electrophoretic mobilities and an immunodiffusion assay (why not a Western blot?) with an overt apology for weak cross-reactivity of the antiserum used.

However, leaving all of that to one side, the strangest thing about this is the sporadic appearance of the proposed chymosin: although 4/5 were scored as chymosin positive in the 1st experiment, is it likely that 2 of these would apparently contain little pepsin? And in the second experiment (the immunoassay) only 5/17 scored positive for chymosin.

Evidently no-one has ever reproduced this result, and the evidence for the pseudogene (but no active gene) is very strong. I vote that humans do not produce a chymosin.

Update
Having read Bryan Krause's answer: if the human gene product was lacking an exon's worth of amino acid sequence then presumably it wouldn't have an electrophoretic mobility that was closely similar to the calf protein.


Which area of neuroscience\biology deals with the effects of genetics and drug discovery based on brain microcircuits? So the title I chose might be a bit too broad or even misleading compared to the specific example I have in mind, but I couldn't choose something longer or more specific than that, so I apologize if that's the case!

Due to its close connection to Autism Spectrum Disorders (ASD) and even some personality dimensions in psychology and my interest in these topics, I was reading an article about the reward circuit (cortico-basal ganglia reward network: microcircuitry, Susan R Sesack and Anthony A. Grace, 2010) which in my opinion is a pretty nice article and as the title suggests talks about the different parts of the cortico-basal ganglia network mostly at a fairly high level of detail (e.g. nucleus accumbens, ventral tegmental area, prefrontal cortex, etc), their interconnections, some physical characteristics of those interconnections, the associated neurotransmitters for the different parts and connections, and some of the functional implications of these topics, and also presents a couple of nice diagrams depicting the afferents and efferents of this circuit. as far as I understand and perhaps obviously, most of this data comes from primate and mouse data, however I would imagine there could be a lot of similarity in humans, and we also approximately know from cognitive neuroscience or other disciplines the general function of some (if not most) parts of this circuit.

The question that came to my mind is, which area of neuroscience or biology deals with modeling and simulating this circuit at this level (not necessarily at the neuron to neuron level) to understand it better, and also understand the effects that genetics or environment could have on it, so that ultimately we might for example come up with a treatment for ASD? is it more related to systems neuroscience, computational neuroscience, systems biology, or even bioinformatics and computational genomics?

Thanks in advance!

Basically you are sketching a situation where:

Brain circuits are modeled (Computational Neuroscience), which often depends on anatomical (Neuroscience, Biology), structural imaging and functional imaging (Neuroimaging) and electrophysiological data (Electrophysiology). Various other disciplines may come into play (Histology, Pathology, Anatomy, etc.).
Genetic (Genetics, Molecular Biology, Cell Physiology) and environmental effects (Behavioral Psychology, Medicine, Psychiatry) also encompass a wide list of expertise, out of which a small handful is mentioned in bold.
The realm of drug discovery harbors Medicine, Toxicology, Organic Chemistry, Pharmacology, perhaps even Physics and likely a host of others.

In short, your question could, perhaps, better be phrased as 'What Biomedical fields of research disciplines are not related to Drug Discovery?


Accommodation mechanism. Can anyone explain how contraction of the ciliary muscles causes relaxation of the zonules? Please explain it anatomically i.e. the attachments of ciliary muscles and its relation with the accommodation process.

I think the problem you're having is in the way you're thinking that all contracted muscle shortens, and all relaxed muscle lengthens. But the cilia is different. The ciliary muscle is a circular or radial muscle (like the orbicularis oris of the mouth.) Thinking of it like a sphincter muscle is much more helpful.

The ciliary muscle is attached at its periphery to the lens by suspensory ligaments (aka the zonules). Think of the the lens, the suspensory ligaments, and the ciliary muscle as a single unit with only two components whose length can change dramatically: the cilia and the lens. The length of the suspensory ligaments is more or less fixed.

This may be counterintuitive, but for seeing at a distance, the ciliary muscle relaxes, and the muscle in effect becomes "thinner" (think of the capitol letter O in a thin font, or think of a shpincter muscle; when the latter relaxes, it becomes thinner and more spread out). This means the "decreased distance" taken up by the ciliary muscle must be made up for by the suspensory ligaments and the lens: The tension on the suspensory ligaments increases, causing the lens to assume a flattened shape.

For near vision, the opposite occurs; The ciliary muscle contracts (think of the letter O now very bolded - it takes up more of the fixed distance.) This allows the ligaments to relax, allowing the lens to assume a more rounded shape.

Does that make any sense at all? I hope so, because it is essentially how it happens.

I did find a YouTube video; unfortunately it explains it pretty much like I did varying in a few details.

Morphological Study of the Accommodative Apparatus in the Monkey Eye Way way complicated; it's better to just believe me.


Utilising Mycorrhizal Association We know that mycorrhizal association helps the plant to absorb nutrients.
Why can't this association be exploited in agriculture ?

Can't we add spores of the specific fungi to specific plant and enjoy the benefit of this association as we would not have to add many fertilizers ?( We could add organic manure whose main drawback is the time it takes to release nutrients. The fungi could probably solve the problem.)

Mycorrhizal fungi are often used in small-scale agriculture for just that reason.  If you search mycorrhizae on amazon they sell it by the tub.  I think its especially used in organic gardening for just what you said, the slightly less-processed organic fertilizers are harder to take up by plants without their mycorrhizae partners.

I'm not sure about how widespread the practice of applying mycorrhizae is in large-scale non-organic farming.  Judging by how big of a problem fertilizer runoff is, my guess is that a lot of companies have decided that their bottom line is best served by just swamping everything with artificial fertilizers.  I'm not sure how mycorrhizae is produced either, it might really be prohibitively expensive to scale production of it up that much.


Can stomach acid destroy a virus? I was reading about a viral list of dubious coronavirus tips on The Verge and reached this tip:

  “Even if the virus gets into your mouth, drinking water or other
  liquids will wash them down through your throat and into the stomach.
  Once there, your stomach acid will kill all the virus,” one tip reads.
  Loren Rauch, an emergency room doctor in Los Angeles who has a
  master’s degree in epidemiology, told Mother Jones this advice was
  “totally bogus.”

I asked a friend, who has a PhD. in cell biology, about this and she said that it's true that a virus would be killed by the stomach acid (i.e. due to high acidity, or low pH value, of stomach acid which could easily break the structure of the virus); however, she added that it's NOT true to think that drinking water would wash the virus from your respiratory system (i.e. trachea or lungs) into your stomach, so drinking water regularly does not necessarily help if it's in your respiratory system.

I was a bit confused since the doctor referenced in the article considered the whole advice as totally false; on the other hand, my friend thinks at least part of the advice, i.e. the virus being killed by stomach acid, is true.

Now, my question is not limited to coronavirus and I am not seeking medical advice or treatment here. I just want to  know if my friend is scientifically correct, i.e. whether stomach acid is able to destroy the biological structure of a virus (any virus, and not necessarily coronavirus)? And if so, how does this work biologically?

Study on MERS coronavirus and HCoV-229E: "rapidly lost most of the infectivity in fasted-state simulated gastric fluid (FaSSGF; pH 2.0)" but "survived FeSSGF" (fed state, which is less acidic). See Figure 3. IOW, on empty stomach, the gastric acid rapidly deactivate the MERS coronavirus and the 229E coronavirus, but if there is food in the stomach then the virus survives.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5687858/


If a blocker prevents repolarization, will the neuron be stuck in a depolarized state forever? Potassium channels help to repolarize the cell after depolarization. But if the potassium channels are blocked, potassium ions cannot flow out of the cell to increase the membrane potential. Thus, one would expect that, at least for some period of time, the cell would be "stuck" in a depolarized state.

How long can this state last? Can a neuron go on indefinitely in a depolarized state if potassium ion channels are blocked? Will it find some other way to depolarize the cell? Will the cell die?

The voltage-gated potassium channels are there only to swiftly repolarize the membrane potential. Ultimately it is the Na,K-ATPase that has to pump the various ions back where they belong (Na out, K in), also when potassium channels are active. So when the potassium channels are blocked, the Na,K-ATPase will restore the membrane potential, albeit in the order of seconds instead of milliseconds.


Order of samples for RNA extraction I want to extract RNA from various tissue samples, liver, gut etc, in different treatment groups. Due to the large amount of samples I will extract in sets. I am wondering, in reducing the potential for contamination whether it will be better to extract by tissue type or by treatment?

What you do not want to do is prep all your control samples on one day, and all your treated samples on another day, because you will not be able to separate differences caused by treatment from differences caused by batch effect.  I'd worry more about that than from cross contamination.  Since you probably aren't comparing the different tissues to each other, batch effect between tissues won't be much of a problem.  So do all your spleen samples, treated and untreated, on one day, all your kidney samples the next, etc.


Is viral single-stranded RNA in the absence of reverse transcriptase infectious? In a medical microbiology textbook I'm reading (Murray et al, 1994), the authors state the following:

The retrovirus genome has a 5' cap and is polyadenylated at the 3' end. Although the genome resembles a messenger RNA (mRNA), it is not infectious because it does not encode for a polymerase that can directly generate more mRNA. The genome consists of at least three major genes that encode for the enzymatic and structural proteins of the virus: gag (group-specific antigen), pol (polymerase), and env (envelope). At the end of the genome are long terminal repeat (LTR) sequences

From this, I interpreted that because viral RNA doesn't encode an RNA polymerase, it is not itself infectious. However, if a cell were to be injected with retroviral single-stranded RNA alone, wouldn't this RNA be translated into proteins (including reverse transcriptase) as if it were normal mRNA into a protein? If this were correct, then the single-stranded RNA has all the information in itself to propagate the virus. Single-stranded RNA needs to be reverse-transcribed into the host's DNA before being transcribed into mRNA that can be translated.
Is there something different between viral RNA and the mRNA transcript that makes one translatable and the other not?
Source: Murray, Patrick R et al, Medical Microbiology (1994), Second Edition.
EDIT/UPDATE
I contacted the author of this chapter (Dr. Ken Rosenthal) and gained some more insight into how this hypothetical (injecting plain retroviral RNA into a cell) would play out. His answer is that yes producing new viruses possible but not probable. The reasoning for this is as follows:

The main reason that a new virus would likely not be created is that for the genome to make a new virus, reverse transcriptase is needed. Without reverse transcriptase, cDNA can't be made. Suppose that a ribosome was able to make reverse transcriptase with naked retroviral RNA and this newly made reverse transcriptase stayed near the ribosome. It would have difficulties making new cDNA from the original RNA template. One of those challenges is that cDNA synthesis needs a specific primer on reverse transcriptase.
The translated retroviral RNA would likely be degraded due to their finite lifespan in the cytoplasm.
There would need to be enough viral proteins translated to form a capsid. This would be unlikely considering the lifetime of the RNA in
Even if there were enough proteins in the cytoplasm, these proteins would then have to remove the RNA from the ribosome to encapsidate it. This is also unlikely.

Considering this, the microinjection of naked retroviral RNA would be an inefficient process to cause an infection.

In RNA viruses with a single-stranded genome, this RNA can be positive or negative sense. Positive sense RNA is directly translatable by a ribosome, while a negative strand RNA cannot be directly translated and therefore non-infectious. It either has to be converted to a positive strand RNA with the help of an RdRP (RNA-dependent RNA polymerase, carried in the virion) or reversely transcribed into a DNA which then serves as the template for generation of translatable mRNAs. In either case, this RNA is non-infectious in absence of the necessary proteins.
Note that positive strand RNA has to be propertly capped in order to be translatable. This is also not always the case - some viruses generate or steal the cap from the cellular mRNAs once uncoated in the cell.
Another aspect worth mentioning is that positive-sense retroviruses usually code for their genes in multiple reading frames and make heavy use of splicing to produce their proteins. Thus, directly translating their positive sense RNA is not sufficient for infection.
From Chapter 3 in Viral ecology:
For plus-strand RNA viruses except retroviruses, translation of the viral RNA
follows immediately after uncoating. The viral RNA extruded from the capsid is then
used by the host translation machinery for directing protein synthesis (Fig. 9).
For all other viruses, whether of DNA or RNA genome, the step immediately following
uncoating is either transcription of the genome yielding functional mRNAs or
reverse transcription of vRNA yielding proviral DNA (retroviruses).

References:

Viral Ecology
Principles of Virology


Is a Linker sequence mandatory in primers for PCR Cloning? I have designed the primers for PCR cloning, but i was not getting any colonies after the ligation. One of our colleagues said, that the restriction digestion might not be working as there is no linker sequence before/after the restriction site in the primer. What measures should I take to be successful in the cloning?

This is the website you need, and yes, most of the time it's better to have several extra bases at the start of your primer.

https://www.neb.com/tools-and-resources/usage-guidelines/cleavage-close-to-the-end-of-dna-fragments


Why are the organs for reproduction and urinary excretion combined? We eat food for getting energy to our body parts, and we excrete the wastes through urine, feces, and perspiration.

Why has nature combined the urinary tract with the genital system (urogenital system) in humans?

Developmentally, the urinary and genital systems (typically you will hear them referred to as "urogenital system") are derived from the same embryonic tissue, the intermediate mesoderm. The embryonic kidneys are drained by the mesonephric duct in both females and males. This embryonic tissue also gives rise to the ovaries and testes. The mesonephric duct degenerates in females, and becomes the ductus deferens in males. A second tube, the paramesonephric duct develops in both, but degenerates in males. The female paramesonephric duct becomes the uterine (Fallopian) tube.

Embryonically, the ureter, which drains the adult kidney is connected to the mesonephric duct. This connection is maintained in males, so that both urine and semen share a tube (urethra) for some of their exit pathway. In females, the paramesonephric duct and urethra are separate, so there are two openings.

In males, sphincter muscles and autonomic control prevent the simultaneous expulsion of urine and semen.

This system has worked acceptably well in mammals for at least about 200 million years (and in humans for the last 4 million or so), so I think it's not correct to call it a mistake. It's not how you would consciously design such a system, but evolution doesn't have a conscious designer.

Here are some slides that cover the embryology of the human urogenital system.


Why do you need you room dark for melatonin release? There is a light pollution movement that says lighting at night obstructs melatonin production. They say:

  What makes you fall asleep are changes in the level of the hormone
  melatonin circulating in your body. During the day, light stimulates a
  part of the brain. This brain part (known as the suprachiasmatic
  nucleus) tells the pineal gland to decrease the melatonin level when
  it is light out and to increase it when it is dark. The brighter the
  light, the bigger the decrease and the darker the dark, the bigger the
  increase of melatonin. By making your days lighter and your nights
  darker, you can improve both the quality of your sleep and the amount
  of time it takes you to fall asleep.

and recommend all kind of protection against the light,

  Dark Nights: Make your nights as dark as possible. Draw the curtains,
  close the shades and keep the lights off. Try a sleep mask if you
  can’t get eliminate enough light. The darker your night, the quicker
  you will fall asleep.

Do I sense the light by the whole skin surface or only open eyes? If you sense by eyes, which are closed during the sleep, then what is the problem?

In other words, the question is: is the sleep mask sufficient for melatonin secretion or you need to cover the skin?

update What if I close only one eye? I tend to do this when the blinding sun shines. Does such light eject melatonin?

The release of the hormone melatonin is responsible for the feeling of sleepiness. It is released by the pineal gland and production starts when the light fades, as it's production is inhibited by light stimulation of the retina, the onset of the production is called dim-light melatonin onset.

Read more about this at this previous answer.

This study on blind people will show you that the light entering the eyes is the (main at least) regulator of melatonin rhythms. They took blind people, 19 of whom could perceive light and 30 who could not, and showed that 14 of 19 light perceivers had normal melatonin rhythms while 23 of the light-blind people had abnormal or unclassifiable rhythms.


How are our senses dimmed during sleep? Our senses are not as sensitive during sleep compared to wake. There is an arousal threshold during sleep that only when it is overcome will it wake a person up. My question is how is this arousal threshold lowered as sleep progresses? And how it is raised again during the latter stages of sleep?

At night several changes occur in the body due to absence of sunlight and other surrounding changes. The biological clock inside the body performs certain function in a healthy body whenever changes are sensed.

There are many receptors in our body located on cell membrane. They are made up of proteins and their function is to receive information from neurotransmitters. This information will be sent to specific part of the brain. If we take sensory information then it is Parietal lobe. This lobe receives the sensory information from all over the body and responds to it when body is active. During sleep, the senses that go through the thalamus, are shut down by gating either in the Nucleus Reticularis Thalami (NRT) or in the Thalamus itself. GABAergic inhibition of the thalamus, most likely deriving from the NRT is probably a part of the reason that sensory stimuli doesn't penetrate during sleep.

This is also influenced by release of hormones in the body whose level when rises in the blood causes certain changes in the concentration at some regions such as receptors which gets blocked temporarily and stops signaling the brain. There is a study on how muscle relaxes when we sleep can be found here Muscle sleep. So it is all the neurotransmitters job at the receptors which stops signals going into brain but internal to the brain it will be active controlling other routine works which it has to do when we are asleep.

The main thing to note here is the 5 different stages of sleep such as non-REM and REM sleep. During those stages several changes take place in the body. The below website gives an excellent insight into different changes happening inside the body when body takes rest at night.

Please refer to "What happens to your body while you are asleep".


Can the activity of a specific gene in a cell artficially be increased? While there are many gene regulation mechanisms from the cell itself, I was wondering whether it is possible to increase the gene activity in a living cell permanently (so that the protein that it codes for is produced in higher amounts) using methods of biotechnology (i.e. no external factors)? Are there any studies or experiments regarding this topic?

There are technologies available for inducing higher (or lower) gene expression in cultured mammalian/human cells as well as in bacteria. The state of the art is CRISPR-mediated gene activation/repression, where you fuse a transcription activation domain to a Cas gene in a CRISPR-Cas system (usually Cas9), and provide a guide RNA to target genes of interest. This Cas gene is made "nuclease-dead" so that it can only target but not cut or degrade DNA (as opposed to natural CRISPR-Cas systems that do both), and serves to bring the transcription activation domain to your gene of interest, which leads to an increase in transcription of that gene.

Check out this paper for an earlier example of such a system in cultured cell lines. The field has advanced quite a bit since then, and people have successfully activated genes in mouse lines


Preventing Diabetes by preventing stress? I have came to know that taking a lot of stress increases the risk of Diabetes, and patients of Diabetes are adviced not to take too much stress, am i correct? if yes then I am unable to understand that how stress affects the level of glucose in our blood?

Prolonged stress leads to elevated levels of cortisol. Cortisol interacts with insulin action and blood glucose levels in various ways, essentially promoting hyperglycaemia.


How do tight junctions in stratified squamous epithelia affect nutrient supply? In histology we know that epithelium tissue isn't vascularized so it takes the nutrition from Lamina propia (CT) via diffusion and in other hand we know all epithilial cells have tight junction which inhibits the flow of substance so how can it diffuse nutrients between themselves because of the tight junction how can they distribute nutrients, same way in capillaries which are endothelium  how interstitial fluid passes throw endothelial cells because of thier tight junction?

Tight junctions function to occlude the baso-apical flow of small molecules. However, tight junctions do not always completely seal a cell's lateral surface. In addition to regulating diffusion, tight junctions promote cell polarity. Establishment of polarity and prevention of water loss are the major roles of tight junctions in stratified squamous epithelia.

In simple epithelia, transcytosis allows the flow of molecules through a cell with tight junctions. However, stratified squamous cells do not use transcytosis for nutrient supply.

In the stratum granulosum, skin cells lose their nuclei and become non-viable. In the stratum lucidum, an oily layer is produced by exocytosis.

It is the loss of nuclei, organells, production of an oily layer at the stratum granulosum and lucidum that contributes most to the death of skin cells, not the limits of nutrient diffusion.


Clarify pre-column pressure vs. system pressure vs. backpressure for prepacked columns used with the äkta purification system Background: I am using the Äkta pure system for protein purification, with prepacked columns from GE-healthcare. Just to take one example, I use the HisTrap 5 mL column (IMAC: immobilized metal affinity chromatography). I understands the effects of over-exceeding the pressure limits of a column, and therefore vigorously set the pre-column pressure to 0.5MPa everytime I use the äkta. However, I am starting to question or how I should think about the different pressure, and if 0.5MPa is correct for the different columns I am using.

I was taught to always set the pre-columns pressure, which makes sense since as far as I can tell – this is the actual pressure inside the column (pressure felt by the resin). However, If I open the documentation on the HisTrap 5 mL column from GE-healthcare, I can’t seem to find much about the pre-column pressure limit. I also find the terms max-backpressure limit in the documentation for the column, and system pressure.

Questions: How is the system pressure different from the pre-columns pressure? Should I calculate the pre-column pressure myself as an effect of the size and length of the tubing leading to the column? Is there a good article or webpage that goes through this theory at a basic level?

It seems obvious, but how can backpressure be created in a system that is not closed and goes one way (or perhaps the Äkta is creating the pressure)?

Is there a good article or webpage that goes through this theory at a basic level?

Yes, Chapter 7 of the manual linked to by Andreas Tosstorff is a good source, and is also the source of the images below. The manuals for your ÄKTA system and the HisTrap columns discuss pressure in some detail as well.

How can backpressure be created in a system that is not closed and goes one way?

This is a physics question and, not being a physicist, I can't go into detail. However, I also use the ÄKTA system for FPLC and may be able to provide some form of an answer. Any fluid moving through tubing experiences some resistance from, for example, friction between the fluid and the tubing walls, bends in the tubing and obstructions like filters, mixers, valves, etc. Even though the system is open at one end, there is resistance to the flow of fluid through it which creates backpressure. The largest sources of backpressure in the FPLC system at low flow rates are filters, flow restrictors (if installed) and the column itself.

How is the system pressure different from the pre-columns pressure?

The system pressure for the ÄKTA is measured at the pump. This measurement in itself is not very informative. The pressures that are important as far as keeping your column safe are the pre- and post-column pressures (the pressure measured immediately before and after the column, respectively), and the difference between these two (the pressure across the column). Your column has two pressure limits:

Hardware pressure limit: this is the maximum pressure the column itself will withstand before there is a risk of failure. I know this from experience after a malfunctioning valve gave 4 times the maximum hardware pressure to my column. In my case, failure meant the top of the column blowing. The pre-column pressure should not exceed the hardware pressure limit.
Resin pressure limit: this is the maximum pressure the resin within the column can withstand before collapsing. The pressure across the column should not exceed the resin pressure limit.

Should I calculate the pre-column pressure myself as an effect of the size and length of the tubing leading to the column?

Some ÄKTA systems are capable of measuring pre- and post-column pressures directly. Mine is not, and I don't know about yours. In the case where pressure is measured at the pump, the pre-column pressure is equal to backpressure between the pump and the column (caused by the tubing/filter/etc.) subtracted from the measured system pressure. To determine this, you essentially disconnect the top of the column, run the system under your intended conditions and record the measured pressure (this is the backpressure generated before the column). The manual for my columns (HiTrap Q) explains this step by step, and yours may as well.

The manual also explains how to determine pressure across the column in a similar manner. However, in my experience, the flow path after the column is relatively unrestrictive (unless a flow restrictor is installed), and its contribution to backpressure is relatively be negligible. Thus the pressure across the column is reasonably equal to the pre-column pressure, which is also reasonably equal to the measured system pressure. Furthermore, listed in every manual I read is some statement to the effect of:

  The maximum pressure over the packed bed (Δp) is an approximate limit. It is dependent on the characteristics of the chromatography medium and on sample/liquid viscosity. The measured value also includes the pressure generated by the column tubing. For many columns, the recommended flow rate is a better guideline for protecting the packed bed.

In fact, the manual for my columns doesn't even list the resin pressure limit and it took substantial digging to find out what it actually is. I always run at the recommended flow-rate and set the system pressure alarm at the resin pressure limit (0.3 mPa in my case versus 0.5 mPa hardware limit) without any of the corrections mentioned above. However, depending specifically on your system and usage, it may be necessary to make them.


Can a gene be split between different genomic locations several kb appart? Can you have exons and introns of the same gene separated by hundred of kb in a genome? If so, how is the full mRNA assembled in such distance?

I'm working on plant mitochondria and I've seen an annoted gene that is cut between very distinct part of the genome.

Yes you can have exons and introns of the same gene separated by hundred (even thousands!) of kilobases.

Here is an example for the human genome:
"On average, there are 8.8 exons and 7.8 introns per gene. About 80% of the exons on each chromosome are < 200 bp in length. < 0.01% of the introns are < 20 bp in length and < 10% of introns are more than 11,000 bp in length."

Source: https://www.ncbi.nlm.nih.gov/pubmed/15217358

For the splicing process, it is not really a problem for the distance. Let me reframe the questions by challenging the assumption you are making: long distances in a sequence correspond to long distance in space.

Actually, DNA/RNA molecules are can have a lot of tertiary structure for example, G quartets for DNA, hairpin structure for RNA.

Source: https://upload.wikimedia.org/wikipedia/commons/5/5d/ATPC_secondary_structure.jpg

Long sequence distances are a poor indication of the real distance in space. Thus although from an engineering point of view it is incredible what molecular splicing can achieve mechanistically speaking. As far as I remember, the length for the intron/exon is important for the efficiency/timing of the splicing process (I might be wrong here on the specifics).


How some virus are able to reach the CNS? I know that the lymphocytic choriomeningitis virus (LCMV) could provoke meningitis and encephalitis when this virus reaches the brain. However, there are other viruses like Varicella (VSV), Cytomegalovirus (CMV) or Herpes (HSV) that are able to reach the brain, hence, to pass trough the blood-brain barrier (BBB) and damage the central nervous system (CNS).

1) Since the blood-brain barrier allows only the free diffusion of some molecules such as water, some gasses and lipid soluble molecule, I was wondering by which mechanism a virus is able to pass trough the BBB.

2) Since the CNS is an immuno-privileged space (where basically the immune system is down-regulated), how does the body eliminate a virus that had reached the brain?

some viruses like rabies get into the peripheral nerves, and travel through those to the spine , unimpeded by any obstacle.


Use of sunlight in biological processes Sunlight is used by green plants in photosynthesis, but it is also used by animals in the synthesis of Vitamin D. Are there any similarities between the two processes and how is the light energy actually used?

We don't get it from the sun, it's synthesized.

Humans can get it...

via nutrition.
via synthesis in the skin, which depends on UV radiation. Sun is the major source of it (the radiation, not the vitamin), and synthesis in the skin the major source of the vitamin. However, it needs further modification in the liver or kidney to become bioactive. UV radiation is necessary and directly causing the opening of a cyclic molecule structure, changing a cholesterol to a previtamin D3.

For more details see chapter 'Biosynthesis' at https://en.wikipedia.org/wiki/Vitamin_D


How can a heart of human work if one of its valve is not working? Yesterday I went to a hospital and heard a doctor say that one of the heart valves of a patient is not working. However, the patient was still alive and was healthy; the patient could walk and talk too. I could not understand it because I have read that all valves of heart are extremely important. I have tried searching on google but all I could find was heart attack problems.

It is not possible that one of the valve is completely closed and the person is still alive without being in ICU. I think what the doctor was trying to communicate to the patient was that one of the valves is in the process of complete closure. There are three main types of diseases associated with heart valves :-

1- Blood flows backwards
2- Heart valve opening becomes narrow
3- upper condition may lead to complete closure

For details see the following link:-

http://www.nhlbi.nih.gov/health/health-topics/topics/hvd
http://en.wikipedia.org/wiki/Pulmonary_atresia

Hope you understand. :)


Questions regarding PCR Background:

From Genomes:

The temperature of a PCR mixture is first set at 94 °C so that denaturation of DNA can happen. Then it is reduced to 50–60 °C, which results in some rejoining of the single strands of the target DNA, but also allows the primers to attach to their annealing positions. After this DNA synthesis begins as the temperature is raised to 72 °C, the optimum for Taq polymerase.

  In this first stage of the PCR, a set of ‘long products’ is synthesized from each strand of the target DNA. These polynucleotides have identical 5′ ends but random 3′ ends, the latter representing positions where DNA synthesis terminates by chance.
  [Subsequent cycles give] rise to ‘short products’ whose 5′ and 3′ ends are both set by the primer annealing positions.

Now Wikipedia says:

  [...] Final elongation: This single step is optional, but is performed at a temperature of 70–74 °C (158–165 °F) (the temperature range required for optimal activity of most polymerases used in PCR) for 5–15 minutes after the last PCR cycle to ensure that any remaining single-stranded DNA is fully elongated.

Questions:

I’m wondering that if the shortening of the length of new DNA is purely by chance. From Wikipedia it appears that the length of the DNA synthesised can be controlled by the temperature of the mixture?

  To carry out a PCR experiment, the target DNA is mixed with Taq DNA polymerase, a pair of oligonucleotide primers, and [...]

A pair of primer cannot support the increasing number of PCR cycles, are primers added later/ throughout the process?

Besides it seems to me that the temperature of the mixture has to be changed according to the phases of the cycle. Is it changed? How is it determined that which phase of the cycle the DNAs are in?

P.S. I'm not sure if this post should be broken down into two posts or more. Suggest if you feel that's necessary.

Ideally amplification happens between the two primer pairs and results in one product. However, complicated secondary structures, the depletion of some of the reagents may cause pauses and fall off of the polymerase. This happens often later in the reaction and results in shorter products. This final amplification step is introduced to finish all these shorter products.
A pair means the combination of a forward and a backward primer (see the image below from here). Bothg primers are added in a concentration high enough that both are not depleted and enable long PCR runs. No primers (or other reagents) are added during a standard PCR reaction.

The temperature of the PCR reaction is changed through 1 reaction cycle: First you start with the denaturation of the DNA at 94°C, then cool down to anneal the primers (typically between 50 and 60°C, depending on the primers), followed by the amplification step at 72°C (it'S length depends on the length of the amplified DNA piece, Taq polymerase processes about 1kb/min) (see figure below from here). This is one cycle and you know where you are, because the PCR machine counts this cycles.


What is the basis for the determining sex from position of adult pelvis? I've read that a person with enough knowledge of anatomy can tell the difference between a "woman" who is a slim man that is very good with makeup and an actual woman.

They usually claim to be able to tell the difference between the two by certain things like digit ratios and pelvic position. Is there any basis to these claims? The one I'm specifically interested in is the "position of the pelvis", as that is the most recent example of the claim I've seen. This is a direct quote from a  novel that I'm reading.

EDIT: it looks like I phrased the question badly. As anongoodnurse stated, I'd like to know if there's any basis for telling if a living person is a man or a woman by looking at them.

An example is if you dress up a slim man with a feminine looking face, get a make up artist to make the face look like a very attractive woman, and put that man in a little black dress, would a person knowledgeable about human anatomy, for example a GP MD, OBGYN, mortician, or Sherlock Holmes (kidding), is there any basis for that person to be able to say: "nope, that's a dude".

"Position of the pelvis" is pretty vague, but there are very clear differences in pelvic morphology between females and males. This sexual dimorphism looks like:

Female pelves are wider and flatter, which I think you could tell from surface anatomy. Of course if you could palpate, then you could tell for sure.


Problem with an analogy (Cell Membrane) I'm studying biology for the first time seriously. I've been reading OpenStax College's material.
In the section of "The Cell Membrane", I have the following problem:

Choose the answer that best completes the following analogy: Diffusion is to ________ as endocytosis is to ________.

filtration; phagocytosis
osmosis; pinocytosis
solutes; fluid
gradient; chemical energy

I chose number 1, but the site says the correct answer is number 2. Could someone please explain why?

[EDIT]

I chose number 1, because diffusion and filtration were passive ways to transport, while endocytosis and phagocytosis are active. I didn't not take in to account that 2. fitted better, because the osmosis part was confusing me.

Osmosis is the diffusion of water.  Pinocytosis is the endocytosis of liquid/water.


Lost Ability to Regenerate Body Parts during the Transition from Amphibians to Mammals Why have higher-order animals lost the ability to regenerate body parts during evolution? Wouldn't it be better for survival? What is the evolutionary theory behind it?

Regeneration of limbs in amphibians is an adaptation where new limbs are generated by dedifferentiated cells. This process is tightly linked to the embryonic program which, in most animal cells, is a difficult program to access once terminal differentiation has occurred (but it's possible, e.g. induced pluripotent stem cells).

Of note, amphibians have a unique life cycle that includes metamorphosis. It is thought that organisms with more diverse stages in their development may have increased potential for regeneration. Mammals, after birth, do pass through multiple stages of development, but these stages are largely continuous.

So the quick answer is: mammalian limbs are made up of terminally differentiated cells (and specialized stem cells) with high barriers of reprogramming. They're difficult to reprogram because there hasn't been strong selective pressure to do so. Limb regeneration might seem like a great adaptation, but it doesn't seem to be that important for the success of mammals. Additionally, selection for "maintaining a full set of functional limbs" could evolve many different ways. For example, primates may have evolved behaviors or reinforced anatomy that reduces their risk of injuring a limb. Also, larger animals are probably less likely to have limbs removed just given their size. And if they do, it may have little effect on their reproductive fitness. A legless amphibian probably finds few, if any, mates.

Yun Gates, and Brock. Regulation of p53 is critical for vertebrate limb regeneration, PNAS 2013


Humidity for wood rotting If I put a piece of wood in a humid environment (basically humid air), it will start to rot. Does the humidity influence the rotting speed, and if so, what is the relation between the rotting speed and humidity?

Rotting is a biochemical reaction: basically catabolism (breaking down of complex compounds to simpler compounds). Cellulose or lignin or any other structural polysaccharide will not undergo spontaneous hydrolysis. This reaction is catalyzed by enzymes produced by the microorganisms like fungi and bacteria (the term for these decomposers is saprophyte). Saprophytes prefer to grow in humid and warm environments.

So the primary role of humidity is to promote the growth of decomposers. Simultaneously it provides the water required for the hydrolysis.


Which DNA sequence will have higher melting temperature: CCCCCC... or GCGCGC...? I tried this service to calculate temperatures. The nearest neighbour method consistently gives larger results for sequences like GCGCGC over sequences like CCCCC or GGGGG, while other methods don't give a difference. Is it nearest neighbour's feature or is there indeed a difference in melting temperatures?

The dependence of melting temperature on different dinucleotide pairs was experimentally measured; the meting temperature calculator is based on those results. Based on these results, you would see that a GC dinucleotide pair would differ from GG and CC pairs. Possibly, this is because of steric effects and stacking conformations.

SantaLucia (1998; author of the nearest neighbour model) has referred to different experimental studies from which the values were obtained, in the Table-1 of the paper.


Difference between KEGG Pathway and Module (from KO mapping) At the KEGG otholog mapping query page I can map pathways and modules. I can't seem to find an extremely low level description of the difference between the two. I think I understand what a pathway is. I can't seem to find any definition or description of what a module is.

A pathway shows all the reactions required for the synthesis / metabolism of a given product.  A module is a functional unit that can be utilized in a pathway, and some modules are common to many pathways.  For example, look at the tetracycline biosynthesis pathway 00253.  This pathway has a description at the top that includes this excerpt:

  Tetracyclines contain a linear tetracyclic skeleton, which is formed from a malonamate starter unit and malonyl-CoA extender units through a common polyketide pathway [MD:M00778].

Confusingly, that "common polyketide pathway" is actually a module, Type II polyketide backbone biosynthesis, acyl-CoA + malonyl-CoA => polyketide or M00778.

Note that this module is included in other pathways:

  map01056 map00253 map01100 map01130

Looking at the drop down menu at the bottom of the module page, we see that the Reference Module contains multiple different KEGG Orthologs that perform the same function in different systems.

Choosing an organism from the drop down menu, the specific Orthologs used by that species are highlighted.

So, you can see how separating pathways into modules can help in identification of these components in other organisms, even if the full pathway does not exist.


Isotype control antibodies in Flow Cytometry In a Flow Cytrometry, one can add an Isotype Control Antibody to allow another antibody to bind more specific to the cells.

My question is, how can the Isotype Control Antibody add specificity to the other antibody?
My thought was, that the Isotype Control Antibody binds to all the antibody receptors, but with a "weak" binding. When the other antibody (e.g. CD73) tries to bind, it can make a stronger binding with the CD73 antibody receptor, kicking the Isotype Control Antibody off it.

However i'm entirely not sure this is correct... Could anyone explain how the Isotype Control Antibody helps the other antibody (eg.g CD 73) to bind more specific?

I don't believe that the Isotype Control Antibody makes the antibody bind more specifically but rather ensures that your signal is specific to your antibody.

The Isotype Control Antibodies tend to bind to the non-binding domain of the antibody, typically the constant (Fc) domain. By measuring the concentration of the control antibody, you can determine what percentage of your light signal comes from your primary antibody and not from non-specific binders to your light source.

This is very similar to having secondary antibodies in your assay.

Random link showing that I'm not making stuff up


How do members of cryptic species know who to mate with? According to Wikipedia:

  In biology, a cryptic species complex is a group of species which
  satisfy the biological definition of species—that is, they are
  reproductively isolated from each other—but whose morphology is very
  similar (in some cases virtually identical).

How do members of these species know who to mate with?  Or would they unknowingly mate with incompatible partners?

As both @Rory M and @Alexander Galkin suggest, there are various non-visual mating behaviors to allow these species to select mates and also allow taxonomists and researchers to identify these species. And they hit on the two major ones, courtship rituals (mating calls, throat bulging, dancing) and pheromones.

Let's have a look at some two examples:

The widespread amazonian frog Allobates femoralis is now being approached as a species complex, with mating differences between the biologically distinct species varying from mating call note differences to cephalic amplexus (head grabbing during mate selection) and other various behavioral differences.[1]
Some crickets mate preferentially based on their species-specific song. Though, there is probably some genetic mixing with those crickets.

I think it's important to note that the species are cryptic because we as humans have decided they're hard to tell apart. Now, that similar morphology is also potentially difficult for predators to tell apart, or may be used by one or both species to parasitize on the other, it may be kept similar by sexual selection, or it may just not have great selective pressures to change. But the important part is that "cryptic species" is a box that we've created to describe traits we see.

Cryptic species as a window on diversity and conservation is a decent overview paper. (it's avaliable here if you don't have journal access)


Differential gene expression analysis between species I have RNA Seq data from mouse and human skin ( 2 replicates each) and want to compare the expression of the orthologous genes to find any which are differentially expressed.
I have quantile normalized the gene expression matrix across all 4 samples (2 mouse + 2 human). I eventually want to calculate the log fold change in expression of all orthologous genes between the 2 species. However before I do this, I should control for gene length, right? Will this be enough to give me an idea of the differentially expressed genes or should I be employing more sophisticated methods?
Any comments would be helpful. Thanks a lot.

It depends on what type of data you have, really. There are methods developed solely for quantifying relative expression based on count data, such as using edgeR or limma-voom.

You don't need to correct for gene length to estimate fold-changes of relative expression, what you need to do is normalise by library size first (and in the process obtain log2 ((counts + 0.5)/1e+06) and then, following quantile normalisation, you can just calculate mouse - human or human - mouse to give you an estimate of fold change.

I still would recommend using something a bit more sophisticated like limma-voom for this task, though, because that also will enable you to get stuff like false-discovery rates for your fold changes.


What alternatives are there to the amyloid hypothesis? Given the recent failure of the Bapi clinical trial, there is a lot of questions that have arised from he amyloid hypothesis. However, I can't really think of many other mechanisms that don't involved plaque formation via protein aggregation.

What are the other dominant proposed mechanisms for the biochemistry of Alzheimers?

Reference: Alzheimer’s Drug Fails Its First Big Clinical Trial. Unfortunately, the results of the study have yet to be presented at a medical conference but will be in September.

Alzheimer's disease is a very complex field, and I am going to restrict my answer to two particular areas: the neuritic plaques and the neurofibrillary tangles. This area is also of interest to me, hence the protracted answer.

The two pathological hallmarks of Alzheimer's disease, first described by Alois Alzheimer in about 1906, are the extracellular neuritic plaques and the intracellular neurofibrillary tangles which occur (exclusively) in the brain of humans with this disease.

The Neuritic Plaques (Amyloid Precursor Protein and β-Amyoid)

[References to the information given below may be found in Price & Sisodia (1998) and in Lowery et al. (1991)]

The major component of the extracellular neuritic plaques is a small, appromimately 4 kDa protein known as the β-Amyloid (Aβ),  or A4-protein.

The Aβ, whose tertiary structure is that of a β-pleated sheet, is itself derived by proteolysis (see below) from a much larger protein known as the Amyloid Precursor Protein (APP).

A number of isoforms of Aβ are known which contain between 36 and 43 amino acids, the most common of which are  Aβ40 and Aβ42.
The Amyloid Precursor protein (APP) is a very large protein (≥ 695 amino acids) of unknown function which is a normal component of brain. It is predicted to have a single transmembrane span.

A number of isoforms of this protein are also known, which contain  695, 714, 751 & 770 amino acids.

The AA751 and AA770 isoforms contain a domain (Kunitz domain) homologous to a class of protease inhibitors, strongly suggesting the proteolysis plays a key role in normal function, and perhaps in (abberant?)  Aβ formation.
One of the cleavages which produces the Aβ, that catalyzed by γ-secretase, occurs within the transmembrane-spanning domain of APP.  How the protease has access to its substrate within the lipid bilayer is a major source of interest.

Researchers who believe that neuritic plaques and  Aβ hold the key to Alzheimer's disease are known as baptists. Their counterparts, who believe that the neurofibrillary tangles are key, are known as tauists, for reasons that will become obvious (see also here).

For the past number of years, baptists have been to the forefront. In my view, the tauist story is even more interesting, and must surely be important in any final understanding of Alzheimer's disease.

 Neurofibrillary Tangles, Paired Helical Filaments and Tau Protein

Examination of the neurofibrillary tangles under the electron microscope revealed that they had a twisted ribbon-like structure which was called the paired helical filament (PHF) (Kidd, 1964; Wisniewksi  et al., 1984).

PHFs are practically insoluble and for a long time this impared progress.  However, extraction using the detergent sarkosyl, followed by sequence analysis and immunological investigations, produced a  major surprise:

  A component of the paired helical filament is the
  microtubule-associated protein tau (Goedert et al., 1988;
  Wischik et al., 1988), a most unusual and interesting soluble protein
  which had already been purified to homogeneity and extensively characterized by Kirschner & co-workers
  (Weingarten et al., 1975; Cleveland  et al., 1977a, 1977b).

A perusal of pubmed shows that at this stage interest in tau increased dramatically!

  It is now accepted that microtubule-acssociated protein tau in a
  hyper-phosphorylated state is the major structural component of the
  paired helical filament (Lee et al., 1991; Kosik & Greenberg, 1994).

Some key properties of tau are the following.

Tau was first isolated as  a series of closely related proteins (isoforms) which co-purify with porcine tubulin during successive cycles of polymerization/depolymerization (Weingarten et al., 1975).  On an SDS gel, one sees (with bovine brain tau) 4 bands quite close together from (say) 58 - 64 kDa.
Interaction with tubulin is the only known 'normal' function of tau.  It promotes the polymerization of tubulin into microtubules under polymerization conditions, for example (Cleveland  et al., 1977a, 1977b).
Tau is encoded by a single gene, located on chromosome 17, and differential mRNA splicing gives rise to the brain isoforms (six in humans and four in cow) [Andreadis et al., 1989; Goedert et al., 1989; Himmler, 1989], and a single high molecular weight tau ('big tau') in peripheral tissues (Goedert et al., 1992).
Tau contains a series of imperfect amino-acid repeats, located in the C-terminus of the protein.  These repeats are thought to be responsible for microtubule binding (see, for example, Lee, 1990).
Although tau occurs in a hyper-phosphorylated state in the PHF, and may be phosphorylated in normal brain, phosphorylation is not necessary for formation of paired-helical filaments (Goedert et al., 1996).
The tau gene may be knocked out without any visible alteration of phenotype! (experiments done in mice) (Harada et al., 1994).
Mutations in the tau gene are not known to cause Alzheimer's disease, but are associated with very rare 'taupathies', such as an inherited dementia called frontotemporal dementia and Parkinsonism linked to chromosome 17 (FTDP-17; possibly identical with Pick's disease) [Hutton et al., 1994].
The crystal structure of tau has not been obtained to date.  Current thinking is that the soluble form of tau is mainly a random coil (see von Bergen et al., 2006).

The fact that tau can be knocked  without serious consequence, together with the lack of mutations causing Alzheimer's,  has led to much criticism of the tauist story.

However it still is the major structural component of the paired helical filament (neurofibrillary tangles), and must surely be a key player in the understanding of Alzheimer's disease.

This is not to imply that Aβ and tau are the only shows in town.  As stated above, the field of Alzheimer's disease is very complex

An allele of Apolipoprotein E (ε4 allele) is genetically associated with an increased risk in late-onset Alzheimer's, for example (Corder et al., 1993).

Mutations in the presenilin genes are also associated with the disease (Sherrington et al., 1995).  Presenilins form part of the γ-secretase protease complex involved in Aβ formation (see Takeo et al., 2012).

I do not know enough about these fields to comment any further (although this does not usually stop me).

It should be emphasized, however, that most cases of Alzheimer's disease are sporadic, and only a small subset has a genetic component. It is a disease of the brain, and of aging. There is no known cure, no known cause and no reliable (biochemical) pre-mortem test (although a clinic diagnosis may of course be made).

References

Andreadis, A., Brown, W. M. & Kosik, K. S. (1992) Structure and novel exons of the human tau gene. Biochemistry, 31,  10626-10633.
von Bergen, M, Barghorn, S, Jeganathan, S, Mandelkow, E.M., Mandelkow, E.  (2006) Spectroscopic approaches to the conformation of tau protein in solution and in paired helical filaments.  Neurodegener. Dis. 3, 197-206.
Cleveland, D. W., Hwo, S.-Y. & Kirschner, M. W. (1977a)  Purification of tau, a microtubule associated protein that induces assembly of microtubules from purified tubulin. J. Mol. Biol. 116, 207-225
Cleveland, D. W., Hwo, S.-Y. & Kirschner, M. W. (1977b)  Physical and chemical properties of purified tau factor and the role of tau in microtubule assembly. J. Mol. Biol. 116,  227-247.
Corder, E.H., Saunders, A.M., Strittmatter, W.J., Schmechel, D.E., Gaskell, P.C. Small, G.W. Roses, A.D., Haines, J. L. & Pericak-Vance, M.A. (1993) Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer's disease in late onset families. Science 261, 921-923.
Goedert, M., Wischik, C. M., Crowther, R. A., Walker, J. E. & Klug, A. (1988)  Cloning and sequencing of the cDNA encoding a core protein of the paired helical filament of alzheimer disease:  Identification as the microtubule associated protein tau. Proc. Natl. Acad. Sci. USA  85, 4051-4055. [pdf]
Goedert, M., Spillantini, M. G., Jakes, R., Rutherford, D. & Crowther, R. A. (1989) Multiple isoforms of human microtubule associated protein tau:  sequences and localization in neurofibrillary tangles of alzheimer's disease  Neuron 3, 519-526.
Goedert, M., Spillantini, M. G. & Crowther, R. A. (1992) Cloning of a big tau microtubule associated protein characteristic of the peripheral nervous system. Proc. Natl. Acad. Sci. USA 89, 1983-1987. [pdf]
Goedert, M., Jakes, R., Spillantini, M. G, Hasegawa, M., Smith, M.J. & Crowther, R. A. (1996) Assembly of microtubule-associated protein tau into Alzheimer-like filaments induced by sulphated glycosaminoglycans. Nature, 83, 550-553.
Harada, A., Oguchi, K., Okabe, S., Kuno, J., Terada, S.,  Ohshima, T., Sato-Yoshitake, R., Takei, Y., Noda, T. & Hirokawa, N. (1994). Altered microtubule organization in small-calibre axons of mice lacking tau protein. Nature 369,  488-491
Himmler, A. (1989)  Structure of the bovine tau gene:  alternatively spliced transcripts generate a protein family. Molec. Cell. Biol.  9,  1389-1396.[pdf]
Hutton, M., Lendon, C. L., Rizzu, P., Baker, M., Froelich, S., et al. (1998) Association of missense and 5'-splice-site mutations in tau with the inherited dementia FTDP-17. Nature  393, 702-705.
Kidd, M. (1964) Alzheimer's disease - an electron microscopical study. Brain 87,  307-320.
Kosik, K. S. & Greenberg, S. M. (1994)  Tau protein and alzheimer disease. In Alzheimer Disease.  Terry, R. D., Katzmann, R. & Bick, K. L., eds.  pp 335-344.  Raven k. Press, New York.
Lee, G. (1990) Tau protein:  an update on structure and function. Cell Motil. Cytoskel. 15, 199-203
Lee, V. M.-Y., Balin, B. J., Otvos, L. & Trojanowski, J. Q. (1991) A68:  A major subunit of paired helical filaments and derivatized forms of normal tau. Science 251,  675-678.
Lowery, D.E., Pasternackj, J.M., Gonzalez-DeWhitt, P.A., Zurcher-Neely, H.
Tomich, C-S. C., Altman, R.A., Fairbanks, M. B., Heinrikson, R. L.
Younkin, S. G.  & Greenberg, B. D. (1991) Alzheimer’s Amyloid Precursor Protein Produced by Recombinant Baculovirus Expression. Proteolytic Processing And Protease Inhibitory Properties.  J. Biol. Chem. 266, 19842-19850.  pdf
Price, D. L. & Sisodia, S. S. (1998) Mutant genes in familial alzhiemer's disease and transgenic models. Annu. Rev. Neurosci. 21, 479-505.
Sherrington, R, Rogaev, E.I, Liang, Y, Rogaeva, E.A, Levesque, G, Ikeda, M, Chi, H, Lin, C, Li, G, Holman, K, Tsuda T, Mar, L, Foncin, J.F, Bruni, AC, Montes,  M.P, Sorbi, S, Rainero, I, Pinessi, L, Nee, L, Chumakov, I, Pollen, D, Brookes, A, Sanseau, P, Polinsky, RJ, Wasco, W, Da Silva,  H.A, Haines, J.L, Perkicak-Vance, M.A, Tanzi, RE, Roses, A.D, Fraser, PE, Rommens, J.M, St George-Hyslop, P.H. (1995)  Cloning of a gene bearing missense mutations in early-onset familial Alzheimer's disease. Nature, 375, 754-760.
Takeo, K, Watanabe, N, Tomita, T, Iwatsubo, T.  (2012)  Contribution of the γ-Secretase Subunits to the Formation of Catalytic Pore of Presenilin 1 Protein.  J. Biol. Chem. 287, 25834-25843
Weingarten, M. D., Lockwood, A. H., Hwo, S.-Y. & Kirschner, M. W. (1975)  A protein factor essential for microtubule assembly. Proc. Natl. Acad. Sci. USA  72, 1858-1862. [pdf]
Wischik, C. M., Novak, M., Edwards, P. C., Klug, A., Tichelaar, W. & Crowther, R. A. (1988)  Structural characterization of the core of the paired helical filament of alzheimer disease. Proc. Natl. Acad. Sci. USA,   85, 4884-32768. [pdf]
Wisniewski, H. M., Merz, P. A. & Iqbal, K. (1984) Ultrastructure of paired helical filaments of Alzheimer's neurofibrillary tangle. J. Neuropathol. Exper. Neurol.,  43,  643-656.


Natural Killer Cell and Cancer NK cells are very effective in destroying circulating cancer cells before their extravasation into the organ, However they have only a minimal inhibiting effect on already established micrometastases.
Anyone knows why ?
Regards.

So we know that NK cells work by receiving activating signals through receptors, and then degranulate such that cytotoxic molecules enter the target cell, and induce apoptosis. NKG2D is such a receptor, and cells that are becoming transformatively stressed by mutations and the like upregulate expression of NKG2D ligands on their surface for elimination. This is one example, and NK cells have different subsets of activating receptors, such as NCRs. NKp30 and NKp44 are examples of NCRs and activate NK cells through detection of heparan sulfate compounds on the surface of tumor cells. The question, then, is what happens to cancer cells that can: (1) downregulate NK cell receptor ligands on their surface, or (2) abrogate NK cell receptor function in their vicinity?

In an earlier study, it was shown that mesenchymal stem cells broadly inhibit NK cell activity through activity of prostaglandin E2 and indoleamine-2,3-dioxygenase, which downregulates each of the three aforementioned NK cell surface receptors. A later study using melanoma cocultured with NK cells again came to the conclusion that the same cancer cell secretions would inhibit NK cell activation in their vicinity.

By the same token, if we consider a cancerous cell that upregulates MIC expression, NKG2D receptors will recognize this and activate the NK cells. A cancerous cell with a truncated MIC that lacks an extracellular domain will fail to activate surrounding NK cells through that pathway. Keep in mind: many mutations go into making a cell cancerous, and many more go into giving it enough fitness to avoid getting killed from the start. These are just examples of critical pathways that result in immunoevasion.

As for why are small masses more immunoevasive than single cells? This goes into a sort of power in numbers logic. A single tumor cell doesn't produce as much inhibitor compounds as a mass of tumor cells. This is an interesting concept because in the hunt for pro-angiogenic compounds, a problem for a while was you would remove a large mass, and a smaller unknown mass would quickly begin to grow. They found that although large masses secreted more pro-angiogenic compound, the tumor cells also secreted so much inhibiting compounds that smaller tumors in the vicinity were effectively inhibited. Once the large mass was removed, this inhibition got lifted.


Can someone link me to resources on the efficiency of sticky end ligation? I really would like to know if sticky end ligation could potentially be performed with very high efficiency, and which factors influence that.  However, I can't find any papers on the subject, even though I'm sure they exist.  I was hoping someone would know of some literature.

The best resource for troubleshooting ligations I found (and use frequently) is this NEB page.  That is assuming you've already referred to the instructions provided with the enzyme you're using.   In my case it's T4 Ligase, again from NEB.   It's helpful to check the FAQs and the references listed on that page.    Also, you can make use of their Molar Calculator tool on Ligation setting (see more from first link).

Good luck with high efficiency!


How big should the human population be, as predicted by body mass? I would guess there is a theory in biology which states that the population size for a given species is inversely proportional to the body mass of individuals in that species.  In other words, there are zillions of ants, billions of mice, millions of deer, and just a few elephants.

If humans existed in a "state of nature" (i.e., were not able to manipulate their environment more than any other mammal), what population size would be predicted by their ~70 kg body mass?

(Assume that the human population has spread globally.)

I imagine we would fall somewhere between the wolf and bear populations.

It is certainly possible to use general relationships to predict human population density or abundance. The relationship between population density/abundance and body size is an old topic in ecology that falls within the field of allometrics (how different features of organisms scale with body size). A closely related allometric relationship is Kleiber's law, which deals with the relationship between body size and metabolic rate.

Your assumption of a generally negative relationship between body size and abundance is correct, and the relationship is approximately linear on a log-log scale. As mentioned in the comments, the exact shape of the regression will depend on what organism groups are included, since the scaling relationship is known to differ between taxa. However, to get a reasonable ballpark figure we can look at a the classic paper by Damuth (1981), which include 307 mammal herbivores. The scaling relationship found there is:

$$D = 10^{4.23}*W^{-0.75}$$

where density (D) is in individuals per km2 and body weight is adult body mass in grams. Using your example of 70kg for humans would result in a predicted density of 3.9 individuals/km2. The scaling coefficient -0.75 (or -3/4) is often labelled "Damuth's rule", and is usually also found when pooling both ectotherms and endotherms.

However, remember that this regression was based on primary consumers, i.e. mainly herbivore grazers. Alternative data for groups of mammals can be found in Peters & Raelson (1984). That paper presents regressions for both carnivores+omnivores as well as for all groups of mammals (herbivores, carnivores, omnivores). The relationship for carnivores + omnivores (CO) is:

$$D = 15.7*W^{-1.15}$$

and the regression with all groups is (HCO):

$$D = 40.7*W^{-0.859}$$

In both of these regressions body weight is expressed in kg. Using the CO regression results in a predicted human density of 0.1 individuals/km2, and the HCO regression gives a human density of 1.1 individuals/km2.

Looking at these values, it is reasonable to assume that the predicted "natural" population density of humans lies in the range 0.1 - 4 individuals/km2, but certainly biased towards the lower part of the range. I suspect that a regression looking only at primates would predict an even lower value, so I would not rule out values below 0.1 individuals/km2.

To get a grasp of what this means in actual population numbers, we can extrapolate the densities to the entire earth. If we use the predicted density from the carnivore+omnivore model in Peters & Raelson (1984) and the entire land area of the earth, which is ~150 million km2 (Wikipedia: Earth), the predicted human population would be about 18 million. Using the high estimate from Damuth (1981) would correspond to about 600 million people. However, remember that this is using the entire land area, including deserts, mountain ranges and arctic areas.

Another point of reference is the estimated historical human population density during the Paleolithic, when we lived as hunter-gatherers. I have often seen population densities in the area of 1 per mile2, i.e. 2.6 individuals per km2. These estimates are naturally very uncertain, but shows that the allometric scaling relationships seem to provide at least reasonable order-of-magnitude estimates of "natural" human population density.

It is also somewhat enlightening to consider that our current human population size of 7 billion corresponds to the predicted population size of a 380 gram carnivorous mammal (using the CO relationship from Peters & Raelson (1984)), making the unrealistic assumption that this mammal has managed to colonize all land areas on earth. This shows pretty clearly what an outlier modern humans represent.

The generality of these types of relationships for predicting densities of individual species can however be questioned. For instance, the regression relationships also differ between climatic regions (see Peters & Raelson (1984) for more), and, as indicated in the comment by @remi.b, it is also unclear what population states that should be included. For instance, should only population densities in "ideal" habitats be used, when we know that population densities of the same species can differ by orders of magnitude in different habitats? It is also unclear if/how to consider the effects of modern humans. Silva & Downing (1995) also argue that the scaling relationship is nonlinear on the log scale, with a more shallow slope for larger species, and also find essentially no relationship between body size and density within some groups of species. More recent papers have also highlighted that studies on global relationships between density and body size often mix-up several different processes and relationships, see White et al (2007) for an overview on this.


Do DNA viruses have their own DNA dependant DNA polymerase? There's an exception to the rule that all DNA viruses need to get to the nucleus in order to replicate. Poxviruses do not require to get into the nucleus because they can make protein from their very own DNA-dependant-RNA-polymerase.

That is fine. But then, how do they make new DNA (for daughter virions)? Do they also have their own DNA-dependant-DNA-polymerase?

So here are my questions -

Does the pox virus also have its own DNA-dependant-DNA-polymerase? If yes, is it unique in having so?
How about other DNA viruses? The rule that they need to get into the host nucleus - is it for making protein using the host DNA-dependant-RNA-polymerase or for replication using the host DNA-dependant-DNA-polymerase? Or for both?
Do all other DNA viruses need to get integrated into the genome to be able to replicate, and do so along with the cell? Are there instances where the host DNA-dependant-DNA-polymerase is expressed at times other than the cell's S-phase?
Are there viruses that replicate inside the cell's nucleus without being integrated into the genome?

I know that's a lot of questions! Hope someone does help.

Note: Discussion limited to those viruses infecting eukaryotic cells. Also excluding Hep B (hepadna virus).

Probably I won't be able to answer all of your questions satisfactorily, but let's begin one by one.

Does the pox virus also have its own DNA-dependant-DNA-polymerase?

Yes. See this article from Wikipedia:

The replication of poxvirus is unusual for a virus with double-stranded DNA genome (dsDNA) because it occurs in the cytoplasm, although this is typical of other large DNA viruses. Poxvirus encodes its own machinery for genome transcription, a DNA dependent RNA polymerase, which makes replication in the cytoplasm possible. Most dsDNA viruses require the host cell's DNA-dependent RNA polymerase to perform transcription. These host DNA are found in the nucleus, and therefore most dsDNA viruses carry out a part of their infection cycle within the host cell's nucleus.

If yes, is it unique in having so?

Actually no. Hepatitis B virus also has its own DNA polymerase. And there's also the classic example of retroviruses: they have an RNA-dependent-DNA-polymerase (but yes, you can't consider it since it isn't a DNA-dependent-DNA-polymerase). See this wikipedia article:

Some viruses also encode special DNA polymerases, such as Hepatitis B virus DNA polymerase. These may selectively replicate viral DNA through a variety of mechanisms. Retroviruses encode an unusual DNA polymerase called reverse transcriptase, which is an RNA-dependent DNA polymerase (RdDp). It polymerizes DNA from a template of RNA.

Another example, as mentioned by @David in comments, is the Herpes simmplex virus (HSV) which contains a bunch of its own enzymes for DNA replication on its own. See this article:

Herpes simplex virus (HSV) encodes seven proteins necessary for viral DNA synthesis—UL9 (origin-binding protein), ICP8 (single-strand DNA [ssDNA]-binding protein), UL30/UL42 (polymerase), and UL5/UL8/UL52 (helicase/primase).

The rule that they need to get into the host nucleus - is it for making protein using the host DNA-dependant-RNA-polymerase or for replication using the host DNA-dependant-DNA-polymerase? Or for both?

Umm, both. Viruses (generally; there might be exceptions) need to reach to the nucleus of host to replicate as well as transcribe their DNA. See this article (emphasis mine):

Most DNA viruses replicate in the cell nucleus, which is where cellular replication and transcription proteins are localized. After infection, the nucleocapsid of DNA viruses is therefore usually delivered to the nucleus where uncoating occurs. An exception is poxviruses, which replicate in the cytoplasm of infected cells.
The first stage in the viral replication cycle is expression of the viral early genes. Transcription of these genes occurs using cellular RNA polymerase II and cellular transcription factors. These proteins bind to the viral DNA in regions called early promoters/enhancers, and promote synthesis of the early pre-mRNAs.
Once the viral early genes have been expressed, and the cells have been induced to enter S phase, viral DNA is replicated. This occurs in the nucleus of infected cells, and gives rise to new viral genomes. Many hundreds or thousands of new viral genomes can be produced in the nucleus of a lytically infected cell.

Are there instances where the host DNA-dependant-DNA-polymerase is expressed at times other than the cell's S-phase?

I think it has already been answered in your 2nd question. No, and the exception is the poxvirus itself. Again see the same article (emphasis mine):

Most DNA viruses replicate in the cell nucleus, which is where cellular replication and transcription proteins are localized. An exception is poxviruses, which replicate in the cytoplasm of infected cells.

Are there viruses that replicate inside the cell's nucleus without being integrated into the genome?

Wait! There's a difference between being inside the host cell's nucleus and being integrated into the host genome. Integration of the viral genome into the host genome requires a special enzyme called integrase and, you know, DNA viruses don't have integrase because they don't need it. So your question can be changed a bit to Are there viruses which replicate inside the cell's nucleus by getting integrated into the genome? Now, I could find only one such example i.e. Ectocarpus siliculosus Virus (EsV).

Ectocarpus siliculosus virus-1 (EsV-1) is a lysogenic dsDNA virus belonging to the super family of nucleocytoplasmic large DNA viruses (NCLDV) that infect Ectocarpus siliculosus, a marine filamentous brown alga...the EsV-1 and FirrV-1 genomes encode a large putative integrase/recombinase for which no counterpart exists in current protein databases. Only the Tyr-recombinase domain at the carboxy terminus of this enzyme is similar to phage integrases. Therefore, this enzyme might be involved in the integration and/or recombination of the integrated viral fragments.

References:

Pox virus

Hepatitis B virus DNA polymerase

Herpes simplex virus

Herpes Simplex Viruses: Mechanisms of DNA Replication

Wikigenes: UL9, ICP8, UL30, UL42, UL5, UL8, UL52

Reverse transcriptase

Viral Life Cycles in Cells

Integrase

Ectocarpus siliculosus Virus-I


Book/source for learning bioinformatics, focused on genomics? Does anyone know of sources for learning bioinformatics, focused on genomics? I would like to learn alot of skills I could apply potently in the workforce if I ever became adept at the fields. My computer science knowledge is weak, and my biology knowledge is mediocre, but i find the topics to be interesting. I have read "The dynamic Genome, A Darwinian Approach, by Fontdevila, and it was a bit rough for me. I have also read some of a introduction to genomics textbook, by Arthur M Lesk, and found it to be very "Academic".

Unix and Perl to the Rescue by Keith Bradnam and Ian Korf is an excellent introductory book and guide for bioinformatics (Linux and Perl) in genomics. It includes exercises and starts with the very fundamentals. You will still need some basic understanding of genetics and biology though.


What is this discarded exoskeleton from? This morning I was looking round the garden and found this sticking out of a pit in patch of soil, next to the wall of the house (in a trough sort of thing). I came to the conclusion it must be part of an insects exoskeleton that was discarded or part of a pupae. Can anybody identify what this belongs to? My location is in the south-west (Wiltshire region) of Great Britain. I'm just interested in what exactly I've found!

I can't be certain, but it is probably the pupal shell of a crane fly (daddy longlegs, Tipula palidosa). Here is an image to compare, and you can find lots more with a Google image search.

In the UK at least, these are colloquially referred to as leatherjackets and if you find one in soil before the adult has emerged it will often twitch.


Cnidarian life cycle, a case of ontogenetic polymorphism? Cnidarians have a complex life cycle which usually goes as follows:

Egg hatches larva.
Larva settles on sea bottom and transforms into a sessile polyps.
Polyps undergoes strobilation and asexually buds off juvenile, free-swimming medusae.
Medusae eventually mature and reproduce sexually to beget new eggs.

Given the morphological and physiological disparity between the three forms (larva, polyps, medusa), and how each form comprises a distinct stage in the cnidarian's development (i.e. ontogeny), would it be accurate to say that the cnidarian life cycle is an example of "ontogenic polymorphism"?

Sure it would.  I would usually use holometabolous insects as an example of this (egg, larva, pupa, adult), but Cnidarians certainly fulfill the basic requirements encapsulated by the phrase "ontogenic polymorphism." It appears that the pressures of finding/establishing food sources and escaping predation in competitive environments has driven both Cnidaria and Insecta toward this evolutionary strategy, though that is a field of active study still (at least in insects).