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Does the cell internal temperature changes in response to a change in external temperature?
Background
Some species are homeotherm (internal temperature is not affected by a change in external temperature) and some are poikilotherm (internal temperature changes in response to external temperature). These concepts apply to individual levels.
How about cells (unicellular cells as well as cell in a multicellular organism)? I know that cells react to temperature change. For example, the amount of cholesterol in the cell membrane can vary in response to temperature in order to keep a membrane fluidity roughly constant (ref). But that doesn't prevent the internal temperature to change.
Question
When the external temperature of cell changes, does it affect the internal temperature? I am hoping that the process is general enough so that I don't have to specify a particular organism. If it is needed to talk about a particular organism, then consider a yeast for example. How does the internal temperature of a yeast vary with a change in the external temperature?
EDIT
My knowledge in Physics being very limited, I didn't even think of Fourier's law before reading @Eli Korvigo's answer and comment and @AMR's comment. So let's make some calculations:
If we consider a spherical cell of area $4\pi r^2$, where $r$ is the radius, then the loss of heat is $4\pi r^2 \cdot \Delta T \cdot K$ (Fourier's law), where $\Delta T$ is the temperature differential and $K$ is the thermal conductivity. Then the ratio of heat production $H$ over the thermal conductivity $K$ (in order to deal with this change of $\Delta T$ °C) is $\frac{H}{K} = 4 \pi r^2 \Delta T$. If $r = 10^{-6}$ meters and $\Delta T = 2$ °C, then $\frac{H}{K} ≈ 10^{-11}$. Am I right?
Is this ratio really not realistic for a cell? The thermal conductivity for water is $k=0.56 \frac{W}{m\cdot K}$(ref.) and the heat production per cell is $34 \cdot 10^{-12}$ W (ref.). So the ratio is of the order of $10^{-11}$ as well! Am I right?
So is it really impossible for a cell to regulate its temperature?

When you do cell/tissue culture, you learn to work fast so that you do not keep your cultures out of the incubator for very long. You make sure it is set for 37* and that your CO2 take is not on empty. In short cells are adapted to the environment they evolved in. Mammal cells do not respond well to dry, too cold or too hot environment and oxygen and about 5% CO2 to culture. Bacteria are pretty sturdy and have a broader range where they can survive, but they generally won't grow outside oh their ideal range. For E.coli, against that is 37* as they evolved in mammalian digestive tract.

Think about it this way. You reach a few hundred meters from the summit  of The Matterhorn as night falls in January. You can sleep exposed, in a tent, or in a tent in a cocoon sleeping bag, or in a tent with sleeping bag and a few climbing partners. Option 1, you will probably be severely hypothermic in the morning or possibly dead. Option 2 you probably won't be much better off. Option 3 you should be okay, though you may be apprehensive about unzipping the bag in the morning. Option 4 the temperature of the tent will likely also be warmer than the ambient temperature outside.

I understand that cells (unicellular or not) have their ecological niche. But it is not because you have such niche that you won't evolve so to regulate your inside temperature in order to expand over this niche (as mammals do for example). So I think the question remains (Are cells (yeast for example) able to regulate their inside temperature).

I would say that there is a range of response to the environmental change that the cell experiences, but no individual cell has the capacity to regulate temperature. They can respond to the change, but you need systems to actually control temperature. Multicellular organisms are greater than the sum of their parts, so even though systemically we (warm-blooded animals) can make modifications to metabolic activity that regulates out core temperature, it is the result of the collective response more than that of any individual cell.

And that is just considering Mammals. There are some very large reptiles who are not capable of maintaining their body temperature, even though they have the critical mass to do so. Their response to cold is hibernation, or in the case of the really large ones, dinosaurs, extinction.

And I know that you are aware of these things but I think that you are so focused on the technical specifics of your question that you are forgetting what you know about why multicellularism arose in the first place. An argument can be made that prokaryotic cell walls are adaptations to the extremes of the environments that they experience, but does that mean that they are actively managing the situation or are just adapted to a broader range of environments as they have to go it alone, for the most part to survive and pass on their genes?

Homeothermic multicellular organisms have special tissues that burn resources to warm up (usually this involves breaking the electron-transporting chain at the final stages of respiration to transform all chemical energy into thermal energy). And they have special tissues (fat) and enough body mass (this is more about the volume/area ratio) to keep this energy from dissipating. If you recall physics, any unicellular organism has insufficient body mass to accumulate thermal energy for any perceptible amount of time, hence it's useless to burn resources that it can spend to adapt to lower temperatures, i.e. synthesise cold-shock proteins, modify membranes, restructure metabolism. This is basically the same reason why small mammals and birds have to eat all the time to stay alive.

As you can see, the smaller you get the more energy you need to burn (hence increase ${O}_{2}$ consumption) to maintain body temperature. That's why we don't see truly homeothermic insects (some of them can warm up for short periods of time) or other small animals.

Thnks for your answer +1 You said any unicellular organism has insufficient body mass to accumulate thermal energy for any perceptible amount of time, hence it's useless to burn resources that it can spend to adapt to lower temperatures That means that there is absolutely no control over internal temperature at the cellular level in comparison to the extra-cellular temperature. Is that right? That'd be great if you'd have a reference.

@Remi.b I don't mean this is impossible, but thermodynamically irrational. This statement directly follows from the Fourier's law. A cell is simply too small, hence any energy spent to warm up will dissipate immediately. Don't forget about the energetic capacity of water.

Eli's answer makes sense, but here is an example. If you put a substantial mass of yeast in a cask with crushed grapes or wort, they will initiate fermentation to produce alcohol for beer or wine. If you look at a temperature, the temperature within the vat will be higher than the ambient temperature. With enough mass, the yeast produce enough heat to warm the container that they are in. However a culture on a petrie dish would likely generate insufficient heat to overcome the effects of the ambient temperature of the surroundings.

Thanks a lot for the comments as well. I plugged a few numbers into Fourrier's law to see if it is plausible for a cell to regulate its temperature (See edit). Please let me know if that sounds correct to you and whether you still think it is impossible for a cell to regulate its own temperature.

@AMR exactly With ENOUGH MASS, the yeast produce enough heat to warm the container that they are in. Indeed, a culture might get significantly warm, that's why many bioreactors have cooling systems, but a culture is not a unicellular organism :)

@Remi.b there are two possible flaws in your estimations (I can be wrong, since I don't have time for a thorough analysis right now): 1. You applied a 1D approximation to a 3D case; 2. you reference heat production per cell in a culture during growth (=> a lot of spare resources to burn) - the value is not relevant to an isolated cell (and that is the model we are talking about as far as I believe). As you might've noticed Over an 8.5 h period, cell numbers increased by 9% and heat production per cell by 18% - the heat production per cell correlates with the number of cells.

The second is indeed a potential problems in my calculations (+1).

@Remi.b My pleasure. As for the mathematical part, you can't apply that linear approximation to a 3D case. If you really want to estimate the heat loss, you have to solve the integral form.


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Pathogenesis of Group B Streptococci and C5a
I am thinking the pathogenesis of the C5a in GBS.
I think the pathogenesis happens like

C5a-peptidase in acid environment (Sialic acid, capsule) $\to$ cleaves C'-derived Neu chemoattractant C5a $\to \downarrow$ alternative pathway of Complement.

However, this part cleaves C'-derived Neu chemoattractant C5a is not clear to me.
I think this means that C5a-peptidase cleaves Neu C5a from the previous complement reaction that inhibits the next coming alternative pathway of complement.
How does this pathogenesis of GBS happen?

I think "neu" must be an abbreviation for "neutrophil".
C3a and C5a are both chemotactic peptides that recruit cells to sites where complement activation is occurring. C5 is a substrate for the C5 convertases formed in one of the three complement pathways (classical, lectin, alternative). C5b, the other product of this cleavage goes on to form the membrane attack complex.
C5a peptidase is a Streptococcal product which destroys the C5a peptide before it can recruit neutrophils and other agents of cell-mediated immunity. Streptococci also produce an inhibitor of the membrane attack complex.

source: Stack Exchange

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

sort: votes


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Can too low oncotic pressure lead to Third spacing and Edema?
I know that low oncotic pressure is associated with many pathologies.
I am interested how it is associated with Third spacing.
My professor says that it can permit edema formation.
The opposing pressure of oncotic pressure is hydrostatic pressure.
So that would suggests mean that the blood pressure is too high if low oncotic pressure and thus fluid would like to go to the third spacing (not sure) and edema.
Can too low colloid oncotic pressure lead to Third spacing?

Yes it can! Its a very important cause of third spacing a.k.a. peripheral oedema, mainly due to decreased protein.
Below is a list of causes of peripheral oedema due to fluid moving from the vascular bed to the peripheral spaces gathered from the following source: http://www.patient.co.uk/doctor/Peripheral-Oedema.htm
Immobility: Increased fluid pressure from venous stasis. Varicose veins.
Obesity: Increased fluid pressure from sodium and water retention; should not to be confused with non-pitting lymphoedema.
Cardiac: Increased fluid pressure: right heart failure, constrictive pericarditis.
Drugs: Increased fluid pressure from sodium and water retention: calcium antagonists, non-steroidal anti-inflammatory drugs (NSAIDs), prolonged steroid therapy, insulin.[1]
Hepatic: Decreased oncotic pressure: cirrhosis causing hypoalbuminaemia.
Renal: Decreased oncotic pressure from protein loss, and increased fluid pressure from sodium and water retention: acute nephritic syndrome, nephrotic syndrome.
Gastrointestinal: Decreased oncotic pressure: starvation, malabsorption, protein-losing enteropathy (eg Crohn's disease, ulcerative colitis, tumours of stomach and colon, coeliac disease and other intestinal allergies).
Pregnancy: Increased fluid pressure both from sodium and water retention and venous stasis from pelvic obstruction.
High-altitude illness: Oedema of face, hands and ankles may occur.
Idiopathic oedema: Associated with cyclical high lymph volume overload, or dynamic insufficiency: usually in a woman aged 20-40 years. Variable and not related to menstrual periods. Diagnosis is based on the exclusion of other causes of oedema.
Post-thrombotic syndrome: Late complication of deep vein thrombosis (DVT) which occurs in up to two-thirds of patients. May present with pain, oedema, hyperpigmentation, and even skin ulceration. May result from remaining venous obstructions, from reflux, or both. Rate of reflux is highest during the 6-12 months after an acute DVT. It may be temporary and self-limiting or not resolve and persist at variable severity.
Pitting localised limb oedema:
DVT: Compression of large veins by tumour or lymph nodes.
Following hip replacement or knee replacement.
Local infection, trauma (including burns, which may also cause generalised oedema because of protein loss), animal bites or stings.

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


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How many systemic reactions in inflammation?
I have this sentence in my notes

Inflammation consists of two local reactions and one systemic reactions.

which is difficult for me to accept.
Two local reactions are vascular and cellular.
I think there are two systemic reactions too:

White blood cell response
Acute-phase response

How many systemic reactions there are in the inflammation?

There are two systemic reactions in inflammation too: mediated by leucocytes and acute-phase response (proteins).


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Does an increase in cancer cell traction forces increase metastasis of the cancer cells?
I am not very familiar with biology, but I have read some articles about cell traction forces lately, where the cells are cancer cells. I found this very interesting, so I thought it might be nice to read about the relationship between cell traction forces and metastasis for cancer cells. I thought that an increase in cancer cell traction force should indicate that there would be more metastasis. I have looked at two references, but one of the articles says that increasing the cell traction force increases metastasis [Kraning-Rush et al. (2012)], while the other says the opposite [Indra et al. (2011)]. Both are experimental articles.
My question is therefore:
Is it correct that most often, an increase in cancer cell traction forces would increase metastasis, or should it most often decrease metastasis?

The second link cannot be accessed without login. Could you provide an accessible link at least to the abstract (maybe NCBI)? Thanks!

@AlexDeLarge http://pubmedcentralcanada.ca/pmcc/articles/PMC3870281/

You have pointed out in your question that two different research groups have differing conclusions about your question.  The answer is not known which is why they are studying it.
Their differing results probably turn on how cell traction force is defined and the experimental system used to measure it.  It may not even be consistently ture - for example metastasis via the lymphatic system may be mediated by different properties than metastasis through the bloodstream or local tissue invasion.

Thank you for your reply! Okay, that makes sense. Do you have some references about that metastasis via lymphatic system or bloodstream might give different different conclusions on the force exerted from the cells?


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Possible to cause the cells to produce less/no chemicals?
I have a question regarding cells producing chemicals, e.g. some metabolite, inside the body. Is it possible to inject something (at least theoretically possible, and maybe practically possible in the future) into the body to inactivate these chemicals (e.g. enzymatically), or inject something which makes the cells produce less/none of the chemicals?

I just mean that I would like the chemicals to decay very fast so that it does not affect the traction force exerted by the cells any more.

Okay, but do you believe we can do something to increase the decay rate of the chemicals without killing the cells?

Welcome to Biology.SE! I tried to clarify your terminology in an edit - does that capture what you mean? Please feel free to further edit. And does that make things clearer for you, @GerardoFurtado?

It will depend on the metabolite, metabolic pathway and the cell of interest.

Okay. I am thinking about cancer cells distributed inside of a spherical collagen gel.

Basically all of pharmacology consists of something that can be injected, consumed, applied topically, etc to cause cells to produce more of something or less of something.


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Can you please identify this beetle?
Can you please identify this species of beetle? It was about 2 cm (or 0,8 inches) in size. Photo is from Greece, Europe.

Could you please add the (estimated) size of this beetle?

about 2 cm ,  0,8 inches.

It looks a bit like a Phyllopertha horticola (Garden Chafer, from Scarabaeidae), with the antenna hidden, but 2 cm is too large. It could be a related Scarab beelte though, or you are overestimating the size (which is common with insects, when you dont actually measure them). The picture is a bit dark to judge though.

Definitely a scarab, likely Subfamily Cetoniinae. You should post an answer @fileunderwater

The insect in the Photo is a beetle (order Coleoptera), in the scarab family (family Scarabaeidae). It is most likely in the Genus Phyllophaga (June or May bugs) or Phyllopertha (garden chafers).  Beetles such as this are commonly referred to as "Chafers" feeding on plant leaves and flowers during the day. One of the defining characteristics in the photo is the apparent "Hairiness" (setae) visible at the sides of the insect body. I am inclined to agree with the good observations expressed in the comments.  It likely to be a garden chafer Phyllopertha horticola. Some helpful links are below.
https://en.wikipedia.org/wiki/Phyllopertha_horticola
https://en.wikipedia.org/wiki/Phyllophaga
https://www.flickr.com/photos/72271115@N02/galleries/72157651475342046/?rb=1#photo_14184003066
https://www.flickr.com/photos/odonataman/14184003066/in/gallery-72271115@N02-72157651475342046/
https://en.wikipedia.org/wiki/Scarabaeidae


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Chromosomally different D. melanogaster sperm
I know that D. melanogaster have 4 pairs of chromosomes and crossing over is absent in males. Denoting autosomes as Ai,j where i is chromosome no. and j are homologues (1 and 2) I am solving the total no. of chromosomally different sperm as 8. I am assuming it as 2x2x2. Can anyone verify my answer?


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Identify this beetle from Bangladesh
Location: Bandarban, Bangladesh

It is from Coleoptera (beetle), right?

Where did you find this insect? Inside your home? If so, where? What "habitat" was this insect in?

This appears to be some species of beetle (order Coleoptera) in the Bostrichidae family.

Commonly called auger beetles, false powderpost beetles, or horned powderpost beetles.

 Xylopsocus capucinus
Identification to species can be difficult, but fortunately for you Sittichaya et al (2009) created an illustrated key for IDing species associated with South Asia.
Based on their key and visual characteristics of your specimen, my guess is that your specimen is Xylopsocus capucinus

 Source: Sittichaya et al 2009 . a. lateral view; b. elytral declivity; c. intercoxal process of the 1st abdominal ventrite; d. dorsal view.

Description: 3-5.5 mm long; 1.4-1.7 mm wide. Shape is cylindrical and similar in general appearance to other common species of the family Bostrichidae.
Distribution: throughout South and Southeast Asia from India to the Indonesian archipelago.
Hosts: apparently polyphagous attacking almost any woody plant in suitable condition.
Phenology: adults emerge mainly
between May and November.

Like most false powderpost beetles, the head cannot be seen from above as it is downwardly directed and hidden by the thorax:

 Source: UFL IAFS

Sources:

Sittichaya, W., Beaver, R., & Ngampongsai, A. (2009). An illustrated key to powder post beetles (Coleoptera, Bostrichidae) associated with rubberwood in Thailand, with new records and a checklist of species found in Southern Thailand. ZooKeys, 26, 33.
Woodruff RE, Gerberg EJ, Spilman TJ (2005). A False Powder-post Beetle, Xylopsocus capucinus (Fabricius)
(Insecta: Coleoptera: Bostrichidae). University of Florida, IFAS Extension Publication No. EENY-179.
Institute of Food and Agricultural Sciences, University of Florida, 4 pp

This appears to be a Powder-Post Beetle (order Coleoptera, family Bostrichidae); a local reference is needed for further identification.

Please provide a reference for your identification if possible.

The post by @theforestecologist gives you a good example of how a well-researched answer to a species ID question looks like, even though your ID is also correct - as far as I can tell, and that is the problem: it needs some effort for me to check even though answers should be self-explanatory. Please try to give more comprehensive answers.


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Does hunger necessarily mean that we should eat?
People feel hunger sooner after they eat food that consists mostly of carbohydrates. For example, if someone eats a good portion of rice then most likely they will be hungry after a couple of hours. But should they eat again in such a case or is it just deception because of blood sugar hikes?


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Which mushroom is this?
I found those mushrooms in my garden in Luxembourg and I was wondering what species they might be.

Where is your garden? Also, the picture is not very good for species determination (several pictures from top, bottom, showing the shape of the hat etc would be better), and I would be sceptical against most advice to eat/not eat based on that picture.

Mountains, Luxembourg area

@fatmau - Please don't ask strangers on the internet to give you advice with such potentially devastating consequences if they are wrong or want to troll. While death is probably uncommon, varying degrees of hepatitis is common, with hospitalization being a frequent event. Get a good guidebook to edible mushrooms and follow the instructions for identification carefully. There are only a handful of mushrooms that can be identified as perfectly safe with one look at a single view.

I added the location and removed the question for advice.

That mushroom is from the Boletus family with sponge gills. A Red Cracked Bolete.
Only one sponge gill toadstool neighbor of the boletus family mushrooms has ever been know to kill a single person, or require a liver transpant, because, if you get an amanite wrong, you can survive, but only with a liver transplant. It is said that: if you found an Amanite, and put a triangle of it in your mouth and spat it out, it may taste fairly scary, but it will not kill you or even make you vomit or Hospitalizeded, although you may experience some discomfort, as long as you spit it out entirely and not swallow it.
In temperate climantes, The only boletus that are quite noxious are the red and beige ones which sometimes smell ghastly are in the family of the devil's bolete. There are other boletes that can make you vomit or ill, i.e. some blue and yellow ones. some boletes are strange and interesting such as the pepper boletus which can be used to flavor a dish because it produces very hot pepper flavor same as capsiacin.
Your mushroom is clearly a Red-Cracked bolete, which make sludgy, insipid soup, they have no texture, gelatious, flavorless, are extremely common, have yellow gills changing to blueish grey, and small red cracks often appear in the top which has the habit of cracking when ripe, hence the name, red cracked bolete. it is harmless and quite a waste of time to cook. https://www.google.fr/search?q=red+cracked+boletus&num=100&source=lnms&tbm=isch&sa=X&ved=0ahUKEwiWn7Ljg9fVAhXDJlAKHe-HADwQ_AUICigB&biw=895&bih=530
The only boletus: sponge-gill toadstool (tail and cap) mushroom ever implicated for someone's death (by artery malfunction in the gut) was a woody tough red one related to boletus satanicus: https://en.wikipedia.org/wiki/Rubroboletus_pulcherrimus
Anyone trained biologist who can identify species from books, has a good chance of never falling ill from Boletus species, as long as he makes very positive identifications of mushrooms that don't have potential deadly or noxious look alikes. many mushrooms like the death cap are particularly deadly because they can be mistaken for small farm agaricus in field edges. especially angel of death and Panther-Cap, which smell of humus, earth, and apples.
The main identifier on a red cracked bolete is the squishy texture, not fibrous, and the velvet. dryish, textured large sporing body which starts as pine colored and matures to olive or bark colored.


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What is the name of this tiny creature?
Place: South India,
Metropolitan, Year: 2017; Night Time.
Size: 1-2 cm (Very Tiny)

Looks like a moth.

It's 'Indian skipper'. Family :Hesperiidae.
Source: http://abeautiful-butterflys.blogspot.in/2010/04/hesperiidae-butterflies-of-india.html

This is not a skipper. Skippers are bigger, have a different shaped body and a different wing pattern, as can be seen from your picture.

From the posture, it looks like it can belong to Geometridae (Larentiinae). But I haven't been able to find a species that has that particular color.

Definitely a moth; possible families are Pyralidae, Crambidae, or Thyrididae (Window-Winged Moths); the first two listed (Snout Moths) are less likely and would be eliminated if a photograph showing the front of the head were available and it turned out that the palps were not elongate and projecting.

Arthur, I've noticed you've provided a handful of species ID answers lately. All of your answers are short, lack references/support, lack photos, and typically don't try to identify beyond the family level. These answers will all likely get downvoted as they do not represent the effort or specificity that are typically expected on this site (and desired by the asker). Please start expanding upon your answers or simply providing your posts as comments instead. See here for a guide to writing good answers on this site. Thanks!


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Fermentation of bananas
I may have access to huge quantities of freshly picked bananas. Searching the web, I have found that the sugar content of the average banana is 14g of fructose (could stand to be corrected on this) which should in principle allow for fermentation. The bananas are in no way processed. My questions now are:
(1) How suitable are bananas for ethanol or methanol fermentation?
(2) How exactly is the fermentation workflow? I presume the bananas would be chopped?
(3) considering point (2) what effect would the banana skin have on the fermentation process? Would it be better to ferment the whole fruit including skins or remove the skin before fermentation?
Hope someone can help

Welcome to Biology.SE. I edited your question to improve the structuring and clarify a bit. Please feel free to further edit or re-edit.

How to make banana wine seems like a good start: http://www.celebrationgeneration.com/blog/2011/10/13/how-to-make-homemade-banana-wine/comment-page-1/

I'm voting to close this question as off-topic because this question isn't about biology, even if it induced a solid answer.

Fruit Moonshine is quite desirable :)
Peel the bananas. Good workflow here:
http://www.moonshiners.club/banana-moonshine-recipe/
It takes considerable work especially in large quantities. Furthermore, check legality and read up on methanol poisoning.  Don't poison yourself!

That's impressive!

Is it too late to change my username to Banana Moonshine?


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How can a pathogenic bacterium be avirulent?
Streptococcus pneumoniae R6 is a pathogenic bacterial strain but it is avirulent. How can a pathogen be avirulent. What does it mean if a pathogenic bacterium is avirulent?

Streptococcus pneumoniae is a pathogenic species. Streptococcus pneumoniae R6 is an avirulent strain of this species. Presumably this means that specific virulence genes that are present in virulent strains of Streptococcus pneumoniae are missing or mutated in the R6 strain. In fact the most likely difference would be that virulence factors are encoded by a plasmid that has been lost in the avirulent strain.
The use of avirulent strains is a common strategy for studying pathogenic bacteria, although obviously it precludes studying mechanisms of pathogenicity directly.

Details as to what render the strain avirulent detailed here. Namely, the lack of a capsule.


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How can one calculate "probability of possessing a ‘perfect’ profile" from "typical optimal genotype frequencies"?
Can anyone please explain how the "Probability of possessing a ‘perfect’ profile" was calculated from "typical frequency of optimal genotype" in Table 1 in this paper?
Paper link here

They appear to have simply considered each allele independently. This means that if there are say 2 alleles for a trait, and they are both present at a frequency of 0.1 in the population, then you have a 0.01 chance of having both of them. This is probably an okay assumption for their purposes (in reality some might be linked and would associate non independently). Their point is simply that as the number of alleles go up, having all the best ones becomes increasingly unlikely.

Makes sense, but still I am not able to figure out the math here. Can you please be kind enough to take an example from this table and explain how the probability was calculated?

seems like i cracked it .. thank you so much for the explanation


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What is the difference between hsa-miR-33a and hsa-miR-33b?
Does anyone know what is the difference between two miRNAs like hsa-miR-33a and hsa-miR-33b? The last letter in them shows what?
Also, if we know that hsa-miR-33a targets gene A, can we say that hsa-miR-33b targets gene A, too? or can we say that it is much probable that hsa-miR-33b targets gene A since hsa-miR-33a targets A?

They are paralogs i.e. they have high level of sequence homology. They may have the same seed sequence too (see this). The paralogs can have same targets if they have same seed sequence but it is not essential in all cases. However, the extent of homology required for this kind of classification is poorly defined. miRBase still follows the guidelines mentioned in this (quite old) article:

When such a candidate is so similar in sequence to the known miRNA
  that the probe designed to detect it would surely cross-hybridize with
  the known miRNA, criterion A need not be satisfied, and the candidate
  can be annotated as a variant form of the known miRNA, provided that
  the candidate itself meets criterion C, and there is also very high
  confidence that one of these paralogs is a confirmed miRNA (i.e., its
  classification is supported by at least three of the listed criteria).
  When there are two or more mismatches between the miRNA paralogs such
  that probes could differentiate between the species on Northern blots,
  criterion A must be satisfied experimentally. Sometimes partially
  overlapping cDNA sequences are identified from the same locus; these
  are assumed to represent differentially processed products from the
  gene.

mind that homology is a 0 or 1 term. I mean two sequences are homolog or not. Its better to use "similarity" instead of "homology".

@MySky not really. Percent homology is a commonly used term.

The term "percent homology" is often used to mean "sequence similarity". The percentage of identical residues (percent identity) or the percentage of residues conserved with similar physicochemical properties (percent similarity), e.g. leucine and isoleucine, is usually used to "quantify the homology". Based on the definition of homology specified above this terminology is incorrect since sequence similarity is the observation, homology is the conclusion. Sequences are either homologous or not.

look at this page: https://en.wikipedia.org/wiki/Sequence_homology


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miRNA targets mRNAs
If we observe that a miRNA, say hsa-mir-233, targets a mRNA, say XXX, in a given tissue in disease condition, can we say that always hsa-mir-233 targets mRNA XXX regardless of type of tissue and disease condition?

miRNA's can be tissue-specific, and their mRNA target can also be tissue-specific. I'd be careful about generalizing.

by tissue-specific, you mean miRNA may target mRNA in tissue A, but not in tissue B?

To avoid confusion, yes, the miRNA can be targeted to it's specific mRNA if it ends up in another tissue. To me there are some confounding factors that may alter it's net effect in different tissues or disease states.

First you have to define what you really mean by miRNA-X targets mRNA-Y. If you mean direct targeting then there are assays to verify it.
To verify if the miRNA can potentially target the mRNA independently, what is routinely done is a reporter downregulation assay (usually luciferase). You clone the 3'UTR of your target mRNA downstream of the reporter gene and check the activity of luciferase in the presence and absence of miRNA. You do that by co-transfecting the miRNA and the luciferase construct, collecting the cell lysate after some time (typically 12/24/36h post transfection) and measuring luciferase activity using bioluminescence counter. This just establishes the molecular possibility of targeting but does not really say if the same actually happens in a given tissue.
Reporter assays like this can be modified for in-vivo conditions too. Express the reporter-3'UTR construct in your organism (or specific tissue). Use another reporter with a mutated target site in the 3'UTR which abolishes miRNA targeting and compare the activities of the two. In zebrafish, people also use modified-backbone oligonucleotides (morpholinos) to mask the target site such that the miRNA can no longer target the mRNA. This assay is called target-protection assay.
There are other assays which do not involve reporter genes but actually capture miRNA and mRNA bound to the Ago-complex. This is done by protein-RNA crosslinking followed by immunoprecipitation of the protein (Ago) which is then followed by sequencing of the bound RNA. See this post for more details. These assays will give you tissue specific information but they only tell you if a miRNA and mRNA are bound together. They do not tell whether the mRNA activity is downregulated or not.
Targeting of the mRNA by miRNA, in-vivo (which has already been established by ectopic reporter assays) depends on many factors, the foremost of which is the relative concentrations of these molecules and the competitors. To produce an effect, the miRNA has to be in sufficient concentration for each of its target (if the miRNA has many targets then the per-target availability will go down).
So, if a miRNA-X actually targets i.e. downregulates a mRNA-Y in a specific condition, it need not do it in another condition. However, we would still say that mRNA-Y is a valid target of miRNA-X if it is so in at least one condition and better if it has been validated using reporter assays (ectopic).

mRNA targeting mechanism is highly specific and depends on various factors. the target mRNA and miRNA complex is highly conserved even from an evolutionary point of view.There are many in-vitro studies which shows the importance of miRNA concentration.Now under any kind of disease state the normal functioning of cells is hindered and this directly effects the level of transcription. the rate can either increase or decrease.
mRNA target region for miRNA in the 3'UTR region is highly specific, and its dependent on base pair complementarity between mRNA and miRNA, due to which the miRNA-mRNA duplex remains exclusive. there are multiple miRNAs which have been found for one particular mRNA, if u go through the database TargetHumanScan database(http://www.targetscan.org/) u will find many miRNAs for one particular mRNA, and vice-versa.
The concern here is not weather any mRNA can be regulated by the particular miRNA, but, whether its positive regulation or negative regulation which is needed by the cell at that particular diseased state.

miRNA hardly ever cause positive regulation. They are primarily repressors.

As well as the above, it's worth noting that the usage of 3' UTRs and polyadenylation sites can vary from tissue to tissue, so that an mRNA might have the cognate miRNA binding site in one tissue, but not another.


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Help identify this worm-like thing
Many instances of this worm-like creature were found in a water system for a mountain cabin in the Sierra Nevada mountains of the US, in late June / early July.  The water system collects water from an enclosed spring.  Can you help identify this creature?
Clues:

The worms have two "points" on their heads.
They can stretch out and be long and thin, or when poked (or are resting) they contract into a small blob.
Here is a picture of a single worm with markings shown.

Here is a picture of a few worms, somewhat contracted.

Here is a movie of them moving, in natural light.
Here is a movie of them moving, with backlight.
Here are pictures of their undersides and their internal structures.

Whenever I pull some out of the water and put them into a tupperware with the same water, they only survive for around 24 hours, after which they seem to disintegrate.  Here is a picture of about 20 of the worms after about 24 hours, the bulk of them have halfway-decomposed and form a heap in the upper right.  After another day it'll just look like debris in the water, you wouldn't even recognize that there were worms in it.  There is a piece of bacon in there because some suggested putting it there to test if they were leeches, but this disintegration happens repeatably and regardless of the bacon; please ignore the bacon.

Someone suggested that they are trematodes, but there are no snails, frogs, or other creatures in the storage and collection sections of the water system;  we have looked very closely.  There may be something within a 30-foot section of pipe, but we doubt it.

Can you help us identify this creature?  Even just possible families of creatures or general categories would be helpful for us.

My first thought, based on the two "points", is that they're slugs, but I think most water slugs live in salt water. This page seems to suggest that freshwater slugs are all tropical, but might have a useful lead.

Are leeches supposed to like bacon ? I thought they needed fresh blood.

@bli - leeches are attracted to odors as well. In swampy areas, it's not uncommon to find a leech or two on a carcass that's been in the water.

I am not too sure but this looks like Polycelis sierrensis.
Though it is apparent that the worm in your pictures is a tricladid planarian, I was not too sure about the species and the geographical distribution.
However, from the Smithsonian list of freshwater planarians in North America, I deduced that this should be Polycelis sierrensis which is found in California and Nevada (Kenk ,1973).
The EOL page on this species also concurs with the geographical distribution. Moreover, the shape and dimensions of the worm, as described in EOL, matches with that of the ones you have got.
I could not find a picture of P. sierrensis but this is how a general Polycelis looks like:

Wow, a google image search for Polycelis sierrensis shows this image as the first result, at least for me.

@user151841 Same here. But the caption just says Polycelis sp. but this one does look like the worms in the question.

Thanks so much for taking the time to answer, WYSIWYG.  We really appreciate it.

The overall shape appears to match that of a flatworm or planarian, but those don't have eyestalks. Also, in the images you posted, none of the worms appear to have the characteristic eyespots of a flatworm, although they DO look planarian-like in some photos:

If they didn't look so thin, I'd say they were common garden slugs. We get them all the time down in Southeast Texas, and they're attracted to humid areas, especially wetness. They usually have thicker bodies, though:

I've never put salt on a planarian before, but the behavior you describe is exactly what happens when a common slug hits salt. They curl up into what looks like a wad of gum, then shrivel up into a blackened husk. On the other hand, slugs are definitely NOT mountainous creatures. And they're definitely NOT leeches, which we also get down in Southeast Texas.
Based on your location and the images, you're probably looking at some sort of freshwater planarian. They're most likely in the source spring itself.

Their capacity to elongate / contract and their two head lobes make me think they are Planarians.
The two points  on their heads must be their eyes: https://en.wikipedia.org/wiki/Simple_eye_in_invertebrates#Ocelli_or_eye_spots


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Can stress echocardiography show coronary blood flow difference before and after exercise?
Stress echocardiography means a pair of cardiac ultrasound imaging examinations, before and after exercise. I assume that coronary blood flow is increased after exercise. Is cardiac ultrasound technology capable of showing this blood flow difference?

Update: I emphasize that my question concerns stress echocardiography, i.e. two echocardiography sessions before and after exercise (or pharmacological stress test) - not simply echocardiography.

Coronary artery disease thickens the wall. Flow is dramatically affected by thickness (radius to the fourth power). In an echo you observe the heart muscle i.e. does it contract normally using the surrounding muscle and baseline as a comparison. If the wall is thickened, this will cause a decrease in perfusion which will result in the heart muscle contracting abnormally. Xaqron is right, it doesn't show you flow directly, but what it does show you is a quick and cheap way to estimate if the artery is blocked enough that it will cause a noticeable difference. If the heart muscle doesn't beat that means it really isn't getting oxygen (but could be because of abnormal conduction), and if it beats suboptimally it is getting less oxygen than it requires.

No, echocardiography is not sensitive enough to do so. For tracing coronary arteries directly flow angiography is the choice.

To a related question of mine AndroidPenguin yesterday answered that with stress echocardiography we could "see how it responds to increased exercise (does the blood flow increase by the same amount everywhere?)". Was AndroidPenguin wrong?


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Why is elevated homocysteine considered a risk factor for angina?
Elevated homocysteine levels are listed among risk factors for angina. How is homocysteine related to the heart? Or the coronary arteries? How do these relationships make it a risk factor for angina?

In his answer to a related question Alan Boyd has given the mechanism how homocysteine inhibited (1)Protein C activation and the (2)binding of free thrombin, both ways promoting coagulation and thrombosis. According to the answer of Xaqron below there are further mechanisms. Not all of them are linked to angina yet.

Homocysteine:

Causes endothelial dysfunction and damage
Accelerates thrombin formation
Inhibits native thrombolysis
Promotes lipid peroxidation through free radical formation
Induces vascular smooth muscle proliferation
Promotes monocyte chemotaxis

Many observational epidemiological studies indicate that individuals with higher Homocysteine levels have increased risks of cardiovascular disease.

How can the effects on lipid peroxidation, smooth muscle proliferation and monocytes lead to angina?

Did you mean thrombUS formation (rather than thrombIN)?

@winerd: No, if it accelerates thrombus formation then it would be more dangerous. I meant thrombin formation as already said in answer.

I guess that the effects on endothel, thrombin and thrombolysis may contribute to coronary thrombus formation, and that's the link towards angina. Am I right?

@winerd: Mechanism is unknown at the time but these factors make a good basis for thrombus formation. Your questions are more medical than biologic, consider voting on Medicine in area51

@Xaqron I'd say this is on topic for us.  I can see how the factors you've listed would be clear risk factors for myocardial infarction but, with the possible exception of 5, I'm not seeing a clear link to Angina (stable or otherwise).  Could you elaborate further?

@RoryM: Smooth muscle proliferation => lower internal diameter of vessels.

Citing a reference for this would make for a slightly stronger answer as well, just a suggestion, though.

@Xaqron: RoryM mentioned 'smooth muscle proliferation' as the one where (s)he sees a link, not where (s)he does not.


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Why do conker flowers grow upwards?
Most trees I know that have their flowers in groups hang these groups down. I noticed, however, that conker flowers grow upwards!
I guess that growing against gravity requires special effort, so conker may benefit somehow from growing the flowers upwards. Is this true? What's the benefit?

The main and maybe the only reason for me looks to be phototropism. Also read heliotropism though I can't guess if this is a factor with regard to the conker tree.

I would think that this is a inherited morphological trait within the subfamily. And I doubt it requires additional effort.

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


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By what mechanism does coeliac disease cause excess fat in the feces?
Wikipedia states that “Severe coeliac disease leads to the characteristic symptoms of pale, loose and greasy stool (steatorrhoea)”. However thumbing through the causes and the pathophysiology it did not become clear to me what leads to this key symptom.
By what mechanism does coeliac disease cause excess fat in the feces?

Coeliac disease is an immune disorder resulting from a reaction to ingested gluten (a protein found in wheat, barley and rye). It is associated with inflammation of the small intestine resulting in a generalised reduction in the capacity for digestion and absorption. According to this paper:

Celiac disease is associated with pancreatico-biliary disease. Postulated mechanisms include reduced gallbladder emptying due to impaired cholecystokinin release and pancreatitis due to malnutrition.

Cholecystokinin is a peptide hormone that is produced by specialised cells in the small intestine and which stimulates the production and release of pancreatic enzymes and bile. Digestion of fat is critically dependent upon the emulsifying properties of bile salts in bile, together with pancreatic lipase. Any breakdown in this stimulatory pathway would result in reduced capacity for digestion of dietary fat.
Failure to digest fat results in fatty stools (steatorrhoea) which is one of the classic symptoms of the disorder.

I think the quoted text is quite interesting, but I'm not inclined to think that is the primary mechanism at play here.

Alan has covered some of it, but to add an illustration of the malabsorption piece of it, below left you can see a "normal" slice of small intestine, where the villi (finger like projections) are covered in enterocytes (the purple "bricks" along the border of the finger), which are responsible for the uptake of lipids (and their eventual "packaging") after they have been emulsified with bile salts in the intestinal lumen.
The offending gluten causes an autoimmune reaction over time that damages these villi as well as the enterocytes (as seen on the right side of the diagram), leaving a flattened area (hence far less surface area for absorption), and disrupted lipid packaging, so the unabsorbed lipids continue through the intestine into the stool.

from Cell Biology at Yale

So, there is no doubt that if fats are digested in the small intestine of sufferers they will not be absorbed due to the damage illustrated. However, the question remains - do the fats actually get digested at all, because if they don't then they wouldn't be absorbed anyway, even if the villi were still intact.

I always thought steatorrhea was the emulsified fats, but I may be incorrect on that.  Completely undigested fats would do a greater deal of damage to the colon and rectum, I think, as was the case when they had potato chips with Olean (sp?) in the mid 1990s.


text:
What's seen when stress echocardiography shows ischaemia? Can this happen without angina?
What can be seen on the screen when stress echocardiography (a pair of heart ultrasounds before and after exercise) suggests ischaemia? Can this happen without chest pain?
Illustration from Wikipedia:

A number of things can be seen. Ischaemia is typically caused by the narrowing of blood vessels that prevents perfusion (blood flow) to the heart or other organs. When the heart muscle doesn't get enough oxygen, the walls of the heart might not "beat" (i.e. contract) properly. We observe this and thus can tell if a coronary artery is reduced or blocked or fine. It doesn't give absolute numbers of how blocked it is, although observation of the way the muscle moves can give some indication. Contrast can further allow us to visualise the wall with more detail, giving a clearer indication of coronary artery disease in the vessels that supply this part of the heart.
Pain is caused when the heart muscle is really suffering, which doesn't occur unless the vessels are seriously blocked. They're so great that even if about 70% of the artery is blocked there is almost no effect including chest pain. In fact it is silent, which is quite worrying also. However, when the heart is most stressed, we can potentially detect decrease in perfusion from small changes in the contraction of the heart.

Many thanks for the answer. Is injecting a dye a usual part of standard stress echocardiography? Or is a dye injected during stress echocardiography under some special conditions?

Your answer makes me think me that ischaemia should be visible with plain echocardiography. Is the second echocardiography after exercise important?

You answered that in stress echocardiography we "see how it responds to increased exercise (does the blood flow increase by the same amount everywhere?)". 10 days ago Xaqron answered "echocardiography [was] not sensitive enough to do so". Was Xaqron wrong?

You can't visualise it directly. Basically you compare the baseline (at rest) to the stressed heart. What you specifically compare is the motion of the walls. The important word here is "compare". Without a baseline you can't see as much. Contrast (i.e. the dye) enhances visualisation where it is difficult to see wall thickening.

I've updated the answer to make it more clearer. You can't tell the flow difference directly, but you can indirectly by measuring the differences in the way the heart contracts. As there's a lot of other factors at play (oxygen concentration of the blood, anaemia etc.) you can't simply equate flow and the observations on an echo. As you are keeping most of these variables constant by doing a before and after, the only thing really affected is flow which is decreased dramatically by thickening of the blood vessels, which you can thus measure.


text:
Can a fungus become resistant to a chemical such as Potassium Permanganate?
A friend used potassium permanganate solution to treat tinea on the hands/feet but after some initial success, the tinea seems to be making a comeback. Could the fungus develop resistance to potassium permanganate?

I hardly doubt it. The desinfective effect is based on the production of reactive oxygen species. The problem is that the solutions used for this purposes are not very stable. Did you always use fresh (or at least relatively fresh) solution or did you get it once and used it for the whole time?

@Chris, aha, you may be onto something there, the solution was mixed once and then used over a few days, so maybe it lost it's efficacy over time.

It is also possible that the fungus could have produced ROS scavengers to survive. What percentage of KMnO4 ??

@WYSIWYG, roughly 5 grams to 5 liters of water, ( so about 0.1% solution? ) . What would be effective strategies to overcome the ROS response.  Would (a) increasing the sol. strength and/or (b) increasing the duration of submersion and/or (c) increasing the frequency of submersion (number per day) help? Of the three, (b) and (c) would appear to minimize the skin corrosion/discoloration and hence be preferable to (a). Thanks for your input.

@WYSIWYG The cells definitely have some enzymes to overcome ROS. Thats why you have to use relatively fresh solutions, otherwise the cells can handle them.

No, it won't, but my experience that KMnO4 is not very effective against fungus. He should try something else, e.g. some pharmaceutical or essential oils like orange, cinnamon, clove, thyme, etc... As long as he is not diagnosed by a dermatologist it is not really sure that he has fungal infection, e.g. once I had warts misdiagnosed by a general practitioner as fungal infection.

I don't think a fungus would develop resistance to something so quickly.
As Chris suggested in the comments, it could be because "The disinfective effect is based on the production of reactive oxygen species. The problem is that the solutions used for this purposes are not very stable." So, if fresh solution haven't been used, it may be ineffective.
As commented by @inf3rno, fungal infections could be much deeper and hence, "treating" them superficially may not help much.

If it would be effective, it has no use, because it affects only the fungus which is on the surface of the foot. Fungal infections can be much deeper...

Fungi cannot develop resistance that quickly. Potassium permanganate is only used to clean wounds. Therefore, the reimmerging of the fungus may be because it wasn't killed in the first place. I suggest antifungal cream should be used generously to kill the roots of the fungus in his hands/feet.

The OP is not asking for medical advice. We discourage both asking for and giving medical advice.


text:
What's the name of the fibrous strands that hold the seeds in a pumpkin?
If you cut open a pumpkin, the seeds are suspended inside the pumpkin by some fibrous, slimey strands. You can see them in the middle of this sliced-open pumpkin:

I'm writing a post for the Cooking.SE blog, and am trying to find out the proper botanical term. Someone suggested that might be called the endocarp, but I want to make sure and also see if there is a more specific term.
Edit
In "Morpho-Physiological Aspects of Productivity and Quality in Squash and Pumpkins (Cucurbita spp.)" §C.1, I see this:

In the central portion of the fruit, a mass of tough fibers, together with vascular strands connected to the seeds, comprise the placental tissue. The endocarp is made up of small, thin-walled cells that form a membranous tissue that adheres to seed, becoming a transparent skin on dried seeds. (emphasis added)

Am I reading correctly that the name for this part of the pumpkin is "placental tissue", and that the endocarp is just a thin layer on the seeds themselves?

I have also found some sources that suggested this is the placenta, but couldn't find a good example like a figure with an arrow pointing to that and saying "placenta". Googling "pumpkin placenta" gives bubkes.

@Bitwise if you try "fruit placental tissue", you get more results... I think pumpkins are fruit from a botanical standpoint, right?

They are indeed berries.

This part of the fruit is called "Endocarp". It does not become more specific as that, as far as I know.
http://en.wikipedia.org/wiki/Fruit_anatomy

From the article I quoted in the edit, it sounds like the endocarp is actually the thin film directly attached to the seed, not the fibrous stuff around it. Am I reading the article incorrectly?

@leonardo Where do you see that on the site? I can't find pumpkins mentioned anywhere. Wikipedia lets me know pumpkins are berries, and that site describes the mesocarp and endocarp as the "fleshy or juicy tissue", so that sounds like the part of the pumpkin you eat...

@leonardo http://en.wikipedia.org/wiki/Berry lists pumpkins. http://en.wikipedia.org/wiki/Squash_%28plant%29 says that squash are berries. So now I'm even more confused...

"Berries" are just a certain classification of the anatomy of a fruit, it has, as far as i know, nothing to do with the phylogeny. Apples are also berries, as well as Bananas and Oranges.

"Berry" is a good example of a perfectly normal English word that has been used with a different but related meaning by scientists (in this case botanists), and that pedants delight in pretending therefore doesn't have it's original (less precise) meaning. So pumpkins are certainly a kind of squash, and squash are generally considered berries by botanists AFAIK. Obviously they aren't considered berries by civilian English-speakers, but that's because normal English-speakers aren't interested in their anatomy.

... so in everyday English they're squash (not berries), whereas to a botanist they're squash (and also berries).

Each strand connected to a pumpkin seed is a funiculus (plural funiculi). The funuculus attaches the seed to the fruit placenta. This photo shows three areas of placenta, the spongy areas that the three clusters of seeds are around. The endocarp is the inner fruit layer; I'm not sure but here it either blends in to the mesocarp (the main flesh of the pumpkin) without a distinct boundary, or it helps make up the spongy tissue in the very center (or both!).


text:
Does a specific blood group enhance the Plasmodium growth?
I am maintaining Plasmodium falciparum cultures for past 6 months. For the blood culture, usually we lab members take turns  and donate blood for the culture. I observed that the parasite's normal growth cycle were fast and more healthy in B+ blood, little slow in AB+ blood. But on the whole the culture was maintained good but I really observed fast stage transitions in B+.
Is this really possible? Does a specific blood group have an impact on Plasmodium growth? Did anyone notice the same issue?
Thanks.

It is a well documented observation that Plasmodium (vivax and knowlesi) infection is dependent on the Duffy blood groups [1].
Individuals lacking the Duffy antigens (Fya and Fyb) have lower susceptibility to malaria. Plasmodium expressed Duffy Binding Proteins facilitate in establishing the initial contact between the merozoite and the RBCs.
However, Plasmodium has evolved to break this dependence on Duffy antigens [2, 3].
For, the ABO blood group system, it has been observed that the blood group-O is associated with lower severity of P.falciparum malaria in adults  [4, 5], which possibly happens because of reduced rosetting (binding of infected RBCs with uninfected RBCs) [5].

References:

Dean L. Blood Groups and Red Cell Antigens [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2005. Chapter 9, The Duffy blood group. Available from: http://www.ncbi.nlm.nih.gov/books/NBK2271/
Ménard, Didier, et al. "Plasmodium vivax clinical malaria is commonly observed in Duffy-negative Malagasy people." Proc Nat Acad Sci, USA 107.13 (2010): 5967-5971.
Mendes, Cristina, et al. "Duffy negative antigen is no longer a barrier to Plasmodium vivax–molecular evidences from the African West Coast (Angola and Equatorial Guinea)." PLoS Negl Trop Dis 5.6 (2011): e1192.
Cserti, Christine M., and Walter H. Dzik. "The ABO blood group system and Plasmodium falciparum malaria." Blood 110.7 (2007): 2250-2258.
Rowe, J. Alexandra, et al. "Blood group O protects against severe Plasmodium falciparum malaria through the mechanism of reduced rosetting." Proc Nat Acad Sci, USA 104.44 (2007): 17471-17476.


text:
What happens if both forward and reverse primers have same Tm?
One of the key rules in primer designing is that Tm (melting temperature) of forward and reverse primers should be in the range of ±5°C. For example, if Tm of forward primer is 62°C, then reverse primer should be either 67°C or 57°C.
What happens if both the primers are having same Tm?
Is this to be considered as perfect score of finding correct primers set?
Thanks

It is actually good if both the primers have the same Tm (Melting Temperature) because you would basically want both primers to anneal at your Ta (Annealing Temperature) which is generally set as Tm-5. If the Tm(s) don't match, then your Ta should be set according to the lower Tm.


text:
What makes urine smell acrid?
Occasionally, after someone's been, there is an awful acrid smell lying about long after them. What causes this? The food that they've eaten? Urea less dilute due to dehydration?
If it helps I've noticed it only with older males.

Acrid or like ammonia?

Acid (not ammonia on the basis that it doesn't smell like cat urine).

Urea could be one. Also, be aware that there are other sources of urine. Asparagus is a famous one. I am still amused because I once thought something was really off with me ( a male, not older yet) when my urine smelled. I panicked and then found out that it was because I had consumed asparagus in a prior meal.
I am not sure if urine starts smelling differently in certain older males, but take diet into consideration.

Urine on the ground smells when there is no rain. Water evaporates, but solutes in it do not. Rain washes solutes deeper into the ground.
In the urine of a healthy person it is urea and bilirubin that smell.
Other causes of smelly urine:

Certain foods, like asparagus, onions, garlic and coffee can add to urine odor.
Dehydration (more concentrated solutes)
Untreated diabetics secrete glucose and ketones in urine
Urinary tract infection
Liver disease

Here's one source:
http://www.healthline.com/health/urine-odor#Diet


text:
Have people in Africa already started evolving resistance to AIDS?
Are people living in areas where AIDS is rampant (for e.g. Africa), less likely to die from it than they once were because some of the people without genes/mutations that give them resistance already died off?
Is there any data on this?

HIV-resistence is indeed a thing (see Pancino et al., 2010 for example).

You seem to focus on African populations but there are non-african countries that have quite a high HIV prevalence too such as Jamaica, Haiti, Russia or Ukraine. Generally speaking, the highest prevalence are in southern Africa (Swaziland, Bostwana, South Africa, Namibia, Lesotho, etc..) though. Swaziland has the highest world-wide prevalence with an impressive frequency of 26.5% of the 19-42 years old people being infected (wiki)

Your comments on parasite evolution are wrong and your question is therefore opinion-based. Highest resistance will not select for lowest virulence. You might want to read on the subject. Here are two related posts on Biology.SE: Viruses selected by evolution (which is a horrible title btw) and Why do parasites sometimes kill their hosts?.


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connect three coding sequences with IRES
To express two proteins at once in mammalian cells, expression vectors carrying an IRES (internal ribosomal entry site) are available. Does anyone know any attempt to express three proteins using two IRESs or more. The third gene may be expressed very low, but it may be acceptable depending on experiments if it works.

http://www.ncbi.nlm.nih.gov/pubmed/14667529 :: https://www.abmgood.com/Bicistronic-Tricistronic-Promoter-Lentivirus.html ::
Let me know if this helps!

@Kendall Thank you, the information was useful.

You might be interested in the Foot and Mouth Disease 2A Peptide, a self-cleaving peptide sequence that can be inserted in between two proteins. The proteins are translated as one sequence, but cleaved at the 2A peptide to form 2 proteins. If I'm reading the source right, they used 4 genes in a row with 2A peptides between them. The 2A peptide has the advantage of being much smaller than most IRES elements, while being more reliable than IRES or internal promoters.

Thank you. I asked this question out of curiosity. But you are right. 2A peptide could be convenient to this purpose.


text:
Restriction sites
I would like to know: how many restriction sites does a restriction enzyme use on a DNA molecule? In other words: If a sequence on a plasmid contains the following bases:

ATTGCAGTCTG

and I want to have only the bases in bold as a new, separate molecule, will I need two restriction enzymes (One to cut the molecule between the T and G and another one to cut it between the T and C)? Or one restriction enzyme (that will cut them both)?
It wasn't clear enough in Wikipedia and in my biology book.

Welcome to Biology SE. Do I understand correctly that you wish to remove the bolded-out sequence, i.e., blunt-end cuts resulting in a oligo-nucleotide of 5 base pairs and the rest? The plasmid question - please google...

Yes. I have a question about a plasmide being cut by only one restriction digest, and I want to know if it will remain the same size...

This doesn't make sense... Your comment is a different question altogether. Please be specific in your question.

I have a plasmide (as much as I know - a round form of DNA sequence in prokaryotes). One restriction digest is cutting it - in one or two places. If it will be cut in just one place - the plasmide's size won't change, it will just open, beacuse it's round. If it will be cut in two places - there will be a cut plasmide and a new oligo-nucleotide.

please add the restriction enzyme to your question, that would help. It is all too abstract

Sorry, I confused the word "digest" with "restriction"... English is not my first language. I edited my question. I hope it will be clear now.

Let us continue this discussion in chat.

Which enzyme do you use for this experiment. Some (but rare) enzymes recognize a specific sequence and cut a DNA fragment out digesting both ends of the sequence.

Yes, bacterial plasmid DNA exists as covalently closed circles, both in vivo and after isolation and purification. IF: the plasmid contains one, or more, recognition sites for the restriction enzyme you are using, THEN: yes, if you follow the manufacturer's recommendations for the restriction enzyme digestion of the target sequence(s) on the plasmid, you should observe close to 100 % digestion (i.e., the introduction of a double-stranded cut in the DNA) at all the sites. So  1 site = 1 (linear full-length) fragment, 2 sites = 2 fragments, 3 sites = 3 fragments, etc.

Type II restriction enzymes always recognize palindrome sequences and the enzymes dimerize so both of the strands, Watson and Crick, get cleaved at almost the same time, each by one molecule in the dimer.

I use the enzymes ecoRI and BamHI. How many recognition sites do they have?

I might not fully understand what you want to do, but if you just need that short bold portion, why not have an oligo synthesized and save yourself the trouble of cutting and purifying? And if you're just cutting out that tiny portion, you'll never notice a size difference on the plasmid.

My question was theoretical. I don't need a new molecule syntesized, but a sequence to be cut. I just want to know if one restriction enzyme can cut a sequence from plasmide (and not just opening it to a chain). I put the sequence above just as example (its real size is much larger). There is a question about restriction enzymes in my course, and I would like to know this in order to answer it.

Most restriction enzymes have a 6bp restriction site (some have 8bp site also). So two restriction sites generally have to span 12bp. However some restriction sites can overlap. For example BamHI and SmaI:

BamHI
|______|
GGATCCCGGG
    |______|
     SmaI

In this case the total length has reduced to 10bp. However such combinations are not that common and at max you will achieve a 2-3bp overlap. A restriction endonuclease only makes a single cut. To make double cuts you need two restriction sites.
Even if the sites are non-overlapping there has to be a minimum length of separation otherwise the binding of one enzyme will hinder the binding of the other enzyme in a double digest. A 6 nucleotide gap between the restriction sites should be fine. If there is no gap then double digest may not be very efficient.
You can also have two restriction sites of the same enzyme so that you need not use two separate enzymes.
BTW the sequence in your question does not have any restriction site.
Hope this answers your question.

Just to bring another light to the question: a restriction enzyme cuts a double-stranded DNA two times, but it only cuts it once on each strand.
So yes, you would need two different restriction enzymes to excise the sequence in bold (assuming you want that sequence in double-stranded-form): one enzyme that would cut between the T and the G on the strand that you have represented, and one that would cut between the T and the C on this same strand.


text:
Please Help Identify These Bugs
I live in KwaZulu-Natal, South Africa, and the only indoor bugs I've experienced issues with are fleas, as I have two cats (and a big garden). This morning, however, I put on a fleece top that had been lying around somewhere, got a lift to the store, and returned to suddenly feel a crawling sensation. I lifted up my shirt to find these tiny bugs crawling all over my upper body. I did some Googling, went upstairs and carefully observed my bedding and bed, however, the only evidence I found was a few newborn fleas / flea larvae (which I intend to deal with today). I should also mention that a flock of wild Egyptian Geese have been raising five goslings in my yard, and they get very close to me when I'm walking outside at times. My house is also not carpeted, it has oregon pine floors throughout. I tried to take a photo of the critters, however, they're very tiny and move very quickly, so it was difficult to get a clear shot. Any advice would be greatly appreciated.

How do they differ from the fleas you have?

They aren't fleas. The fleas look like fleas and jump around. These are very tiny, appear to look quite different to fleas, and crawl only. I did some Googling, and the closet thing I have found that looks similar is Book Lice.

Definitely look like book lice (psocoptera) to me. We already have a handful of quesions regarding these: see here, here, and here

Yes, this is a book louse (order Psocoptera). They feed on all kinds of organic matter, and are very common. Fun fact - they are called "book lice" because they are often associated with old books, feeding on the organic glues in the bindings. (they are also called bark lice - I'm sure you'd know why).


text:
Which kind of bird is in the picture?
I am wondering what kind of bird this is. Can you help me?

It is a male Rufous Whistler (Pachycephala rufiventris).

The species is sexually dimorphic. While females are typically dull brown or grey with streaked underbodies, males are predominantly dark-grey with white throats and (in most cases) a black mask that covers most of their head and some of their neck.

Your picture is from : hbw.com.


text:
What is this brown spider with black and white stripes? (Atlanta, Georgia)
Location: Atlanta, Georgia
Spider mostly brown, with black and white stripes. Would fit on a teaspoon.  Ran quickly but not very far when I tried to catch it.
Click to zoom in the pictures below:

It resembles Dolomedes tenebrosus, commonly called the Dark Fishing Spider, and it belongs to the family Pisauridae.

Image Source: Bug Guide
Males are generally thinner in profile than the females, which is well depicted below.

Image Source: Spiders.Us
Based on the pictures provided, you seem to have captured a male Dolomedes tenebrosus.

Based on the OP's description of size, I'd say they found a male (7-13mm)

@theforestecologist I would agree. I have updated the answer to include that information.


text:
Will salting the ground kill insects and spiders?
I want to kill the insects and spiders living in my egress using something non-toxic to humans, dogs. I was thinking copious amounts of salt would kill earth dwelling bugs and what appears to be ground spiders with funnel like webs. The insects seem to be majorly silverfish. I am in Missoula Montana.

I think the bugs are coming from the egress. Here's an internet photo similar to my egress. The ground at the bottom is the area in question.

Not sure what the spiders will do, but salt is toxic for plants. In my place at least (Western Europe), usage of salt would kill the native plants and leave the ground to nettle.

The ground in question is in the egress. I want to stop the whole basement window food chain.

I have had some success with boric acid against an infestation in my bathroom.

Dusting the area with a diatomaceous earth based insecticide ought to do the trick, while being essentially non-toxic. If you want to prevent plant growth there too then of course salt the earth.
See Efficacy of modified diatomaceous earth on different cockroach species (Orthoptera, Blattellidae) and silverfish (Thysanura, Lepismatidae)

As soon as I dumped diatomacous earth on my 5 egress windows, hundreds of millipedes, centipedes, spiders, silverfish, beetles, hornets came up out of the ground and the surrounding grass. Before that was 50lbs of salt, which didn't bother anybody. All the basement windows are beautiful white wastelands. THX @jzx :D

Hahaha, happy to be of service!


text:
How does a single-stranded RNA bind to a double-stranded DNA to form a "triplex structure"?
If you have a single-stranded RNA that is complementary to a double-stranded DNA, how do they interact to form what my prof. calls a "triplex structure"?
e.g.
    UGCUGAUAGCUACG
ACGTACGACTA
TGCATGCTGAT

I don't understand how the DNA can form 2 bonds there?

None of those sequences are RNA. I assume it's the one at the top that is supposed to be?

Sorry I fixed that, yes the one on top is RNA

DNA-RNA triplex formation is well-documented. It was originally analysed in simple model polynucleotides where the DNA has a polypurine strand and the RNA has a polypyrimidine, e.g.
rCCCCCC
dGGGGGGGGGGGGGG
dCCCCCCCCCCCCCC

rUUUUUU
dAAAAAAAAAAAAA
dTTTTTTTTTTTTT

but it is now known to occur in more complex sequences. One of the best studied examples is in the promoter of the human DHFR gene:

Gee, J. E. et al.(1992) Triplex formation prevents Sp1 binding to the dihydrofolate reductase promoter. J. Biol. Chem. 267, 11163–11167

In this work the oligonucleotide GR19 was shown to bind in a triple helix to SpI binding site I in the DHFR promoter (CR19 was used as a control). Triplex formation was detected by gel shift, and the specificity was confirmed by DNase I footprinting.
This effect is part  of the regulation of DHFR - the transcript from a minor upstream promoter binds to the major promoter, see:

Martianov, I. et al. (2007) Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 445: 666-670

The structure of these triple helices involves a combination of Watson-Crick base pairing in the DNA duplex together with Hoogsteen base pairing in the RNA-DNA interaction:

Figure taken from:

Morgan, A. R. & Wells, R. D. (1968) Specificity of the three-stranded complex formation between double-stranded DNA and single-stranded RNA containing repeating nucleotide sequences. J. Mol. Biol. 37, 63–80


text:
What is this insect found in Western Arkansas?
I had my cup of water outside with me, went inside for a few minutes, came back outside and this insect almost found out what was unpleasant about being drunk.
It's 1-2cm long, mostly black, with some white spots on the back. The bottom of the abdomen was also white/gray & black striped.
What did I almost drink?

Update:
I saw another one of these at the park - it's rear legs were positioned like a stink bug, and before I could take any pictures of it, it flew off. It had a sustained flight, like a wasp, rather than say a grasshopper.

A better close-up, something for scale, and a photo of the underside would be helpful...

@arboviral I've added another pic of the cup with a US quarter, since the bug is long gone. The bug was roughly the same size.

That sure looks an awful lot like a cricket.

I've never seen a cricket like that. It was skinnier/longer than a cricket, and I think it may have had wings (though I could be wrong on that). You can kind of see the two white "L" shaped spots on the back - they were quite white IRL.

It could be Gryllus pennsylvanicus.

@SanjuktaGhosh No, that's definitely not it. I've got plenty of crickets and I know them. I actually have two in front of me waiting on my jumping spider to consume them. I actually saw another one of these guys later on at a park but before I could snap a picture it flew off. One thing I noticed was that one that wasn't in my water cup held its bag legs like a stink bug - that distinctive splayed style.

I see. So you are an insect keeper :) . Today somebody asked a question about identification of a cricket and  Gryllus pennsylvanicus was the one, and your insect too looked similar, so I thought I might tell you.

Your comment got me looking again and I found this eastern leaf-footed bug that's very similar. The distinction I see - it's not a straight white bar on the back, and the hind legs aren't "leafy".

Zooming in on the photo showed me an antenna with more than five segments, so definitely not a true bug (and the segmentation being almost clear eliminates crickets as well); the same zoom also showed what seem to me to be short elytra (the front wings of a beetle).  Not knowing where the photo was taken (beyond probably the United States, unless Wayne also collects foreign coins?) forbids me from speculating further.

@ArthurJFrost Western Arkansas

That is not a true bug.  It looks like a beetle, possibly in the group that includes the borers.  Exactly what it might be, though, I don't know.  I've seen that sort of hind leg position before, and noticed it, but I'm darned if I can recall in what.


text:
Finding proteins in DNA sequence
I have to do a task for a university task and I need to understand some things
before figuring out how to do it.
The task is the following:

Find matches of known proteins (DNA-PolyI,II,III) to the specific E.Coli DNA, sequence.

I downloaded in FASTA format the protein sequence of DNA-Poly3 DNA-Poly1 of E.coli (strain K-12) and the entire DNA sequence
of the E.Coli.
I've studied a bit on-line and using the BioRuby gem and the Ruby programming language I wrote a program that translates DNA to protein sequence.
Then I tried to match the known DNA-Poly3 sequence but it did not match. After searching a bit on-line again, I learned about ORF and
and the 6 possible reading ways of each frame. The longer, in terms of codons, ORF conformation is chosen but there's no way of telling for sure that the protein was made using
this frame.
Then I've read about TATA boxes, but I can't use those since they can be found only in Eukaryotic and Archaea.
So how should I proceed in order to solve this problem: How can I prove that the DNA-Poly3 gets produced by a specific area (gene) in the DNA sequence?
Thanks for your time,
ps. Insights and hints are very much welcomed as this is just the tip of the iceberg for me and I'm very willing to study bioinformatics :-)
EDIT: This is an update for info requested in relevant answer
The files I have used are the following:
➜  Bioinfo  ruby dogma.rb
----------------
DNA Length: 4639675
gi|48994873|gb|U00096.2| Escherichia coli str. K-12 substr. MG1655, complete genome
----------------
DNA Poly-1 sample: 928
gi|16131704|ref|NP_418300.1| fused DNA polymerase I 5'->3' polymerase/3'->5' exonuclease/5'->3' exonuclease [Escherichia coli str. K-12 substr. MG1655]

You can download them here: E.Coli DNA and E.Coli DNA-Poly1.
NOTE: My sample protein is DNA Polymerase I (and not 3).

Do you need to write a program that does this or will existing tools be OK?

I should write the program and put up a web interface.

OK, but do you need a totaly new algorithm or can you use existing tools like BLAST? If this is a computer science course, you should implement the algorithms yourself (I guess), if it is a bioinformatics course you should not reinvent the wheel. There are many, very, very good, programs that do what you need already. Is it OK to integrate them into your web interface?

Yes I should not (by any means) re-invent anything. I can use algorithms already in use. I know there are very sophisticated tools for the job. What I really want to know to begin with is how it works, then I can use ready algorithms.

To give a clear example, all my data comes from ncbi (BLAST). How come that I can not match it? I've tried out all 6 possible conformations of ORFs and still I can't "produce" a sequence that matches the DNA-Poly3! :-/

Aren't the RBS and Shine Delgarno sequences a much better search term?

Hello @bobthejoe, could you give me links and offer a quick hint about why are they better suited?

The DNA sequence you have is the entire genome of the bacterium. It contains a multitude of ORFs coding for all sorts of proteins. What you need to do is use BLAST, or much better, exonerate as described in my answer. Translating the entire genome and then trying to find a single protein is both incredibly inefficient and prone to errors as well as very hard.

I am trying to create some results. After reading the manuals - it has an incredible amount of options - I used the following cli: exonerate -Q protein -T dna -E -m protein2genome:bestfit dna-polyI.e-coli.fasta e-coli-K12.fasta  and I'm waiting for it to finish. My hardware is a macbook air i5 1.7 Ghz with SSD.

You are only interested in the best result here since that will be the coding gene. You do NOT want exhaustive (E), that is only useful for highly divergent sequences, not when working on the same species. Try this: exonerate -m p2g dna-polyI.e-coli.fasta e-coli-K12.fasta it took about 2seconds on my laptop and the first result is what you want.

IMPORTANT EDIT : In your particular case, if you are working with bacterial genes, splicing is not an issue since bacteria do not have introns. I am leaving the information here since it may be useful to someone else. However, I recommend you focus on the UTRs since they are probably what is causing you problems.

There are three things that could be causing you problems. I will briefly touch on each one. I will talk about all genes, bear in mind that bacteria have no introns so any discussion of splicing and/or introns and exons is not directly relevant to your problem.
1. UTRs
Untranslated Regions (UTRs) are sequences at the beginning and end of a gene that are not translated into protein. UTRs are regions that are part of the original genomic sequence, they are also part of the mature mRNA (indeed, UTRs are sometimes modified by splicing events, they are exons not introns) but they do not get translated into protein. To illustrate, have a look at this simplified representation of an mRNA molecule:

Only the green exons will make it into the final protein. Introns are spliced out and UTRs are not translated.
Therefore, if you translate the entire gene, you will not get the correct protein.
2. Reading frames
Genes are read in words of three letters (the codons). The sequence ATGTGTACCTGA has six possible reading frames (three on each strand) which can be read and translated as follows:

5'3' Frame 1
    ATG TGT ACC TGA
     M   C   T  Stop

5'3' Frame 2
    a TGT GTA CCT ga
       C   V   P

5'3' Frame 3
    at GTG TAC CTG a
        V   Y   L

3'5' Frame 1
TCA GGT ACA CAT
 S   G   T   H

3'5' Frame 2
t CAG GTA CAC at
   Q   V   H

3'5' Frame 3
tc AGG TAC ACA t
    R   Y   T

DNA is double stranded. The sequence of one strand is complementary to that of the other, therefore if you have one strand you can infer the sequence of its complementary one. Genes can be found on either strand, the two are equivalent biologically. However, sequencing projects choose one of the two strands (randomly) and call it the plus (+) strand and then save all sequences with respect to that strand. This means that sometimes the genomic sequence that you download from a database might be the complement of the actual sequence you are looking for.
3. Names
I once heard someone say in a conference that

Biologists would rather share a toothbrush than a gene name.

While that might be a little exaggerated, naming conventions vary between research communities and species and databases. So, are you sure that you have downloaded the correct gene? Where did you get it from? How did you identify it? Does the sequence also contain up/downstream regulatory regions, promoters, enhancers and the like? If you post the exact sequence you are attempting to use I can give you more specific help.
For example, the first 20 hits when searching for the E. coli DNA Polymerase 3 in ncbi's nucleotide database, are whole genome shotgun sequences. These do not correspond to the gene sequence you are looking for. They are huge pieces of the genome (or even the entire genome) that will contain your gene and many others. Look at the Tools section below for suggestions on extracting your gene from the whole genome.

4. Splicing (irrelevant to bacteria)
Another possible problem is splicing. Lets start with the basics, the process of producing a eukaryotic (bacteria have no introns) protein from a genomic sequence is summarized in the image below (modified slightly from here):

Transcription begins at the transcription start site (TSS) but not all the transcribed sequence is translated into protein. First, the introns are spliced out of the mRNA to produce the mature mRNA (other things like capping and poly-A addition also occur but are not relevant here). So,the mature mRNA contains the exons of the coding gene. This means that a linear translation of the gene's sequence will not correspond to the protein produced. You will need to take splicing into account.
Also, bear in mind that splicing will change the reading frame.
Now, if the sequence ATGT were spliced at, for example, AT/gt (most splice events cut/join at GT/AG sites) and joined with the sequence agATTATT, the resulting (spliced) sequence would be (the splicing process will remove the gt from the first sequence and the ag from the second):
ATATTATT

As you can see, the reading frame has now changed. Where before, in the first reading frame, we had the codon ATG, the canonical translation initiation codon, we now have ATA which codes for isoleucine (I). I hope that is clear,  the main point is that splicing can change the reading frame.

5. Tools
OK, that was the background. Now, what you will need to do is use existing programs that model splice sites and can correctly align a protein sequence to genomic DNA. My personal favorites are exonerate and genewise. On a Debian-based Linux distribution, you can install them with this command:
sudo apt-get install exonerate wise

Then, to align the protein to its gene do:
exonerate -m protein2genome -n 1 prot.fa dna.fa > out.txt

or
genewise -pep -pretty -gff -cdna prot.fa dna.fa > out.txt

In my experience exonerate is (much) faster but genewise is a little more accurate. I usually use exonerate if I am dealing with a whole genome and genewise if I only have a few kilobases of sequence. Both are very good and both will be able to align a protein to its genome of origin.
I will not explain all these options because that is beyond the scope of this site. Have a look at their documentation (which is quite good and clear) and if you still have problems, you could ask a question on our sister site, Bioinformatics Stackexchange
Alternatively, you could link your web application to the ucsc genome browser BLAT service. Click here to see the results when aligning the human
DNA-directed RNA polymerase II subunit RPB1 protein.

Thanks for the answer! I will study the answer in a couple of hours when I'll have time! Thanks for your time!

Just to let you know, the way to give thanks on the Stack Exchange network sites is to upvote the answer and, if (and only if) it answers your question to accept it. Thanks are always appreciated of course, I'm just letting you know how these sites work.  Anyway, you're very welcome :).

The OP asked about an E. coli protein and the E. coli genome. I don't think his problem is anything to do with splicing.

@AlanBoyd ah, you make a good point. Probably down to the UTRs then. I'll edit my answer.

Hello, thanks for the explanation it was enlightening, I will try work on it tonight. Do you know which is the main procedure by which the protein is aligned to the DNA? :-) Thanks again!

Please re-read my answer, I made a substantial edit. You can ignore everything I said about splicing. As @AlanBoyd very correctly pointed out, if you are working on bacteria it is not a factor. As for aligning proteins to DNA, use exonerate or genewise as described. You can also use a genome browser like the ucsc or ensembl.

Sure, already did! Thanks again for the tips!

@terdon I modified my initial question and added some more specific questions! Thanks for your help, it's very very much! You saved me quite some time!

@terdon However, sequencing projects choose one of the two strands (randomly) and call it the plus (+) strand and then save all sequences with respect to that strand. This means that sometimes the genomic sequence that you download from a database might be the complement of the actual sequence you are looking for.What are the serious implications of this method?Please elaborate.Thnx

@Raghavakrishna what do you mean? What method? If you mean the two tools I mentioned, exonerate searches both strands by default and genewise does so if you give it the -trev flag.

@terdon I meant the methods used by the sequencing projects to  choose one of the two strands (randomly) and call it the plus (+) strand and then save all sequences with respect to that strand

@Raghavakrishna I still don't understand what you're asking. Sequencing projects sequence one strand and call that the + strand and then extrapolate the sequence of the - strand. If you have a question about this, please ask a new question so you can explain it clearly and get a full answer.

For what its worth - I have replicated what you are trying to do using a Python script. This is not elegant, but I just wanted to check for you that it is possible, and that there really is a match.
pseudocode is

take the genome sequence
make a reverse complement sequence
for each of the two DNA sequences, for each of three reading frames:
translate the DNA into a single string of amino acids with "*" at stop codons
split the string at "*" characters, call these words
find the first Met residue in each word, the string from that Met to the end of the word is an ORF
if the ORF is >99 (arbitrary cut off) put it in a big list of ORFs
now have a list of all ORFs in all 6 reading frames
search this list for a match to the polI sequence (I actually just looked for the first line in the fasta sequence).

The hit is identical to the entire polI sequence in a CLUSTAL alignment.
Note that this algorithm does not detect any ORFs that cross the breakpoint in the linear sequence representing the circular genome of E coli. Also assumes all initiator codons are ATG/Met but I seem to recall some E.coli initiation codons are GTG/Val

Rather than doing it all from scratch, if you had your own instance of BLAST, you would make a blastable database of your e.coli sequence, and do tblastn, with your putative polymerase protein sequence as the query.
This would find the best matching sequence in the genome, and will work even if there are a fair number of differences between the protein you gave it, and what your DNA sequence actually translates to.


text:
How are lophotrichous flagella of helicobacter pylori produced?
I am thinking the mechanism is something like first adhesins (mucinase).
Howevever, this does not seem to be enough.
How are the flagella of H. pylori produced?


text:
Elevated transaminases after blood transfusion?
This sparks HCV immediately in my mind.
However, there may be other possibilities too.
What can you deduce from elevated transaminases if you only know that the healthy adult patient received blood transfusion in Africa?


text:
Kidney failure → Inhibition of Na+/K+ pump → Heart failure
I read in my biology book:

Due to kidney failure, the concentration of K+ in the body increases. This can lead to heart failure too.

But there wasn't any explanation to the mechanism of this phenomenon. So, I took help of the internet, found out about the Na+/K+ pump and its role in muscle contraction on the Wikipedia page.
But, there wasn't any direct mention of the relation between inhibition of Na+/K+ ion pump and kidney failure. After some brainstorming, I hypothesized the following mechanism:
Due to kidney failure, the aldosterone-catalysed mechanism for keeping the Na+ concentration static in bloodstream stops. So, Na+ ions filtrated by the nephron can't go back to the bloodstream, resulting in a decreased concentration of Na+. Then, the decreased potential difference between intra and extracellular space, in terms of Na+ ions, inhibits the Na+/K+ pump. As muscle contraction is dependent on the Na+/K+ pump, heart muscles stop to work.
Is my hypothesis right?

Basically, you are right... But you should really consider and the HUGE role of the Na+/K+ pump on the neurons... If that pump is blocked from high intra consertration of Na or K the pump won't work and as a result the nerval impulse will be deleted. This means that the Autonomic nernous system of the heart will collapse and as a result you will have heart failure. It is like a machine that doesn't get orders.....

@The_Mad_Fish No, this is not right. See my answer below.

@BryanKrause Ok wait to check your answer.

Hyperkalemia (too much blood K+) caused by kidney failure is because the kidney is not clearing excess K+, and most K+ excretion is by the kidneys. Usually kidney failure alone isn't sufficient to cause hyperkalemia (Lehnhardt and Kemper,
 2011), and note that kidney failure can cause problems via many other mechanisms besides hyperkalemia.
The reason that hyperkalemia causes problems with heart and other muscle function isn't directly because of the Na+/K+ pump, but because of how the electrical potential of cells controls contraction. Cardiac myocytes, like most cells, have a negative resting potential, with high K+ inside and low Na+ and Ca2+ inside, and a resting conductance that is higher for K+ than the other ions. When the cell is depolarized to around -40mV, a rush of Na+ and Ca2+ comes in that further depolarizes the cell and also causes the muscle contraction.
Normally, this "action potential" is terminated by opening K+-channels, which returns the cell to a hyperpolarized/resting state by letting K+ ions flow out, ready to fire another action potential and contract again. However, the resting potential is determined by the Goldman equation and depends on the concentration of each ion both inside and outside the cell. The reversal potential for K+ depends on there being a lot of K+ inside the cell, and very little K+ outside the cell. Therefore, it takes a large negative potential to keep K+ in equilibrium. As the K+ concentration outside the cells increases, the equilibrium potential for K+ gets closer to 0 mV. Eventually, cells can't repolarize after contraction and effectively stay in "contraction mode" without relaxing.
Although the Na+/K+ pump is somewhat dependent on the concentrations of Na+/K+, the typical role for that pump is to push K+ ions into cells and pull Na+ ions out. If blood K+ is high, that will not do anything to prevent the Na+/K+ pump from operating, so suppression of that pump is not having any mediating role in this process.
As a side note, KCl is used in lethal injection in the United States as the final drug administered, which stops the heart by causing immediate hyperkalemia.

Your answer describes the hypercalemia state right? Well that's what and I explained but I thought that the Na+/K+ pump would be blocked and as and you say in your post : "When the cell is depolarized to around -40mV, a rush of Na+ and Ca2+ comes in that further depolarizes the cell and also causes the muscle contraction." I ment that upper but I couldn;t describe it, that's why I posted a comment and NOT AN ANSWER. I will +1 your answer cause it shows extended reseach... can you please edit your answer with links of the sites you found facts? Thank you

@The_Mad_Fish I can add some references, sure, but there is nothing here that isn't widely available on wikipedia. I'm a bit confused by your comment though referring to Na+ and Ca2+ coming in to the cell: that mechanism as I describe it does not have anything to do with impairment of the Na+/K+ pump. Yes, if the Na+/K+ pump was impaired that would be a problem, but that is not the only mechanism to interfere with action potential generation.

Ok I understood where the mistake in my hypothesis was. Thank you for the corrections and for the clarifications. :)


text:
Whitening of hair at old age
Human beings have evolved from their ancestors to their modern forms adapting many changes in structure and I would assume that every change has a significance.
So, what is the cause of our hair turning white at old age? Was it meant for frightening away predators at old age when our body is weak? Or what is it actually?

Not everything what changes has a significance. It can also be neutral - as for whitening hairs. Hairs grey and eventually whiten due to the loss of pigment, nothing else.

It would be incorrect to assume that

every change has a significance

from an evolutionary point of view. In many cases, the changes could be happening at an age where it does not affect it's selection, since it's past the reproductive age. This could certainly be true for greying of hair.
If you want to understand from the point of view of an evolutionary theory, there are at least two possible explanations. One is the Mutation Accumulation (MA) theory. It says that mutations causing late life deleterious effects can build up in the genome more than diseases that cause early life deleterious effects. This is for the simple reason that cases of the latter would be eliminated as they will usually affect in the reproductive period, but chances of a 60 year old grey-haired man to have offsprings is low. In essence, if a trait reduces survival in the post-reproduction period (which is the case here), then the effect of selection is weak for it. So, since grey hair arrive so late, they might not really be selected out.
Another is the Antagonistic Pleiotropy theory. Pleiotropy means a single gene having more than effect. So it says that if a gene improves fitness early on, but causes an undesired effect later in life, it will be selected for in the population. This is simply because the later deleterious effect does not affect the advantage the gene provides at the stage were reproduction happens. So, it is possible that the gene responsible for grey hair may also be making you more fit.
So, in summary, there seems to be no direct advantage of having grey hair. It could be the result of Mutation Accumulation, or the antagonistic pleitropy effects of the responsible gene.
You can read more about it in this and this answer.