Why is GTP gamma S non hydrolyzable? GTP gamma S is routinely used in studies of G proteins to stably activate the G protein. Comparing the structures of GTP gamma S and GTP, the Sulphur atom replaces the Oxygen attached to the leaving Phosphate group. However, this is not the bond that is hydrolyzed (dashed line). What makes it non-hydrolyzable then?

GTP:                    GTPgS:

Gamma thiophosphate-analogues of nucleotides were first synthesized in the 70s (Goody and Eckstein, J. Am. Chem. Soc., 1971) and have been used to decipher many intracellular pathways.

To understand why GTP-γ-S is not (or very slowly) hydrolysed by GTPases, we can look at the structure of a GTPase-GTP complex.

GTP binds to various sites on GTPases. This is the binding of GTP to Rap2A, as described in (Cherfils et al., EMBO J. 1997).

As you can see four different sites bind to the γ phosphate.

From the paper:

  The interaction of Tyr32 with GTP suggests that its general conservation in small G proteins may have structural or functional advantages. Tyr32 is located three amino acids upstream of a threonine (Thr35 in Ras) which is extremely conserved in most G domains. The alpha subunits of heterotrimeric G proteins have a conserved arginine equivalent in sequence to Tyr32, which was shown from crystal structures to interact with the γ-phosphate of GTPγS

In particular, the position of Tyr32 is different, when Rap2A is crystallised with GTP-γ-S. This figure shows the position of the Tyr32 with GDP (A), GTP (B) and GTP-γ-S (C)

  Crystals of Rap2A–GTPγS, whose structure we also report at 3Å resolution, are isomorphous to the Rap2A–GTP crystals. Both structures are essentially similar, except that Tyr32 no longer forms a hydrogen bond with the corresponding atom of the γ-thiophosphate, which is probably the sulfur atom. The Tyr32–γ-thiophosphate distance is 7.2 Å. The conformation of switch I and II and their interaction with the nucleotide are otherwise identical. Thus, the Tyr32–γ-phosphate hydrogen bond forms only in the presence of the true ligand, but is probably not essential for the triphosphate conformation of Rap2A nor for proper binding of the nucleotide. In particular, the position of Thr61 compares well between the GTP and GTPγS complexes.

The author conclude that:

  Our study shows that the complex with the natural ligand GTP is similar to the complex with GTPγS, and thus justifies most conclusions obtained from previous structures of G proteins with GTP analogues. However, the structure of Rap2A with GTP reveals a novel interaction of Tyr32 with an oxygen of the γ-phosphate of GTP and with the amide group of Gly13. In the GTPγS complex, Tyr32 is shifted away from the corresponding atom. The Rap2A–GTP and Rap2A–GTPγS complexes are otherwise identical, and form isomorphous crystals. Thus, the interaction of Tyr32 with GTPγS is prevented solely by the presence of the gamma-sulfur, but the conformation of switch I and II is similar whether GTP or a GTP analogue is bound. GTPγS probably introduces a different charge distribution on the gamma-(thio)-phosphate and/or modifies the polarizability of the β–γ P–O bonds as compared with GTP


How can the layperson test whether a UVC light sold as "germicidal" is a fake or probably the correct wavelength? Are there simple ways to test whether a light is likely short wave / UV-C, or at least whether it is probably a fake?
Real Example:
2 lights are allegedly germicidal and supposedly emit germicidal 254nm radiation.

Light 1 darkens transition glasses and emits the smell of chlorine / ozone.
Light 2 does neither but appears much brighter than Light 1.

Does the ozone smell of Light 1 entail that it at least emits radiation within the UVC band?
Assuming the glasses do darken outdoors and do darken in response to Light 1, given that they do not darken with Light 2, is it safe to conclude Light 2 emits no UV at all?

You can do the banana test to identify if it is real or fake.
Get a green banana and cover parts of it with a sticker you now need to expose the banana with the uv light for about one hour,the green banana will get brown/yellow at the exposed part and stay green under the sticker if the uv-c light is genuine..
It is best to do this in a dark room and the banana can not be in a plastic bag or any covering as this might stop the uv-c light.
The uv source needs to be close to the banana for this to work.
If the color of the green banana stay the same after the test your uv-c light is fake.
Never look directly at the uv-c light and do not shine the light on your bare skin.
source https://www.reddit.com/r/BigCliveDotCom/comments/gj9ymb/uvc_the_green_banana_test/


Where can I find these frequencies for several species? Where can I find frequencies of nucleotides in the DNA for several species?

Since most of the genomes consist of double helix DNA, the only meaningful ratio is GC-content. A comprehensive list of the known genomes that includes GC-content data is available at NCBI (note that default Overview tab doesn't contain the GC-content numbers, you need to select another tab, e.g. Prokaryotes). They also provide an FTP access to the raw data, if you need to process the numbers with software.

If you're interested in particular genomes that are not present in this list, you can calculate all frequencies from the sequence. There are a number of programs to do this. For sequences in FASTA format you even don't need a special software, the analysis can be performed with standard tools, e.g. grep (should be installed in Linux/BSD/MacOSX, obtainable for other systems):

grep -v '^>' sequence.fasta | grep -o '[ATGCatgc]' > tmp
# number of AT pairs
grep -c '[ATat]' tmp
# number of GC pairs
grep -c '[GCgc]' tmp


sex limited genome transmission In general, for dioecious species, a large portion of the genome passed from parents to offspring of both sexes - in mammals the X-chromosomes and autosomes are passed from a mother to both daughters and sons, and autosomes from the father to both sons and daughters. Only the small amount of genes present in the Y-chromosome and mitochondria are inherited solely within one sex.

Is there any species (not just mammals) where most, or even all, of the genome is inherited in a sex-specific trajectory? What is the most sex-limited genome known to researchers?

Is there any species (not just mammals) where most, or even all, of the genome is inherited in a sex-specific trajectory?

Here are a bunch of cases and specific examples that may interest you

There is a species of ants where both genders evolve to be able to reproduce by parthenogenesis (which means that males might be call females as well). In this species, the two genders mate together to create workers that do not reproduce! Therefore, when you look at the phylogenetic tree you can see that males and females are on two totally separate branches as there is reproductive isolation between the sexes in terms of fertile offspring. There is an article by L. Keller on the subject.
In the amazon molly, there are no males. But it is interesting because females need sperm to start the development of their ovules although they don't even use the genetic material of the sperm. Therefore, the amazon mollies need to find mates in sister species. In consequence, they imitate the females of the other species. There is a recent article from Hanna Kokko that investigate with a mathematical model how such system may be able (not cause the extinction of the amazon molly or of the sister species).
Sex-specific segregation distorter. Nasonia sp. may be an interesting case study
Haplo-diploidy. In ants for example, sons receive genetic material from their mother only. They are haploid.
if the rate of sexual reproduction is different from 1 then, females are responsible for more than half of the inherited genes in the next generation.

I apologize for the lack of references $\ddot \smile$


Fish Carcass Identification Can anyone identify the species of this fish carcass?

This photo was taken in Brooklyn, NY. The fish would have presumably been in Gravesend Bay.

The large lozenge-shaped scales suggest me it could be some sturgeon species. The location is compatible with what Wikipedia says:

  In North America, they range along the Atlantic Coast from the Gulf of Mexico to Newfoundland [...]

Specialists may be able to refine a little more the identification, based on location and visible features.


Why is cisplatin a very potent antineoplastic for testicular cancer, but not necessarily for other cancers? Cisplatin (structure below) is a platinum-based chemotherapeutic agent which is very effective in the treatment of some cancers. Its introduction was responsible for improving the cure rate for testicular cancer from 10% to 85% according to the wikipedia page on cisplatin.

However, it is not very effective for other types of cancers; interestingly, ovarian cancer does not respond well to it (Siddick, 2003).

Does someone know why cisplatin is so specific to testicular cancer? I haven't found any sources explaining this.

From the dedicated cisplatin website and Drugbank it appears its use is quite diverse and not confined to testicular cancers. Further, your linked (Siddick, 2003) paper mentions on the first line of its abstract that cisplatin has clinical activity against a wide variety of solid tumors.

Cisplatin.org mentions that cisplatin finds use as chemotherapy against a range of cancers:

  Cisplatin is a chemotherapy drug which is used to treat cancers including: sarcoma, small cell lung cancer, germ cell tumors, lymphoma, and ovarian cancer. [I]t can be a valuable part of a combination chemotherapy regimen. Look at the regimens given to patients and you will often see cisplatin as one of the drugs.

Moreover, cisplatin is explicitly used to treat ovarian cancer:

  Treatment of ovarian cancer involves putting the cisplatin into the peritoneal cavity rather than a blood vessel. The type and extent of a cancer determines the exact dose and schedule of administering the drug.

As to your comment that cisplatin has "magical powers" I can say that it does not. The article that your linked cisplatin wikipedia page refers to (Einhorn, 1990) is a review paper that describes the efficacy of  combination therapies with cisplatin. The high cure rate of 75% was reached when cisplatin was used in combination with etoposide plus bleomycin. The last 10% was theorized to be achievable with 'salvage chemotherapy'. Hence, it is not cisplatin on its own.

In general, it is common practice to use various chemotherapeutic agents in consort, preferably with differing modes of action to reduce the dose of each and hence lessening the side effects.

References
- Einhorn, JCO (1990); 8(11): 1777-81
- Siddick, Oncogene (2003); 22: 7265–79


Why is chloride ion classed as a cofactor for amylase rather than as a coenzyme? I am provided with the two following statements and have to prove which is true and which is false.

$\ce{Cl-}$ acts as a coenzyme for amylase
$\ce{Zn^2+}$ acts as a prosthetic group for carbonic anhydrase

Now, I know that statement 2 is correct.

But, I'm confused why statement 1 is wrong.

I know $\ce{Cl-}$ is the cofactor for amylase, but why is it not its coenzyme?

On the wikipedia page (en.wikipedia.org/wiki/Cofactor_(biochemistry)) a coenzyme is defined as a complex organic cofactor, so Cl⁻ doesn't count. Another thing that disqualifies it as a coenzyme is that the ion is not directly involved in the catalyzed reaction. This amylase contains both a calcium ion, involved in catalysis. The chloride is speculated only to be involved in differentiation between substrates, and is absent in other structures.


Can a plant be induced to accelerate transpiration? Just what the title states.
I wonder whether it is possible to fire a chemical switch - sort-of like injecting adrenaline in a human, to accelerate a particular process in a plant. For example, transpiration.

With high(er) temperatures, especially in drier air with a bit of breeze, a plant will transpire more. While not a chemical solution, it is indeed a mechanism that serves to cool the plant.


Are there journals for theoretical models of protein-protein interactions? Are there respectable scientific journals for publishing models of protein-protein interactions obtained by docking simulations? I would also discuss the biological significance of the particular mode of docking that I found through the simulations, and how it is consistent with available experimental evidence. The point is that my paper wouldn't have any new experimental evidence. Rather, I analyze existing experimental evidence in the literature and demonstrate that the model of interaction I propose explains this data. Are there respectable journals accepting this type of research? Can you post some example journals like this?

Also, can you post some references to good papers like these, hopefully highly cited, if there are any?

Protein-protein interactions is an area of biophysics, so certainly Biophysical Journal (published by Cell) is a nice place to look.

PNAS has a broad range of areas and they pay a lot of attention to nice biophysics and modeling. But also they require (seems to me) experimental evidence.

The Journal of computational chemistry certainly about a lot of simulations and modeling, so see for yourself.

As for publications, the fact that you are asking for references makes me think you haven't done your homework on literature review, as it is always first and foremost job in a research project.


Can the Staph streak method be used for culturing Neisseria on blood agar? What I learned in class:
Normally chocolate agar is needed to grow Haemophilus and Neisseria. The Staph streak technique can be used for culturing Haemophilus on blood agar by allowing the Staph to hemolyze the blood so Haemophilus can grow around it.

My question:
Is there a reason this method couldn't be used for Neisseria as well?

It depends on your species of Neisseria.

N. meningitidis grows on BAP (Blood Agar Plate), with colonies being grey and unpigmented on  appearing round, smooth, moist, glistening, and convex, with a clearly defined edge

You can read more about that here.

N. gonorrhoeae is known not to grow on BAP.
More on that here.


Incomplete Dominance and Probability I have a follow-up question about an in-lecture question (this is not a homework question). As you can see I have already answered the question and the question is closed to further submissions.

In any case, this is my reasoning.

The male has the genotype Gg and BB. Fur color is incompletely dominant so to have black fur this implies the male has the genotype BB not Bb (which would likely be gray).

The female has genotype Gg and Bb because as the question states, the female is doubly heterozygotic.

The two have a FEMALE offspring - this is critical. This means that the male "donates" a copy of his X chromosome to the offspring. Now if the question had asked about a male offspring, then that would mean the male had donated a copy of his Y chromosome instead, and the male would have no "say" in the male progeny's eye color.

So the probability of green eyes between a cross of Gg with Gg is 3/4.

The probability of black fur between a cross of BB and Bb is 1/2 given that there is incomplete dominance.

So the probability of both events occurring simultaneously is 3/4 * 1/2 = 3/8 = 0.375.

Is this correct? Or should I account for the "female" offspring part and half the answer?

The male has a phenotype XGY BB, and the female, XGXg Bb. Thus the probability is 0.25.


Which was the first DNA-based genome to be sequenced? The Wikipedia article on phi X 174 states that:

The phi X 174 (or φX174) bacteriophage is a single-stranded DNA (ssDNA) virus that infects Escherichia coli, and the first DNA-based genome to be sequenced.

But, the article in Wikipedia on Whole Genome Sequencing states:

The first whole genome to be sequenced was of the bacterium Haemophilus Influenzae

So as bacterial genomes are DNA-based, I am confused as to which organism was the first DNA-based one to be sequenced.

Expanding the question to the history of the sequencing of genes and genomes in general, I present a timeline taken from a review by Giani et al., entitled “Long walk to genomics: History and current approaches to genome sequencing and assembly”.

The graphic shows how the size of sequenced genes and genomes has increased since 1965, which reflects developments in sequencing technology that are discussed in this and other articles which may be more accessible. It should be noted that the more modern methodologies are not intrinsically more accurate than earlier ones, but can be employed more rapidly.
I see no value in the “Guinness Book of Records” approach to biology, but to satisfy the poster, the genome of bacteriophage φX174 was the first DNA genome to be sequenced (1977), and that of H.influenzae the first bacterial genome to be sequenced (1995). But the RNA genome of my old friend bacteriophage MS2, was the first genome to be sequenced (1976).
And the first human chromosome to be completely sequenced is not on the graphic as it was only published in Nature a few weeks ago (July 2020) — chromosome X.

Postscript
For the record, the quotation from the whole genome sequencing article is actually a caption for a (gratuitous) image of the bacterium, is unqualified, and, thus, is incorrect. But when reading Wikipedia articles it should be born in mind that they are written by people like you and me. Anyone can edit them, and nobody need check them or correct them. Peer-reviewed papers can also have mistakes, but where they are of this type, the referees should pick them up. (But by the time you read this I will have edited the Wikipedia article.)


What is the difference between tissue engineering and 3D bioprinting? 3D bioprinting is the modified version of the tissue engineering but when we want to describe the both terms, what are the basic criteria or points to make difference between these?

Tissue engineering is research into ways of organizing cells and cell droplet/matrix structures into a useful form, usually for medical applications. In the near future, tissue engineering could refer to rewriting or genetically modifying cells for a new purpose or to enhance their existing function. Even more into the future and tissue engineering could mean custom-building multi-cell structures from scratch on a computer.

3D bioprinting is the practical or laboratory deployment of the first technology mentioned above - a subset of tissue engineering.

In a nutshell:

Tissue engineering = "Come up with a creative way to arrange these cells and cell structures into something useful".

3D bioprinting = "Use the above-mentioned technology to build part of a synthetic organ".


Lack of skin in a certain area of the body --- hypo[what]? Lack of skin in a certain area of the body. How shell I name this?

Hypocutaneousis?
Hypo[somethingElse]?

What is the correct term?

First, this is not an area where I have any education or experience. However, out of curiosity I consulted google and found two genetic castle diseases that should be relevant to your question:

Epitheliogenesis imperfecta (vetbook.org)
Ectodermal dysplasia

Both diseases are very serious, and Epitheliogenesis imperfecta is fatal (due to infections).

I chose not to include any pictures of the diseases in this answer since they often look quite horrible, and some people might find them unsettling. If you click the links there are pictures of the conditions though.

A "similar" condition in humans might be  Epidermolysis bullosa, which is caused by decreased anchoring between dermis and epidermis, which cause a very fragile skin:

  Epidermolysis bullosa (EB) is a group of mainly inherited connective tissue diseases that cause blisters in the skin and mucosal membranes, with an incidence of 20 per million newborns in the United States.[1] It is a result of a defect in anchoring between the epidermis and dermis, resulting in friction and skin fragility. Its severity ranges from mild to lethal.

(Wikipedia)


Which cells produce HCl produced in stomach? Don't these cells get destroyed by HCl? Which cells produce HCl produced in the stomach? Or is HCl produced due to the translation of proteins. Don't these cells get destroyed by HCl?

Since your first question is a quite basic one (the answer is oxyntic cells) and asking two or more questions in the same post is a reason to close ("Avoid asking multiple distinct questions at once"), I'll address only your second question:

  [Why] don't these [oxyntic] cells get destroyed by HCl?

First, it's important to understand that oxyntic cells (from the greek ὀξύς, meaning "sharp" or "acid") do not produce HCl. They actually secrete two separate ions, Cl− and H+ (and, since HCL is a strong acid, one can say that technically there is — almost — no HCL in the lumen, because the ions keep dissociated).

You can find this in any physiology book, but there is a good explanation of the steps in Scientific American (2017):

Potassium ions, K+, diffuse passively from the parietal cell into the lumen.
An active transport pump brings K+ back into the parietal cell,
simultaneously secreting H+ from the cell to the lumen. As much K+
returns by this route as leaks in (1).
Chloride ions, Cl−, diffuse passively from the cell to the lumen, and their negative charges balance the positive charges of the secreted H+.
An exchanger on the opposite face of the parietal cell balances this
loss of Cl− by importing Cl− from the blood in exchange for
bicarbonate ions (HCO3−).
Within the cell, water reacts with carbon dioxide (CO2) to form carbonic acid (H2CO3), which dissociates into H+ and HCO3−.

This image from Lodish (2000) summarises it very well:

Of course, the important factor in lowering the pH (and in eventually killing the oxyntic cell) is the H+ concentration, not the Cl− one. Regarding that, it's worth mentioning that, despite the H+ concentration in the lumen keeps rising, cytoplasmic H+ concentration is never as high as the luminal one, because H+ is being pumped out of the cell.

Second, why don't the HCl (actually Cl− and H+, as explained above) already present in the lumen destroy the mucosa? The answer is the mucus layer.

Still according Scientific American (2017):

  HCl in the lumen doesn't digest the mucosa because goblet cells in the mucosa secrete large quantities of protective mucus that line the mucosal surface. Basic electrolytes, such as HCO3−, trapped inside the layer of mucus neutralize any HCl that penetrates the mucus.

By the way, a similar mechanism explains why doesn't the lysosome has its membrane destroyed by the enzymes it contains.

Sources:

Lodish, H. (2000). Molecular cell biology. New York: Scientific American Books.
Scientific American. (2017). Why don't our digestive acids corrode our stomach linings?. [online] Available at: https://www.scientificamerican.com/article/why-dont-our-digestive-ac/ [Accessed 30 Jul. 2017].


What is the magnification necessary to see pond life My daughter is 5 and wants to learn about Biology. I thought a great start is to see life from pond water through a USB microscope. It would be great if she could see organisms like amoebas, flagellates and ciliates with her own eyes. The microscopes I have seen typically have a zoom range of about 40 to 400x.

Would this range be sufficient to see microscopic pond life?

2019-05-01 Edited: Updated dead links

From the comment section:

I would go with a cheap one with a magnification of ~40X. According to this source, 10-20X is already sufficient to see large protozoans and algae in a pond. Here some suggestions on what you could look at.


Mushroom Identification (USA) I would like some help identifying this mushroom I found in my yard.
Location: Southeast Georgia
Near Pine trees after heavy rainfall
Color: Light brown to Dark Red, biggest is about 4 inches in radius

It is some type of boletus. You would need a spore print and a few more examples to decide which one. They are commonly found under conifers.The books say most are editable and good taste. The couple kind I have eaten had no flavor , not worth collecting. The tubes instead of gills on the bottom of the cap are an indicator of boletus group.


Is it possible to make humans extinct artificially? Verging on the realm of science fiction, my question is that is there any theoretically possible way, biologically/chemically, with which the entire human race can be killed without affecting the rest of the biosphere at all? I am only curious about theoretically possible no matter how unlikely. If we encounter a sufficiently advanced alien civilization bent on our destruction, would it be possible for them to make sure all humans die without harming any other living organism on our planet?

Is there anything biological/chemical which makes us unique or different than other lifeforms on Earth? Something which can be used against us? Or are we just so similar with a bunch of other species that we cannot be wiped out without other lifeforms getting harmed or our destruction cannot be ensured? Is it possible to artificially make humans extinct?

Thanks you.

Trick question. By driving humans to extinction, you almost certainly will be driving all human-specific parasites and pathogens to extinction as well.


If bacteria with recombinant DNA molecules do not survive in gene cloning, how they can be grown into a colony after being isolated? This is as far as my understanding of gene cloning goes. Let's say that the plasimd (vector) in the bacteria contains an ampicillin resistence gene. Through restriction enzymes, the ampicillin resistance gene is cut through and foreign DNA is inserted. This creates a recombinant DNA molecule.

Once many bacteria are introduced to a medium that contains ampicillin, only ones that have no recombinant DNA and functional ampicillin resistance genes will survive and those with the recombinant DNA won't. Through the addition of some chemicals, the surviving bacteria will turn blue and those with the recombinant DNA will turn white. Thus, bacteria with recombinant DNA can be taken and grown in their own culture, the recombinant DNA can be isolated, and research goes on.

However, if all the bacteria with recombinant DNA have been killed because they have no functional ampicillin resistance genes, how can they be 'grown' in their own colony? They're all already dead, aren't they?

The question confuses too many things. The process being described, Lac Z Blue-White Screening, doesn't involve cutting the ampicillin gene, nor do the bacteria with the recombinant DNA or without the recombinant DNA die in the process of the experiment.

The plasmid contains a Lac Z gene involved in creating enzymes that break down galactose. In a test tube, the vector plasmids take up the gene of interest and the recombinant DNA is produced. The recombinant DNA is then added to the medium of bacteria, but only some of the bacteria will be transformed and take up the plasmid vector. In these bacteria, restriction enzymes will 'cut open' a space for insertion in the Lac Z gene, and DNA ligase will seal it up. The insertion of the gene in a bacterium disrupts the Lac Z gene and make it unable to produce the required enzymes to break down galactose. Then, the bacteria are applied to a Petri dish that contains growth media with a derivative of galactose, X-gal in it. When X-gal is broken down by the bacteria able to create the necessary enzymes from their functional Lac Z genes, the bacterial colony will turn blue. So, when you add these bacteria into the Petri dish, only the bacteria without the recombinant DNA will break down X-gal and turn blue, whereas bacteria with the recombinant DNA will not be able to break it down and remain white. This allows the researcher to distinguish between the bacteria with and without the recombinant DNA, and allow them to isolate for the ones with it.


Pneumonia in children after abdominal operations This textbook says:

  Consequently,  young  children are prone to  suffer from pneumonia after abdominal operations, because they resist breathing (being abdominal) due to  pain.  As a result the secretions in the lungs tend to  accumulate,  which may become infected and cause  pneumonia.

Iam unable to find which secretions are they and how breathing removes them from lungs?

I thought it could be pleural effusion but unable to figure out the mechanism involved and how it gets infected if it remains there for long.

Abdominal surgery results in a painful wound that affects the abdominal muscles, which are important for coughing. The Lungs and respiratory tracts constantly secrete mucus that flows upwards to the Trachea then down the Oesophagus. The trachea is lined with a moist mucous-membrane layer composed of cells containing small hairlike projections called Cilia. The Cilia project into the channel (lumen) of the trachea to trap particles. The Cilia constantly move in a manner that pushes the mucus up to help clear the respiratory tract of pollutants, debris and bacteria. Here is a link to show the Cilia Movement:

https://www.britannica.com/science/cilium/media/117814/16442

Abdominal Surgery reduces the efficiency of the cough reflex due to abdominal wound pain, while the Anaesthetic results in an increase in mucus due to the upper respiratory tract trauma, with some anaesthetic drugs also increasing these secretions and suppressing Cilia movement. All that eventually results in secretions being produced at a higher rate than being evacuated leading them to accumulate and resulting in an increased risk of lung infection.


Attaching suspension cells to coverslip during mycoplasma contamination detection I am planing to screen my cell cultures for mycoplasma contamination using the Hoechst 33258 DNA staining method.

This method is suitable for adherent cultures. Is this method suitable for suspension cultures?

If yes, what is the procedure to attach my suspension culture on coverslip and prevent washout of cells during staining.

If you are working with suspension cells, it's always easier to use Flow cytometry but if you want to use microscopy then I would suggest using chamber slides. You just have to put your cell suspension inside the chamber and then stick the cells to the microscope slide. After that you can do whatever treatment you want just by putting in the chamber the proper solution and wash afterwards. The more the steps the more cells you'll lose mostly because of pipetting so try to pipette always at the same corner and be gentle. To stick the cells to the slide your best option is to centrifuge the slide. Unfortunately in my lab that wasn't an option so I just fixed the cells with methanol while there were suspended in PBS and it worked very well. Most of the cells were attached to the slide and the staining was perfect.
Hope I helped. Good luck!


Are corn kernels considered a grain I have seen corn described as a seed, a grain and a fruit.
What are the kernels or a corncob considered to be? A grain, a seed or a fruit?

The grain of corn is known as a caryopsis, which Merriam-Webster defines as:

  a small one-seeded dry indehiscent fruit (as of corn or wheat) in
  which the fruit and seed fuse in a single grain

This image by Encyclopedia Britannica shows that the corn seed, enclosed by the seed coat (testa) is then further surrounded by the pericarp, which consists of the layers of tissue around the fruit.

Therefore, the corn kernel can be described as any of the terms that you have mentioned.


Can denatured GFP show fluorescence? GFP ( green fluorescent protein) can show green fluorescence. And its fluorescence is due to the tri peptide chromophore which is given in below I was wondering, can we observe fluorescence, if we denature it by boiling at 95 degree celsius? Say can we observe fluorescence band in SDS-PAGE?

I assume it can show some fluorescence as it is not due to any cofactors etc.

According to PDB (protein data bank — a repository for protein structures) the chromophore must be protected from interaction with water molecules to fluoresce.

  The chromophore is found right in the middle of the [protein], totally shielded from the surrounding environment. This shielding is essential for the fluorescence. The jostling water molecules would normally rob the chromophore of its energy once it absorbs a photon. But inside the protein, it is protected, releasing the energy instead as a slightly less energetic photon of light.

This means that denaturing the protein will result in quenching of the fluorescence1, so you are unlikely to see significant signal on a denaturing gel.  In fact, as WYSIWYG has pointed out, fluorescence has been used as a marker of renaturation of GFP1.

Reference:
1: R.Y. Tsien (1998) The green fluorescent protein. Annual Review of Biochemistry 67, 509-544.


Do people who have been blind all their lives dream? Do the people who have been blind all their lives dream and do they experience or report "imagery" in the dreams?

Yes, they do. A blog post on the National Geographic website describes the results of a study about how blind people dream.(1) The participants who were born blind did not report any visual impressions. Among those who previously had sight, the number of visual impressions reported decreased with the time since loss of sight.

  Just as there are many ways to take in the world, there are many ways
  to dream about it. Blind people dream, just as they live, with a rich
  mix of sensory information.

  About 18 percent of the blind participants (both congenital and
  later-onset) reported tasting in at least one dream, compared with 7
  percent of controls. Nearly 30 percent of the blind reported smelling
  in at least one dream, compared with 15 percent of controls. Almost 70
  percent of the blind reported a touch sensation, compared to 45
  percent of controls. And 86 percent of the blind reported hearing,
  compared with 64 percent of controls.

  (...)

  Despite these sensory differences, the emotional and thematic content
  of dreams isn’t much different in the blind and the sighted. Both
  groups reported about the same number of social interactions,
  successes, and failures in their dreams. They had the same
  distribution of emotions, and the same level of bizarreness.


Geometric Interpretations of the DNA Double Helix In mathematics, a helix is a shape which has constant curvature and constant torque (see Wikipedia here. What are the biological implications of the DNA double helix having constant curvature and torque, or is there none?

The standard text-book answer to this question is illustrated by the cover illustration of one edition of, well, the standard text book which I reproduce alongside an image taken from a teaching site of my own in which you can view several different aspects of the double-helix in 3D.

[Views of DNA looking ‘down’ the axis of the helix. On the book cover the bases are black filled shapes of purine and pyrimidine structures, in the image on the right the purines and pyrimidines are red and blue outlines, respectively, with the sugar–phosphate backbone shown in white.]
The regularity of the helix (constant curvature and torque) maximizes base stacking, which involves the π–π interactions of the purine and pyrimidine rings. This is important for maintaining the structure of the double-helix and hence facilitating its function. Base stacking is discussed in another question on Stack Exchange Biology, in that standard text, Berg et al. , and in a chemical article in Wikipedia.
Although concerning a single-stranded RNA rather than a double-stranded DNA, I take this opportunity to illustrate the biological significance of base stacking by considering the anti-codon loop of transfer-RNA. As is well-known (see e.g. this StackExchange Biology answer), there is frequently ‘wobble’ at the 5′ position of the anticodon loop, allowing certain non-standard base-pairs at the third (3′) position of the mRNA codon. As the image below shows, this can be partly attributed to the poorer base-stacking at this position in the anti-codon loop (G-34 in the illustration) compared to the other two positions, allowing greater flexibility.

[Anticodon loop of yeast phe-tRNA, created by the author from 1ehz.pdb]


What species of snake found in central Alabama, US? The snake in the image below was found in the attic of a home in a relatively well-forested suburb of central Alabama, south of Birmingham about 20 minutes. It was safely released outside in the wooded backyard area. What species is the snake in the image below?

Some additional details that may be helpful follow. It emitted musk while being coaxed into the box. I don't recall seeing much striping, except near its head, as can be seen in the image below. I did not get a good look at the belly color, but I believe from the glimpses I got that it was similar to the lighter color on its back and sides. It appeared to be close to 3 feet (~90 cm) long.

I attempted to use Google to identify the snake, and the closest matches were various rat snakes. None had quite the same patterning.

Definitely looks like some species of rat snake (genus Pantherophis). Based on the size, location and coloration, I'd say it's a dark variant of a Gray rat snake (Pantherophis spiloides).

It might also be a cross between a black and grey rat snake (i.e., Pantherophis spiloides x obsoletus).

 Source: Todd Pierson

 Sources: Alan Brumbeloe | Bill Funderburk

Description: Adults usually 99-183 cm long; dark to light gray with darker gray or brown blotches

  Unlike other Pantherophis, whose conspicuous juvenile pattern fades into adulthood, gray ratsnakes do not undergo drastic ontogenetic changes in color or markings. These snakes retain the juvenile pattern of dark elongate dorsal blotches separated by four, or more, pale gray body scales, a light gray crown with dark striping that forms an anteriorly facing spearpoint, and a solid band which covers the eyes and extends rearward to the posterior upper labial scales. The venter is usually off-white or pale gray with darker irregular blotches, and a double row of black spots behind the divided anal plate of the vent. The dorsal scale rows around midbody are usually weakly keeled. Because the gray ratsnake shares its range with other members of its genus, hybrids of midlands x eastern ratsnakes are not uncommon. [Source].

Note, According to here one could have a difficult time IDing juveniles between species of rat snakes:

  The juveniles of all subspecies [of rat snakes] resemble the gray rat.

However, your specimen's size indicates it's likely an adult, and therefore its strong patterns preclude the black rat snake.

Distribution:  commonly found in the forests of eastern and central United States, including throughout Alabama:

 Source: Trey Dunn

Behavior: Gray ratsnakes are agile climbers and can be found in tree tops as well as barns/sheds/buildings close to forests

  The gray ratsnake will defend itself by raising its head and bluffing a strike. If handled, these snakes will musk a victim by releasing the foul-smelling contents of their cloaca, and will bite if necessary. [Source].


What happens in the synapse when cocaine administration occurs in the human brain As far as i know when you accept cocaine in your blood some cocaine molecules reach some synapses in your brain and fill some Reuptake tunnels preventing the cell to simply "do not know that fired neurotransmitters have achieved their task" and doing so the cell fires neurotransmitters again becuase "it" simple do not know that "it" have achieved its task.
In this case cocaine molecules fill Reuptake tunnels in Dopamin Serotonin and Norepinephrine
orientated neurons.But since the firing occurs when an electrical signal occur how the neurotransmitters are fired again when such electrical signal does not exist?

If im mistaken in my physiology knowledge explained above please correct me!

You are correct that cocaine "fills the tunnel" (the pharmacology terminology is that it "blocks the transporter").  But it is not an autoreceptor, so the reuptake transporter does not send a stop signal, it just removed neurotransmitter from the cleft.  But once you've blocked it with cocaine, neurotransmitter is not being removed from the cleft so it has a much longer and stronger signaling effect on the post-synaptic neuron.

But cocaine can also block sodium channels, which assist in action potential propagation and that has more of a local anesthetic effect.

The effect you are thinking of would pertain to auto-receptors, not reuptake transporters.  Autoreceptors tend to be more like the post-synaptic targets of the neurotransmitter.


What causes the development of antibiotic-resistant strains of bacteria? I understand bacteria have become resistant to antibiotics due to selection pressures, but how do resistant bacteria process antibiotics when exposed to it, compared to non-resistant bacteria. Also, what research is being conducted to combat bacteria resistant to antibiotics?

Bacteria usually gain resistance mechanisms through horizontal gene transfer (such as conjugation and phage infection). The four main mechanisms in which bacteria elude antibiotics are:

Drug Inactivation: For example, E. coli can produce beta-lactamase that inactivate many lactam based antibiotics such as penicillin.
Alteration of Target Site: Mutations in genes encoding for target sites can reduce drug binding affinity. Example: Random mutations in DNA gyrase and topoisomerase IV reduces binding affinity to fluoroquinolone.
Alteration of Metabolic Pathways: Many drugs target certain parts of metabolic pathways by inactivating enzymes or sequestering substrates. Bacteria can use alternative metabolic pathways or find ways to uptake the necessary nutrients from the environment.
Reduced drug accumulation: Caused by reduced drug permeability or the ability of the bacteria to transport drugs out of the cell (for example, tetA encodes for a tetracycline efflux transporter). They can gain these abilities through conjugation, phage infection (transduction), or uptake of environmental DNA (transformation).

Wikipedia has a pretty extensive and comprehensive article on antibiotic resistance. There's also a good list of references. http://en.wikipedia.org/wiki/Antibiotic_resistance


What are the effects of the common cold in an immunodeficient person? How would the virus causing the common cold (rhinovirus) affect the human body in the absence of a normal immune response? On the linked wiki page it is said that the runny nose and fever symptoms are in fact caused by the immune response, rather than the rhinovirus itself.

Suppose the immune system is severely impaired (immunodeficiency), how would infection with the rhinovirus affect the body? Would the host not develop any symptoms then?

In one small study, rhinovirus in the immunocompromised led to significant mortality from lower respiratory infection:

  Among high-risk patients with cancer, rhinovirus infections are often fatal. In a study of 22 immunocompromised blood and marrow transplant recipients who were hospitalized with rhinovirus infections, 7 (32%) developed fatal pneumonia. The remaining patients had infections confined to the upper respiratory tract. In 6 of the 7 fatal cases, rhinovirus had been isolated in bronchoalveolar lavage fluid or an endotracheal aspirate before death.

Note that this is in hospitalized patients; it says nothing of non-hospitalized patients.

This conclusion has been disputed.

In a slightly larger study among people with hematological cancers (presumed immunosuppressed because of same):

  Respiratory viral pathogens are a common cause of morbidity in patients with hematologic malignancies. ...Both a rapid viral culture with direct fluorescence antibody (DFA) staining and a PCR-based assay (MultiCode-PLx Respiratory Virus Panel) were performed on patients with hematologic malignancies, who underwent collection of a nasopharyngeal swab or bronchoalveolar lavage from October 2006 to April 2007. Eighty-two samples from 70 patients were obtained; all patients had upper respiratory tract symptoms. Respiratory viruses were detected in 10 samples (12%) by conventional virological methods and in 31 samples (38%) by the MultiCode-PLx assay. ...40% of these patients had pneumonia in addition to the upper respiratory tract symptoms. [emphasis mine; note, there is no mention of mortality.]

So long story short, they have stuffy, runny noses, sore throat, cough, etc. Clearly the virus itself causes damage to the mucosa; that is integral to viral replication After entering a mucosal cell, the virus replicates, then the progeny virus is released by lysis of the cell. This damage itself causes inflammation (not the same as an immune reaction), pain, etc. The major difference seems to be a more severe and prolonged experience.

Respiratory Consequences of Rhinovirus Infection
Detection of respiratory viruses with a multiplex polymerase chain reaction assay (MultiCode-PLx Respiratory Virus Panel) in patients with hematologic malignancies


What would happen if there were no SOX9 in an XY human? Would testes be produced? If SRY is functional, can it produce other proteins that can direct the production of testes, which may or may not be sterile?

Quoting the abstract of this paper verbatim:

  Sox9 is an Sry-box-containing gene that encodes a transcriptional
  activator. During mouse gonadogenesis, Sox9 is detected in the male
  gonad at 11.5 days postcoitus (dpc). At 12.5 dpc, testicular cords
  form, morphologically distinguishing the male gonad from the ovary.
  From this stage onwards, Sox9 expression is restricted to the Sertoli
  cell lineage and persists in the adult. Humans with heterozygous
  mutations in SOX9 develop a skeletal syndrome known as campomelic
  dysplasia. Furthermore, most XY SOX9 heterozygotes show variable
  male-to-female sex reversal, implicating SOX9 in testis development.
  Sox9 heterozygous knockout mice die at birth with a syndrome similar
  to that of human campomelic dysplasia. In contrast to humans, XY
  Sox9+/- mice form normal appearing testes. Germ-line knockout of Sox9
  using a conditional null allele provides a tool for generating Sox9-/-
  mice by simple genetic crosses. However, Sox9-/- mice die soon after
  11.5 dpc because of cardiovascular defects. In vitro culture of the urogenital ridges of XY Sox9-/- results in gonads lacking testicular
  cords and Sertoli cell marker expression, but with the expression of
  ovarian-specific markers. Therefore, Sox9 is essential for diverting
  an intrinsically ovarian program of organogenesis toward testis
  formation.

From MGI page on Sox9:

  Null mutant heterozygotes and conditional knockout mutants display
  perinatal lethality with cleft palate, hypoplasia and distortion of
  numerous cartilage-derived skeletal structures, and premature
  mineralization in many bones. Specific conditional knockout mutations
  are sex-reversed.


Can you please identify these yellow dot parasites which grow on non-living surface? Little yellow dot parasites have screwed me for years and I still don't know how to fight back as I don't know what they are. I just know that they are living beings because they grow in number.
Images:

(Click the images to enlarge)
Location: North India
Size: Visible to naked eyes (one dot is approx 0.25 mm in diameter; their colony is upto 5 mm in length or diameter; their colonies aren't perfect circles as seen in the images)
Behavior: They grow on any plastic, metal and glass surfaces (but not on clothes, walls or wood) if they are stored in open (the surface is in contact with oxygen)
Can you please identify it?

This looks like the work of an insect, perhaps a fly.
You can check by experimentation.
Try covering part of one surface with a fly-proof covering.
Take photos at weekly intervals of exactly the same area, compare images.
black-and-white images below from
Forensic Science International 137 (2003) 152–159
"Distinction of bloodstain patterns from fly artifacts"
Mark Beneckea, Larry Barksdale
DOI: 10.1016/j.forsciint.2003.07.012
Bar on images is 1cm


Why heart beats increase when we are in a state of tension even though it is a disadvantage? Suppose a poisonous snake bites you; this will likely cause hypertension, and it will result in your heart rate increasing dramatically.

Because of the high rate of heart beats, your body will make the snake poison circulate throughout the whole body even faster. This will likely bring about death even faster. (definitely 100% disadvantage)

Why do heart beats increase when we are in a state of tension even though it is to our disadvantage?

The heart rate increases due to any acute stress, it is part of the flight or fight response. This is part of the responses that readies the body for rapid extreme effort.

The body is not selective about it, any acute stress causes it. One idea why is that a hormone response is slower than a direct nervous response so the preparing the body needs to happen as fast as possible since it takes longer to complete, compared to an actual identification, decision and movement.

Also remember that only for a small number of snake bites is this counter-productive, for others it does no additional harm but helps get you away from the snake. Snake venoms vary greatly in their effects.


What does units/mg mean for Streptavidin I got streptavidin for surface reaction. The label says "biotin binding: 16 units/mg". What does units/mg mean?

Does it mean "1 mg biotin can bind to 16 units SA"?

How much is the unit here?

16 units/mg means 16 units per milligram of protein.

Many companies, including Invitrogen, define 1 unit streptavidin as the amount of streptavidin necessary to bind 1 microgram of biotin.


Free online image libraries of trachoma I'm looking for an online source with images of the eye disease trachoma. I'm looking preferably for resources from a credible source that have images from each stage of the disease.

According to wikipedia there are two different way to distinguish stage of the disease. One is from McCallan and one from the World health organisation (WHO). For the second one, on WHO website, you can find their grading card with eyes images. You can download it with also a little description.

Hope it helps.


Refer to Ran-GEF as a coenzyme? Ran-GEF facilitates an exchange of GDP for GTP in the formation of Ran-GTP in the nucleus as part of gated import of proteins. Would I be correct in calling Ran-GEF or Ran-GAP coenzymes?

coenzymes are factors that bind to the enzyme so that enzyme can show its activity. In this case conversion between Ran GTP and Ran GDP are caused by hydrolysis and phosphorylation reactions. Ran GEF and Ran GAP are not binding to Ran GTP or Ran GDP.


What is the meaning of deep winter mixing? I was reading a paper about eutrophication and there was a term "deep winter mixing" in which an abundant supply of phosphorus is released to the surface waters. I searched a lot but nowhere I could find a definition for that.

The winter mixing of stratified layers in lakes and seas due to temperature changes can vary in depth, so scientists sometimes say "deeper winter mixing" and "deep winter mixing". Scientists measure the water arising from 300 or from 800 meters depending on the year, so the deeper winter mixing is a relative term. i.e.:
1992, associated with more stormy weather and higher precipitation than usual. This anomaly was the cause for the deeper winter mixing in the Cyprus Eddy (>500 m) than the typical 350 to 400 m reported by Brenner et al. (1991). Exceptionally deep vertical mixing (>850 m) was reported that winter also in the Gulf of Aqaba https://www.int-res.com/articles/meps/167/m167p047.pdf
Here is basic description of winter mixing:
https://teara.govt.nz/en/diagram/11817/water-circulation-in-a-lake

and here is a science paper:
https://www.jstor.org/stable/2259960?seq=1
A wiki page on lake stratification:
https://en.wikipedia.org/wiki/Lake_stratification


When was peptidoglycan discovered? I've searched for some time now, but I can't find a definitive answer. The closest I have gotten is "knowledge about peptidoglycan structures dates back to the 1970s–80s" from this paper.

The discovery of peptidoglycan, as present in the bacterium cell wall took many years.
“The terms mucopeptide, glycopeptide, or murein, used by some authors, are all synonymous with peptidoglycan.” [Ghuysen, J.M. (1968) Bacteriol. Rev. 32:425-64] Among those, Weidel and Pelzer previously coined the term murein [Weidel, W. and Pelzer, H. (1964) Adv. Enzymol. Rel. Areas Mol. Biol. 26:193].
Regarding the organized, higher structure of the peptidoglycan as found in the Gram-negative cell envelope, Salton [Salton, M.R.J. (1994) New Compr. Biochem. 27:1-22] mentioned the following:
“The exact nature of comparable ‘wall’ fractions obtained from Gram-negative bacteria remained a matter of uncertainty until the advent of electron microscopy of ultra-thin sections of bacterial cells as demonstrated by Ryter and Kellenberger [Ryter, A. and Kellenberger, E. (1958) J. Biophys. Biochem. Cytol. 4:671-678.]. The response of cells to the Gram stain procedure and the early chemical analysis of ‘cell wall’ preparations clearly pointed to some basic differences in the properties of the envelopes of Gram-positive and Gram-negative bacteria and the greater chemical complexity of the isolated fractions from the latter organisms [Salton, M.R.J. (1953) Biochim. Biophys. Acta 10:512-523.]. The structural complexity of the Gram-negative cell envelope was clearly resolved in the thin sections of Ryter and Kellenberger [Ryter, A. and Kellenberger, E. (1958) J. Biophys. Biochem. Cytol. 4:671-678.] and established the presence of an outer membrane as a characteristic feature of the cell envelope. The mysteries of the structure of the Gram-negative cell envelope were finally solved with the demonstration of the thin layer (peptidoglycan) between the outer and inner (cytoplasmic) membranes by use of lanthanum-stained thin sections by Murray et al. [Murray, R.G.E. et al. (1965) Can. J. Microbiol. 11:547-560.], and the isolation and demonstration of the thin murein sacculus of E. coli by Weidel et al. [Weidel, W. et al. (1960) J. Gen. Microbiol. 22:158-166.]. Thus, the complex cell envelopes of Gram-negative bacteria were resolved as consisting of an outer membrane anchored to the underlying rigid, thin, peptidoglycan layer or sacculus.”


Why people like to see pornographic scenes, but do not feel the same about eating scenes? This question may seem funny, but I think biology must have good answers.
I think no more explanation is needed.

I really thought about this and searched for an answer, but there is nothing yet.
If you know some thing about or have some thing which may lead to good answer(s) please express.

Also, do animals portray the same behavior in such situations?

For these two phenomena to create the same feelings all of the time, the physiology that engenders these feelings would have to be the same.  All I can do is point out that these have been separate and distinct even in yeast and bacteria and invoke a likelihood argument.

The impulse for hunger is almost as old as living things.  In bacteria, cyclic Adenosine mono phosphate (cAMP) mediates hunger, though this does not appear to be universal.

Sexual reproduction appeared much later - in the single celled eukaryotes mating factors for instance are mediated by the MATa/alpha receptors.

In animals like C elegans the differences persist (hunger, mating).  This is not a precise argument, but there is the entropy argument - the odds of these 2 signals evolving together biochemically or genetically is quite unlikely given how separate they have always been.

That's not to say that eating food can't create a sexual arousal, but it does not do so all the time.  The sexual response appears to be plastic and adaptable to nearly any sort of stimulus.  The fact that in primates and many other animals, the pleasure stimulus is related to both mating and eating might make them seem like similar impulses, but when you go deeper it doesn't seem plausible.  So the two could hypothetically create the same feeling, but if you are asking why doesn't it usually... then there are lots of reasons why.

I find it helpful to reverse the question and ask - what would happen to a species where you could suppress the mating impulse by eating?  Probably not an adaptation that would survive long.


Finding protein motifs by running sequence analysis in protein BLAST I've run the following sequence (bottom of page) in NCBI protein BLAST and its been identified as Zn-dependent alcohol dehydrogenase. Next I want to see what protein motifs are in this protein. Where in the programme is it possible to see the motifs?

Thanks in advance!

Sequence:

MDRNRLAIVFPIFARCISAADFSTDLYLSEIYQQKVVTMKAAVITKDHTIDVKDTKLRPLNYGEALLEIE
YCGVCHTDLHVKNGDFGDETGRISGHEGIGIVKQDGEGVTSLNAGDRASVAWFFKGCGHCEYCVSGNETL
CRNVENAGYTVDGAIAEECIVVAEYSVRVPDGLDPAVASRITCAGVTTYKAVKVSQLQPGQWLAIYGYGR
FRQSSPSICQDMYFNAKDEQLAYYAKELGGADMVINPKNEAAKIIQEKLGGAHATVVTAVAKSAFNSAVE
AIRAGGRVVVVVAVGLPPPEKMDLSIPPRLVLVGIEVLGSLVGTREKEAFQFAAEGKVKPKVTKRKVEEI
NQIFDEMEHGKFTGRMILPTHHIWIVIGWQSFSLYSQDVSQPQIFRLTSISPRYINKRSPKQPSLLKIIR
STKTPNYALITGKRFWKSNIAGYVIPISMKTGISAMKPAEFQGMKVVSSSRTGKGLLLMPVTAPVLHGSS
KAAAIANIVSAGMKRFAATLKMPVIRLTALQKNASSSPNTRSACQMVLILRLPAGSLARVPPIKQRFLSY
SPDNGWPSMATGGLGNLALRYAKTCISTPKMNSSHTTPKSWAAQIWSSIRKTKLPKSFRKSSGEHTRRWR
LLPNPPLTRLLRLSARVAVLLLLSPLVCLLLKKWIAFLLVWCLSVSKSVPWSERGKRRPSSLQPKVRSSR
KLPSVKSKKSTKSLTKWNMVNSQAVYYQPITYGSSAGNRFPYIRKMYLSRRFFDPLSLRDISTKGSHHES
SRHYRSYDRRERHQITPSELRGSASGNRILRGMSYRSPCEKRGFRRNRQNFRARYRYRQAGRGRGYFSEC
RPRQCCMVLQRLRPLRILCQRENALPQRKCRLYGRRYSRRMHRRRRILGPRARWSSCGCQQDHLRGCNHL
SSKGFSATARTMAGHLWLRAVAIPFDMETPRHVFQRQRTARILRQRVGRRRYGHQSEKRSCQNHSGKARG
STRDGGDGCCQIRLLGCGYPRGWPCCCCCRRWSASSKNGFEHSSSFGACRYRSPRFLGRNAGKGGLPVCS
RRGQAESYQASRRNQPNLRNGTWIHRPYDITNPSHILYVMGWYHTACEFTMFHFVKDLVDFFDFTLGNFR
LDLTFGCKLEGLLFPRSDQGTDFDTDKHQTRRNAQIHFFRRRQTNGDNNNNTATRADSLNSRVKGGFGNS
RHHRRVCSPELFLNDFGSFVFRIDDHICAAQLFGVVCELFIFGVEIHVLAYRRARLPKPPVAIDGQPLSG
LLRNLYCFIGGYTRASDPAGNRRIKTIWHADRVFGDDDAFFCYSAVNRITGIFNVAAKRFIPADTIFAMA
AAFEEPCNTGAVTGIQRSNPFPVLLDDTYTFMPNSAGFIAEIPVFHMEIGMTYPAIFDFQKRFPVIQRAF
GVFHVDRMIFSNDGCFHGDYLLLIYLGEIEVSRKICGDTSCEYRENDCQPITIHYMWVGNIIRPVNLPCS
ISSKIWLISSTLRLVTFGLTLPSAANWKASFSRVPTKEPRTSIPTSTKRGGMLKSIFSGGGRPTATTTTT
RPPARIASTAELKADLATAVTTVACAPPSFSMILAASFFGLMTISAPPNSLAYASCSSLALKYMSWHIEG
LDCLNRPPMASHCPGCSETFTALVVTPAQVILLATAGSRPSGTRTEYSATTMHSSAIAPSTVPAFSTLRQ
SVSFPLTQYSQWPQPLKNHATLARSPAFREVTPSPSCLTIPIPSCPEILPVSSPKSPFFTWRSVHTPQYS
ISRSASPFRGRNLVSFTSIVSLVMTAAFMVTTFCYISERRSVEKSAAEIHLANIGKTIASRLRSICDGLV
ISYGLIYHVPFRQRFGFLRLYAWLSAPYLRLQTGRPPFPAFRPRNLGLRYRQAPNEEECSNPFFQEEADQ
RRQQQQHGHPRGPQQPSRRIWQQPSPPSRVLPRAFPEFWQLRFSDPYLRRPTLWRSMRAVHLWRNTCLGI
SKGIATARSHRWPAIVRAVAEKPLLLYRWLHPRKSCWQPQDQDHLARGPSIRRRRCILLLRRQPYNRHFQ
RCGKAFHSRHNIRNGRSLRTMQHWRGHRHSEKPLPRPARYLYLHALKFCRFHRRNPRFSHGDRYDIPRNI
RFPEALPRNSEGVIWCLSRRSYDLRLLSWLPFVDISRRDRGQSKNLRLRYILRIGKRLPADYDP

MOTIF search
First of all this is not possbile in BLAST (at least nog direclty).
There are a lot of tools to search for motifs in your sequence. I think a good way to start is to use MOTIF search. This searches for motifs in your sequence based on infomration in: Pfam, NCBI-CDD, PROSTIE PATTERN and PROSITE PROFILE (you can select which of these you want to use). Further you can also use INTERPRO (which also searches through serveral database, note that INTERPO searching can take a while but will give a nice graphical view). If you want to find new motifs you can use MEME (as suggest by @mxwsn). However to do this you have to find (or have) a set of sequences which resemble your seqence to find motifs. Because off course the algorithm is not able to find motifs in one sequence because it needs to compare a set of sequences to find some frequently occuring motifs, which could be of your interest.
So to summarize you can use MOTIF search (or INTERPRO etc...) to find motifs in your sequence which are already known. Or gather a set of sequences and find new motifs in them using MEME or a similair tool.

However, how did you conclude that your sequence is a Zn-dependent alcohol dehydrogenase? Because BLASTing the sequence you provided will give matches with this enzyme but only covering ~17%. Nonetheless a good way to find information about your sequence is indeed to find motifs and compare the sequence with HMM's or PSSM's of known proteins.
For example MOTIF search will give these results:

PROSITE:
    Zinc-containing alcohol dehydrogenases signature.
PFAM:
    Zinc-binding dehydrogenase
    Alcohol dehydrogenase GroES-like domain
AND A LOT MORE>>>

Searching PFAM will give you this:

Notice that the second domain (Zinc-binding dehydrogenase) is not completely present, more information can be seen in the detail overview:

I would advice to also take a look at how important these "missing" residu's are (e.g. using a MSA and look at conservation). Because your sequence could contain these domains but that does not necessarily mean that this IS A Zn-dependent alcohol dehydrogenase. It could be non-functional for example.


Can more than one antibody bind the same antigen I'd like to clear something up about antibodies that I'm not sure I've understood in the articles I've read. Looking at concepts such as "affinity maturation", "monovalent antigens" and "polyvalent antigens" it seems as if there are multiple antibodies which can bind to the same antigen. (Although I think I'm right in saying that individual antibodies can only bind to one antigen?) However, when I read sentences like "It has been estimated that humans generate about 10 billion different antibodies, each capable of binding a distinct epitope of an antigen" on the Wikipedia page (for antibody) it does make it sound like it's one antibody per antigen? Is this the case? Or is it one antibody per epitope. Either way, to put this question in a nutshell:

Is it true to say that the same substance could bind with (and, therefore, be recognised by) more than one antibody, or not?

Also, if the answer is no, does that mean that antibodies with different binding affinities are classed as the same antibody or not?

Let's clarify the terms. An antigen is a molecule that can be associated with a particular substance (virus, pollen, dander.) When an immunoglobulin or antibody recognizes an antigen it binds to a specific epitope. An antibody recognizes an epitope using its paratope.

Some antigens have multiple epitopes; this means that different antibodies can simultaneously bind to them (if the epitopes are far-enough apart from each other so that binding to one doesn't preclude binding to the others.)

An example from my work is influenza (flu) hemagglutinin, which is a major viral coat protein. Here's a low-resolution structure showing a "head-binding" antibody fragment (actually three of them), and here's a similar structure showing a "stem-binding" antibody fragment. Our immune repertoire (and physiology) greatly predisposes us towards producing head-binding antibodies over stem-binders. Note that each structure has three antibody fragments bound in the same state. Because the head-binder and stem-binder antibodies are well-separated in space they can both be accommodated in a single complex (as is experimentally confirmed.) In this case, up to six antibodies, using two distinct paratopes, could simultaneously bind to a single antigen.

For matured (high affinity and high specificity) antibodies, each binds a specific epitope. The typical state of affairs is then explained "one antibody per epitope" which is overly simplistic because some epitopes can be recognized by multiple paratopes (which would be found on different antibodies.) So a given epitope can be recognized by no antibodies (a new antigen, or one that is poorly immunogenic) or by multiple ones.

  Is it true to say that the same substance could bind with (and, therefore, be recognised by) more than one antibody, or not?"

Yes, that's true.


Does vaccination make the immune system "lazy"? I was having this discussion with a friend over vaccination against the flu. Although he agrees that vaccination against almost all diseases is necessary, he said that flu shots are not. He argued that the immune system is like the muscular system. It constantly goes through training. Flu shots deprive the body from "natural exercise" since, he believes, we need to train our immune system by getting "the right amount" of the real viruses from the environment. In other words, if we do too much vaccination (and flu shots are "too much") we make our immune system lazy.
Is this true? I know that there is a difference between natural immunization and vaccination, is it correct though to say that the latter makes your immune system lazy? I was under the impression that vaccination's function resembles more the way we learn and memory and less the musclar system which can get lazy.

Contrary to many beliefs our immune system needs no "training". It is permanently active and confronted with dozens to hundreds of antigens in our food, from dust we inhale and so on. This all happens to protect our body from the environment and the immune system is pretty efficient with that and certainly it is not getting lazy.

By vaccinating against a certain disease, you generate immunogenic memory against this disease. When you then get exposed to the disease, this memory helps to speed up the immunogenic reaction against the disease - ideally you are not getting sick, in some cases the progression of the disease is much milder.

Further reading:

Wikipedia on adaptive immunity
The front line of host defense from Janeway at the NCBI Bookshelf


Cancer biology: Can tumors form from cells that are genetically identical to non-cancerous cells? Can a tumor begin to form without any genetic mutations? I'm specifically interested in a tumor which could later lead to cancer.

This is a very interesting question, and one that has been at the heart of cancer research for a long time. I think it separates into three issues.

Are there non-genetic mechanisms that can induce uncontrolled cell proliferation?

Yes, at least in experimental settings. There are many viruses that induce proliferation in its host cell, and viral genes / proteins have been identified that can disable the host cell's cell cycle regulation machinery. A well-studied example is the SV40 Large-T gene (from Simian Virus 40); this gene can be expressed in cells to cause cell proliferation in a transient, reversible manner, and it does so by interacting with host proteins, without causing genetic changes. See for example this article.

Can such genetically normal cells progress to form tumors?

It depends on what you mean by "tumor". To my knowledge, tumors large enough to be a serious medical problem are always found to be genetically altered in one way or another. There are plenty of viruses that cause tumors in humans, for example Epstein-Barr and papilloma (HPV) virus, but in all cases viral sequences are found integrated into the host genome. This may be because development of large tumors requires many cell division, and any non-genetic change that drives proliferation is likely to be lost on the way.

On the other hand, HPV virus frequently causes warts, which technically are small benign tumors. As far as I know, no genetic modification of the host cell is required for this to happen; rather, the virus replicates from its own separate DNA while simultaneously driving keratinocyte cell proliferation to cause these growths. So this example shows that small "tumors" can be formed without any genetic cause. Perhaps there is a limit on how large tumors can grow without genetic changes.

Can genetically normal cells form cancer, meaning a malignant (invasive) tumors?

No, as far as I know, this has never been observed. Large, malignant tumors without genetic changes are unlikely for the reasons above. There are cases of metastatic cancer where the primary tumor is so small that it cannot be located, but in these cases the metastatic cells are again genetically altered. Experimentally, it is possible to produce invasive behavior in cell lines by expressing oncogenes like ras, but these genes are mutated to begin with. Also, normal cells have mechanisms that detect such alterations, causing senescence, and they must first be inactivated by mutations. Transformation to an invasive phenotype is not usually caused by viruses, probably because it would give no advantage to the virus (unlike cell proliferation).

For more information, Robert Weinberg's Cancer textbook does a good job of discussing these issues. This article also provides a historical perspective of tumor virology with some interesting pointers.


Are red blood cells prokaryotic? After searching "do antibiotics impact the immune system" I found out that antibiotics target prokaryotic cells. It all made a lot of sense thinking about all those yogurt recommendations you get after taking antibiotics: the collateral damage is on the prokaryotic cells that live with us, but are not "us" as such.

Except I remembered human red blood cells don't have nuclei, so where's my confusion?

(I'm only a biology enthusiast.)

When differences between prokaryotes and eukaryotes are taught in an introductory biology course, a generic prokaryotic cell and a generic eukaryotic cell are typically compared. Cells in a complex multicellular organism, like a human, are quite diverse. Human red blood cells are one example of a highly specialized cell with a mature form that is quite different from the typical eukaryotic cell. Keratinocytes in the epidermis are another example (see Ross Histology, Ch. 15). In both cases, these cells produce large amounts of a single protein, eventually, at their most mature stage, stopping protein synthesis, extruding their nuclei and most other organelles.

The absence of a nucleus or other organelles, however, does not necessarily make either of these cells more susceptible to antibacterial antibiotics. Antibiotics are targeted toward things that bacteria have (positive differences), rather than the absence of typical eukaryotic structures. Almost all antibacterial antibiotics have one of three targets (see Goodman and Gilman Chs. 48, 52-55):

The bacterial cell wall or membrane
protein synthetic machinery
specialized metabolites required by bacteria

There is (almost) no overlap between these structures in bacteria  and structures in any of the diverse array of human cells. The one partial exception is a similarity between the mitochondrial and bacterial ribosome, that may, for example, be responsible for some of the toxicity of chloramphenicol (G&G Ch. 55).


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?

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.


A question regarding trichomes in plants Trichomes in general are features of xerophytic leaves, which reduce water loss by evaporation by trapping water vapor and increasing humidity (as a result lowering the water potential gradient).
BUT I wanted to know whether trichomes also reduce water loss by decreasing "surface area" of the leaf, so that less water loss occurs (considering they occur as finger-like projected structures that occur in large numbers)?

Trichomes can serve the purpose you ask about, but certainly not only that. They also appear on a great many other, some very delicate, plants from many different habitats. Decreasing water loss is only one of a number of different functions they might serve.

But with respect to xerophytic plants, trichomes are still a projection from the leaf surface and so, by definition, increase the surface area of a leaf by a significant amount.  However, it's not the surface area per sé that leads to water loss, it's increased evapotranspiration which can be caused by and mitigated by many different factors, one of which is, indeed, trichomes.

Some trichomes, such as those on Tillandsia species, occlude or reflect light.  This reduction in incident light is primarily what protects the leaf tissue from damage and helps reduce water loss due to heat. Such trichomes may also function, as you mention in your question, by creating a insulating layer of still air around the leaf, thereby reducing diffusion of water vapor away from the leaf and creating a smaller gradient, though this is usually not their primary function.


Why does Thiamine pyrophosphate have phosphates? The reactions that Thiamine Pyrophosphate(TPP) catalyses are associated with the thiazolium ring. Why is pyrophosphate a part of the structure of TPP then? What benefit do the additional phosphates give TPP? Is there some reaction with TPP that does not center on the thiazolium ring?

The diphosphate* part of TPP does not serve any catalytic function but, rather, helps bind the coenzyme to the enzyme. In this respect it is similar to the non-nicotinamide portions of NAD/NADP (think, why the P?), and represents a general theme, rather than a unique instance.

A pertinent paper that I found from an internet search unfortunately requires access to an academic library. This is P. Arjunan et al. J. Mol. Biol. (1996) 256, 590–600, and describes the crystal structure of yeast pyruvate dehydrogenase. I quote the following from it:

  The roles of Asp444 and Asn471 in binding the cofactor to the enzyme, observed in PDC and in their counterparts in transketolase (Lindqvist et al., 1992) and pyruvate oxidase (Muller & Schulz, 1993), conclusively establish the importance of a conserved sequence roughly 30 residues long (Hawkins et al., 1989) starting with GDG and terminating with NN (Figure 8). These residues are among the few highly conserved in all ThDP-dependent enzymes and form the Mg2+ binding site which assists in anchoring the diphosphate to the protein matrix.

And the Figure 8 referred to is a stereo-pair diagram (squint at the centre — with your specs off if you wear them — to see it in 3D):

￼
This also has a Pfam designation. The structure was deposited in the Protein Data Bank as 1PVD, where there is a useful diagram showing the interaction of the protein and magnesium ion with the phosphates:

*The paper quoted refers to the pyrophosphate part as “diphosphate”, which I assume is the standard chemical nomenclature.


Basic step by step methods for PCR & Gel electrophoresis class I'm teaching a class how to do PCR & gel electrophoresis soon and would like it if you could check through my basic step by step instructions - it's a while since I've done one. Is there anything there that is wrong, missing, or should be excluded in the following?

A)    Collect all ingredients from the refrigerator and keep cool (on ice). Leave the TAQ in the freezer until required.
B)    Make master mix by adding all ingredients (ddH20, MgCl2, PCR Buffer, F Primer, R Primer, dNTP) (excl. TAQ)
.......
W)    Take the gel to the UV camera and take a picture. Large DNA molecules move through the gel slowest so will be nearest to the wells.

(The students will use primers they designed to sex 6 DNA samples from 3 species of birds, males should produce 1 band & females 2 bands in the gel)

for the full version see the answer below

I've run a test following this protocol to the letter...

PCR step by step:

Collect all ingredients (excluding TAQ) from the refrigerator and keep cool (on ice). Leave the TAQ in the freezer until required.
Make master mix by adding all ingredients (excluding TAQ) using fresh pipette tips for each ingredient and using the volume specified
in the PCR reaction mix recipe.
Vortex & lightly spin down on a centrifuge.
Add the required amount of TAQ to master mix (insert in to the liquid) and mix using the pipette to draw some liquid up and down.
Add master mixes to labeled PCR tubes in the required volumes as specified by the protocol.
Add DNA to PCR tubes (using fresh pipette tips for each DNA sample) again using the volume specified in the protocol. Label your tubes
carefully (and on both the lid and tube).
Lightly spin down the PCR tubes on a centrifuge.
Run PCR in the thermocycler according to your protocol.
Collect samples from thermocycler and place in fridge until needed.

Gel Electrophoresis step by step:

Make 1xTAE (enough to make the agarose gel and to place in the electrophoresis apparatus).
Make an agarose gel (about 5 mm thick) by melting agarose and 1xTAE in the microwave; allow the liquid to cool a little before adding it
to the mold.
Once the gel is cool, place it in the electrophoresis apparatus, cover it with 1xTAE (just covering the gel) and then remove the comb.
Collect the PCR products from the fridge/thermocycler.
Make spots of loading dye on parafilm. The loading dye is premixed with GelRed so your samples show under UV light.
Add one sample to a spot, mix it by drawing the liquid in and out of the pipette tip, and then carefully add to a well in the agarose
gel. Take care not to puncture the gel or spill any of the liquid out
of its well. Discard the pipette tip.
Repeat the previous step for each sample and for a negative control (master mix and milli-q water instead of DNA). Use a fresh tip for
every sample.
Load PCR Ladder, also mixed with loading dye, in to a well.
Connect the electrophoresis apparatus to a power supply, with negative electrode (black) nearest to the wells containing the
samples.
Set the power to run 80-120 volts.
Wait until about a finger-width gap appears between the blue and purple bands (approximately 20-30 minutes).
Disconnect the power and collect the gel carefully from the liquid.
Take the gel to the UV camera and take a picture. Large DNA molecules move through the gel slowest so will be nearest to the
wells.

And got a perfect result...

The order is Control, female, male, female, male, female, male, ladder. Males have one band, females have two. The final pair didn't show too well on the picture but were clear enough on the screen in the camera room. Thanks for the tips everyone! Sorry the picture is low quality.
Feel free to recreate these guidelines but remember to credit the Biology Stackexchange Community!


Is there some research paper which focus on the influence of using cancer cell as experimental materials on experimental result? Cancer cell is unstable cell and high variation, but there are many experiment use cancer cell as experimental materials. I always wonder how much influence can using cancer cell as experimental materials exert over experimental result?

Is there any study about this? If any, please give me the study paper.

Thanks for any help.

There are several articles on this. You may look at these for a start:

Masters, John RW. "Human cancer cell lines: fact and fantasy." Nature reviews Molecular cell biology 1.3 (2000): 233-236.
Masters, John R. “False Cell Lines: The Problem and a Solution.” Cytotechnology 39.2 (2002): 69–74.
Masters, John R. "HeLa cells 50 years on: the good, the bad and the ugly." Nature Reviews Cancer 2.4 (2002): 315-319.
Holliday, Deborah L., and Valerie Speirs. "Choosing the right cell line for breast cancer research." Breast Cancer Res 13.4 (2011): 215.
Lacroix, Marc. "Persistent use of “false” cell lines." International journal of cancer 122.1 (2008): 1-4.


Simulating substitution rate of neutral mutations I am trying to computationally simulate a population based on the Wright-Fisher model I would like to get to the classic result of the neutral theory of molecular evolution that the rate of neutral substitution equals the rate of mutation. However, the results of my simulations never show that. I will briefly explain my simulation process and how I calculate the mutation and substitution rates. Please let me know if there is something wrong in my procedure.

I have a non-structured haploid population that grows in discrete time steps. I start with a population of N individuals in an environment with carrying capacity K. I use a K-allele model of mutation. At each generation, every individual will reproduce n offsprings and it will immediately die afterwards. A u fraction of offsprings will be chosen randomly to have a single mutation in each generation (u is mutation rate per gene per generation). At each generation, I record how many mutations have occurred and how many mutations have reached fixation in the population (reached frequency of more than 99% of individuals). Thus, mutation rate and substitution rate per generation is calculated as the number of mutations and number of substitutions divided by population size, respectively. With this set up, even with hundreds of repetitions, the rate of fixation will never be as big as mutation rate u.

Where do you think is the problem?
I have struggled with this a lot and I appreciate any help.

Edit:
My code is written in Python. This my pseudo-code:

Parameters: population size, genome_size, mutation_rate, generation_number, fixation_threshold.

'''
Population_size: Here it is 1500
Genome_size: the number of loci that can be mutated. Each locus can be mutated to any of ACTG. Here 10^4
Mutation_rate: number of mutations per genome per generation. Here 0.05
Generation_number: The number of generations that the population grows. Here 1000
Fixation_threshold: The fraction of individuals having an allele in the population so that the allele is considered fixed. Here 0.99
'''

The initial population is created. All individuals are the same without any mutations
A vector to hold the number of mutations and a vector to hold the number of fixations is created

For each generation:
    I determine how many individuals in each generation should be mutated. Here 8.
    I randomly choose  (uniform with replacement) the individuals to be mutated
    For each individual in the population:
        It will produce an offspring. The offspring inherits the genome of its parent, i.e. the mutations of the parent.
        If the individual is among the ones to be mutated, the offspring will receive a mutation that is randomly picked.
            The mutation can be a back mutation
        The individual will die
    I record the number of mutations that occurred (it will always be 8 in this case)
    I record any mutation that has a frequency in the population of more than 0.99 of individuals. This is the number of fixations

I run this code for at least 100 times. I expect that the average number of fixations to be equal to the average number of mutations in each generation, or they converge over generations. Because the neutral theory of Evolution by Kimura predicts that for neutral sites in the genome, substitution rate is equal to the mutation rate.

I don't fully understand how your model works

I don't fully understand how you model your population. Is it a standard $oop$ (object-oriented programming) where you simulate each individual? Or is it a simulation where you already use some mathematical model? You could eventually copy-paste your code. it is probably not very long, right? What language did you use? Do you have only one locus? Do you simulate several positions within these locus? Do you allow for back mutations?

It seems that you allow the population size to change over time and I don't quite understand how your parameter $K$ does limit the growth rate though. You should write down some equations about that. In any case, change in population size will modify the probability of mutation fixation.

Here is probably some important modifications to do on your code

It is a bit hard to comment on your simulations without actually seeing some equations or seeing the code but I really think that you'll need two important modifications in your code.

fix population size $N$.
To simulate reproduction, randomly choose (uniform distribution) individuals (with replacement) from the population. The chosen individuals form the new generation. For example:

In R:

new_pop = sample(old_pop, N, replace=T)

or directly

pop = sample(pop, N, replace=T)

In Python:

from random import randrange
new_pop = []
for i in xrange(N):
    new_pop.append(old_pop[randrange(N)])

When you get your results, don't forget that you're talking about a stochastic process and you may want to run enough simulation or enough independent loci in order to be able to compare with the predictions from mathematical models.


What is this insect that I found under my bed Found it under a hotel bed in Las Vegas, what is it?

It is a Madagascar hissing  cockroach. They are native to Africa, particularly Madagascar. In the U.S. these roaches only invade homes when accidentally brought in via imported furniture or food, although some people do keep them as pets.

https://en.m.wikipedia.org/wiki/Madagascar_hissing_cockroach


What are these little leaves growing on these other leaves? (plant growing near the ocean) I saw many of these plants while hiking on a hill facing the ocean in northern Taiwan. I've included a snapshot of a nearby part of the same trail to show it's rugged, wet, green, and rocky, and another photo of some what looks to be the same kind of plant without these things, and one that has a reddish coloring.

Any idea what these little (~10 mm long) "leaf-shaped" brown/orangish things are, growing from points along two regular rows of bumps that are repeated everywhere? Is this reproduction, if so how does it work?

Also curious, any thoughts on what kind of plant to call this? I don't need a species identification necessarily, but is it a kind of fern?

below: Additional photos, click for full size.

These are really cool, and I am absolutely not certain of this, but I would hazard that they might be some kind of bulbil? Ferns (if I have started my ID correctly) can use them to asexually reproduce. For example the New Zealand endemic Asplenium bulbiferum grows little bulbils on the adaxial surface of its frond.


Doesn't osmosis violate the law of conservation of energy? Osmosis seems very counter-intuitive to me. I will try to explain my doubt with the following thought experiment:

Consider a huge container divided into two by a semi-permeable membrane. We add equal levels of water on both sides. On one side, dissolve some sugar. After some time, there will be a net movement of water to the sugar containing side of the container. This will increase the level of water on one side and decrease it on the other. If we create a huge hole in the membrane (large enough for both water and sugar molecules), then water will rush from one side to the other, equalizing the levels. If we were to somehow place a turbine at this hole, we could generate quite a bit of energy. Where did this energy come from?

I'm no thermodynamics expert, but Ill have a go at this.

The energy comes from the original set up, in which you have created a low entropy state. As the diffusion of water molecules equalises their concentration across the membrane so the entropy of the system will increase. This translates to a negative free energy change. That manifests as potential energy stored in the hydrostatic pressure resulting from the changes in volume, which in turn is available to turn the turbine.

So in the case of an experiment of the type described, the energy is derived from the experimenter who sets up the experimental situation in the first place.


What am I looking at in Franklin's Photo 51 of DNA? Here's Rosalind Franklin's famous Photo 51, the X-ray diffraction image of DNA from which Watson and Crick deduced its structure:

My understanding is that it depicts a short segment of DNA shown from the side (so the axis that the strands wind around would run up and down through the center of the photo). Like this double-helix diagram from Watson and Crick's paper:

I have a lot of trouble connecting the photo to the diagram.

What am I actually seeing in the photo? There are dark blobs at the top and bottom. A diamond shape of dark lines. A concentric circle (or rounded diamond) inside the outer diamond. An X formed from two intersecting rows of 7ish mostly horizontal short lines or blobs. Which of these features correspond to what parts of the DNA molecule?

Well, you said that you...

  ...have a lot of trouble connecting the photo to the diagram.

And that's quite excusable: interpreting that X-ray image is actually very complicated .

All the quotes and images in this answer, except the bulleted list further down, come from this paper (Lucas, 2008), which explains that historic picture in details.

Full disclosure: I always though that that image depicted the X-ray going longitudinally (that is, along the main axis) through the DNA. However, it goes transversely:

  When filamentous macromolecules are packed in a fibre along a fixed direction, the X-ray intensities diffracted by the fibre fall on the observation screen along approximately straight and equidistant lines, the so-called layer lines, perpendicular to that direction. This important concept was introduced by Michael Polanyi in 1921 for the X-ray study of cellulose. (emphasis mine)

These are the so called layer lines (I'm keeping the original paper's legend in all images):

Then, still according to the paper, Crick and others started to hypothesise how would be the X-ray diffraction in a monoatomic helix:

  In 1952, Cochran, Crick and Vand developed an analytical theory for X-ray diffraction by a monoatomic helix. The immediate interest of their theory was to give a transparent, analytical expression of these amplitudes at a time, in 1952, when computers, if at all available, were barely capable of a brute force calculation of the total diffraction intensity.

This is the X-ray diffraction pattern in a monoatomic helix, which is quite important to understand the famous DNA diffraction image later on:

Thus, with that theoretical background, we can understand our famous image:

In this image, a X-ray diffraction image of A-DNA (left) and the more common B-DNA (right) show a periodic pattern in the layer lines.

The diffraction patterns can be interpreted as follows (source):

The layer line separation reveals the value of the polymer repeat period. The decrease of over 20% of the layer line spacing when going from A to B implies an increase of that much in the period: P = 2.8 nm for A-DNA and 3.4 nm for B-DNA.
Look at the sharp, discrete spots observed near the center of the
diffraction pattern for A-DNA along the first few layer lines, these
suggest the crystalline order in the fibre. In the high-humidity
B-DNA pattern, these crystalline spots are absent, suggesting that
the extra water molecules must have invaded the space between the DNA
molecules, freeing them from being locked into crystallites.
The thick arcs at the top and bottom of the B-DNA pattern are found at approximately 10 layer line intervals from the center, implying that B-DNA had 10 repeating units within one period of 3.4 nm. These are produced by the scattering of X-rays by the equidistant, nearly horizontal flat bases separated by 0.34 nm. The A-DNA pattern lacks these big smears, suggesting that the bases in A-DNA are not horizontal, and the number of base pairs per helical period is closer to 11.
The central cross in B-DNA represents the Saint Andrew cross expected
from a helical molecule. The large radius r (1 nm, indicated by the
meridian angle of the cross) and the absence of intensity in the
meridian diamonds indicates that the phosphate backbone is at the
periphery of the helix. This cross appears to be absent in A-DNA,
however, this is due to destructive interference from some of the
inclined base pairs.

Finally, this is an image better relating the double strand structure of the DNA (both A and B DNAs) with the X-ray diffraction image:

Reference:

Lucas, A. (2008). A-DNA and B-DNA: Comparing Their Historical X-ray Fiber Diffraction Images. Journal of Chemical Education, 85(5), p.737.


How would you effect bulk DNA gene therapy for a human? Let's imagine  that we understood DNA programming and our genome very well and realized that there were some significant flaws (we die, we need sleep, etc.) And let's imagine that we understand how to make our genome do what we want, but it's a major refactor.  We're going to have adjust 10-15% of our DNA. (Note this is just a contrived example to suggest why we would want to make such a drastic change - our ability to actually know what changes to make is unimportant for the question.)

How would we replace/or modify this much of our DNA?  It seems the problem is very similar to gene therapy, but on a larger scale.

A few possibilities come to mind.  We could make a virus that would modify our DNA.  Or perhaps we could generate the new genome and inject it into some cells which would then just outlive the others (eg because these cells won't have a Hayflick limit) or will be able to generate lots of new adult stems cells with the "refactored" DNA?

Let's imagine that we understood DNA programming and our genome very well and >realized that there were some significant flaws (we die, we need sleep, etc.) And >let's imagine that we understand how to make our genome do what we want, but it's a >major refactor. We're going to have adjust 10-15% of our DNA.

I think we both recognise that this is a very naive view of biology and the nature of how organismal properties emerge (through multiple levels of systems) ultimately from the genetic code, the information in the genome, and the developmental process.

It is more pertinent and promising to think about treating genetic diseases.

Some genetic diseases are caused by mutations to single basepairs (e.g. the HgbS variant of the haemoglobin beta chain, which causes sickle-cell anaemia).
Other genetic diseases are caused by rearrangements of large segments of chromosomes, and the gene dosage imbalances that arise from this (e.g. Charcot-Marie-Tooth syndrome 1A). Finally, some genetic diseases are caused by a major gene-dosage imbalance caused by having an unusual set of chromosomes, "aneuploidy" (e.g. down syndrome, where chromosome 21 is present in 3 copies).

'Large-scale' gene therapy could be something useful for aneuploidy. Recently, the mechanism for inactivating one X-chromosome in female somatic cells has been applied to silencing the surplus chromosome 21 of Down Syndrome.

In yeast, a 'designer chromosome' has been chemically synthesised, and has been used to replace the corresponding native chromosome in yeast cells.

So although I think the premise of your question is basically science-fiction and naive, it is becoming possible to silence or replace whole chromosomes. More realistically than making our species immortal and ever-awake, this technology could possibly translate to therapies for some genetic diseases. But of course, the problem of retrospectively getting your therapy in to many somatic cells is still there. Engineering zygotes is feasible but has ethical problems - also, where pre-implantation screening is permitted, IVF can simply include genetic selection rather than genetic engineering!


Do neurons secrete multiple neurotransmitters, or just one type? I know that neurons communicate between each other by filling the junction between dendrites with neurotransmitters.

What interests me is if a single neuron only works with one type of neurotransmitter(ex: serotonin), or if it can secrete/receive all of them (serotonin, dopamine, etc).

If a neuron can secrete all, then can all dendrites secrete and respond to all neurotransmitters, or is it one per dendrite (one branch only works with dopamine, another one with serotonin, etc)?

I've googled this for a biology class I taught, and the quick answer is that both possibilities happen in different instances.  Some specialized neurons secrete more than one type, even though the ruling concept used to be one neurotransmitter for one neuron.