Small black slow-moving insect showing up in the home In the past few weeks (winter) I've started to notice these insects crawling about various places of the home.

Slow-moving like a beetle.
Black all over.
Hard to see but they have two prongs sticking out of the front.
I own dogs and cats.
I live in Tel-Aviv, Israel.
I live on the second floor.

Very hard to capture in an image so I tried a video. Here's a Gif:

What is this species?

Based on the hard-looking outer "shell" and elongated nose, this is certainly a type of beetle called a  weevil.

Given the size of the weevil, the time of year and the location of your home (second floor in a large city), I would guess this is certainly some species of nuisance/pest weevil.

Candidates include:

Wheat weevil (Sitophilus granarius)

Range: Worldwide
Food: wheat, oats, rye, barley, rice and corn
Appearance: 3–5 mm long with elongated snouts; reddish-brown
Life History: 36-254 eggs in 5-20 weeks

Rice weevil (Sitophilus oryzae)

Range: worldwide
Food: wheat, rice, and corn
Appearance: 2-3 mm, long nose, brown/black in color with 4 orange/red spots
Life History: 300 - 400 eggs per month [source]
Note: can fly

Maize weevil (Sitophilus zeamais)

Range: cosmopolitan in warmer climes [source]
Food:  corn (maize), wheat, rice, sorghum, oats, barley, rye, buckwheat, peas, cottonseed, other types of stored, processed cereal products (e.g.,  pasta, cassava, other coarse milled grains), and even has been known to attack fruit while in storage (e.g., apples)
Appearance:  2.5 - 4 mm, brown with four reddish-brown spots on elytra, long/thin snout, and elbowed antennae

See this Wikipedia page for a comparison of the rice vs. maize weevils

Life history: 300 - 400 eggs per 36 days

If you've been seeing multiple of them, that likely means they are breeding in some container of grain (wheat, rice or corn perhaps) you have in your home and could be well on their way to an infestation if your grain source is large enough. I recommend you check all sources of dried foods in your home to see if you hear/see weevils in it or coming out of the container.

Given the relatively large number of eggs each female can lay and given the month long generation time, this is an infestation you'd like to stop quickly.

 Note: all info is from the linked/cited Wikipedia pages unless otherwise cited.


Why does ostrich meat look and taste more like beef than chicken? Some time ago I tasted ostrich meat, and what was amazing to me was that the meat very much resembled beef, much more than it resembled chicken, turkey or duck meat. And even more than lamb and pork resemble beef.

The resemblance is both in look, both raw and grilled, and in taste (only tried grilled). I would have thought that the meat of related animals would have similar taste. Why is it that the meat of an ostrich, which is a bird, doesn't taste like that of other birds?

Warning, the following links are to pictures of meats!

A picture of beef
A picture of ostrich meat
A picture of chicken meat

There is a very plausible explanation here.

Basically, it explains that meat colour is due to the protein myoglobin (a haem-containing protein related to haemoglobin). There are two types of skeletal muscle: fast-twitch and slow-twitch (Wikipedia). Slow-twitch muscle is red muscle because it contains lots of myoglobin. Fast-twitch muscle is white muscle, containing less myoglobin. The Wikipedia link explains a little more about these muscle types and their functional differences. Evidently the lifestyle of the ostrich dictates that it have more fast-twitch muscle, and so it has red meat. It isn't unique in this: duck and goose are classified as red meat too.

Incidentally the role of myoglobin is to improve the rate of diffusion of oxygen from the haemoglobin in the capillaries through the cytoplasm of the myocytes to the mitochondria. It has also been suggested that it acts as an oxygen storage mechanism in diving mammals which have very high levels of myoglobin in their muscles, but this storage function is unlikely to be important in other mammals, despite what you may read in textbooks.


What does this biomass measurement mean and how to translate it to volume This is probably a softball question but because of the nature of the term, it's difficult to Google.  I am not a biologist, I am a web developer.  :-)

What does this measurement mean (it is a measurement of biomass production): 50 g m-2 d-1

I believe it means 50 grams per square meter per day - but not sure why there are '-' signs in there.

And perhaps more complicated, it is possible to translate this measurement to volume (either cubic meters or ideally cubic feet)?

50 g m-2 d-1 translates to "50 grams per square meter per day": the negative signs are negative exponents (check a math textbook). This is equivalent to writing

((50 g)/m2)/day

You cannot transform this into volume, doing so would lose the meaning: if you are talking about biomass growth of 50 grams per square meter per day, you are saying that there is 50 grams of new biological material produced within a square meter of land (say, a patch of grassland or forest). Talking about it in terms of volume doesn't make sense because the "height" coordinate doesn't produce additional biomass, since the source of energy is the sun.


Can I identify this black ant queen? I have an ant queen in a jar. This is what she looks like:

Because I'm planning to start an artificial ant nest, I'd like to learn something about that specific species of ant. This particular queen is very common in the Czech Republic, central Europe. It's also very common in cities.

Could you tell what kind of queen is that?
Is there any image reference that would help me find out? Ideally with some location search possibility.

As @skymnige said it is definitely Black garden ant (Lasius niger)


Which landmark paper first described the differentiation of T-cells? T-cells are distinguished from B cells in part by their locus of differentiation/maturation (thymus). This is textbook knowledge, but I was wondering which particular person or people were responsible for making this discovery. I'd appreciate any links to their original papers/works. Thanks a lot!

This paper appears to be a history of the discovery of B/T differentiation and the role of the thymus. I believe that you should find a number of important references therein.
It describes specifically a series of publications in the 1950s and 1960s that may be relevant (section "Identification of T and B cells"), such as this one by Gowans.


How to build a trimeric protein structure from monomeric PDB file? Problem: I have a PDB file, with a monomer, but I would like to show the entire structure - which is trimeric - but I don't understand how to merge/build or combine the monomeric units to its full structure in COOT, SWISS-PDBviewer or pymol?

Here is a link to the protein complex I am looking at

I would appreciate: Guidelines on how to do this (preferably in coot, pymol or Swiss-PDBviewer), or referral to a tutorial that actually goes through this would be great!

For reference: I found some descriptions on how to "build/merge" with Swiss PDB viewer here. And in threads from this discussion I found descriptions of how to do it with other molecular graphic tools as well (although I don't completely understand it)

What I have tried: In the tutorial for the SWISS-PDBviewer ( link ), I am able to follow some of the instructions, but I can't follow them for long:

I upload three of the same PDB file in SWISS PDBviwerer (they are layered on top of each other)
I can access/see the layers in the "layers info"
I am told to open the "text icon" to see the PDB text file, and look for "mtrix" rows - which should come right before the "atom" rows. As cited from the instructions:

  " Scroll down the pdb file until you find MTRIX lines (they are just
  before the ATOM lines). You can see 9 lines MTRIX. They represent
  three transformation matrices, and allow you to build the
  non-crystallographic symmetries of the protein"

I cannot find the "mtrix" rows in the PDB-text file, and am very unsure of how to follow the next instructions (link) after this as well. I am not able to click anywhere in the text file, then I get the error: "sorry can't recognize any clickable information under this pointer..

This is what I see above the "atom" row:

There are no MTRIX cards for that molecule. This seems like the easiest path:

http://www.rcsb.org/pdb/explore.do?structureId=4G3Y

Download Files -> Biological Assembly 1

i.e.:

http://www.rcsb.org/pdb/files/4G3Y.pdb1.gz

And read that file into Coot (should you wish)


How to put a gene under the control of a regulable promoter? Suppose I have a hetrologous (eukaryotic, plant) gene sequence that I want to express in E Coli under the control of a regulable promoter (say the lac promoter induced by IPTG) how exactly does one add the promoter sequence upstream of the gene?

Are there any tools to do this?

e.g. Say this is the gene itself, what sequence modification is needed to put it under the control of the lac promoter? The goal is to induce overexpression of the protein coded for by the gene on addition of IPTG to the medium (if I understand the strategy correctly)

atggctaccg ataatgacag ctctgaaaac cgtcgtatgg gtaattacaa gccgtccatc       60

tggaactacg acttcctgca gtccctggct acccgccaca atatcatgga agagcgccac      120

ttgaaactgg cggagaaact gaaaggccag gtgaagttta tgtttggtgc cccgatggag      180
.................................................................
gagccgttcg tgacgttcaa cctgaacagc gttcgtggtt cccatttctt ttacgagttt     1560

ggtgacggtt tcggtgtgac gaatagctgg accaaggttg acatgaagag cgtcctgatt     1620

gatccgattc cactggatga agaataatga                                      1650

If you're expressing the gene in E. coli, then you're almost certain to be using a plasmid or other ectopic gene vector. There are a wide variety of plasmids available, with many different promoters. With a commercial plasmid, you're not adding in the promoter sequence, but the gene sequence. You pick the promoter you want and then clone your gene sequence into the plasmid's multiple cloning site, which is designed to lie downstream the promoter.

There are a variety of tools to design and order plasmids. A common plasmid repository is addgene and my favorite tool for designing plasmids prior to ordering is APE.

Design the plasmid with APE or another tool, to be sure that everything looks good, then you can order the appropriate plasmid vector and enzyme cut site-flanked gene sequence and go to town cloning.


How to calculate the occurrence of a stretch of nucleotides in a genome? I have seen that the formula to calculate the number of times a given sequence of nucleotides occur in a target genome is derived from that to calculate the expected frequency of restriction sites:
a = (g/2)^G+C × ((1-g)/2)^A+T,

where:
a = probability
g = G+C content of the target genome
C+G = number of G and C in the stretch
A+T = number of A and T in the stretch.

An example was given for the mitochondrial genome and the restriction site for EcoRI (GAATTC). I calculated, based on the example:
a = (0.44/2)^2 × (1-0.44)^4 = 0.0005

given that the length m of the mitochndrial genome is 16 000 bp, the number of occurrences is:
n = am = 0.0005 × 16 000 = 4.92 (against 4.80 reported in the paper).

I then tried to calculate the occurrence of a primer based targeting E. coli: GTGTCCATTTATACGGACATCCATG.
The GC content of E. coli is 50.8%, thus:
a = (0.58/2)^11 × (0.42)^14 = 1.22×10^-6 * 3.24×10^-10 = 3.95×10^-16

and the number of occurrences is:
n = 3.95×10^-16 × 16*10^6 = 6.32×10-9

Looks to me, that the primer should not occur at all in the E. coli genome.
Are the formula and its application correct? Also, I don't like the fact that one needs to know the CG content beforehand (although, one can assume 50% content) and an exponent at the 11th power; is there an alternative formula?
Thank you.

Strictly speaking the question is from the realm of probability theory. If the probability of a nucleotide $X$ in the genome is $p_X$ ($\sum_x p_X=1$), then the probability to encounter a particular sequence, where nucleotide $X$ occurs $n_X$ times, is
$$
\prod_X p_X^{n_X} = p_A^{n_A}p_C^{n_C}p_G^{n_G}p_T^{n_T}.
$$
The formula given in the question is a particular case for $p_C=p_G=g/2$, $p_A=p_T=(1-g)/2$,
$$
\left(\frac{g}{2}\right)^{n_C+n_G}\left(\frac{1-g}{2}\right)^{n_A + n_T}
$$
which is obviously always the case for DNA, where the numbers of Cs and Gs (or As and Ts) are always the same, but the more general formula could serve for RNA or proteins.
What one should keep in mind is that the formula above is for a sequence with a particular order of the nucleotides! If the order is immaterial, and only the content of the sequence matters, the formula has to be multiplied by a binomial factor, which is effectively summing over all the possible arrangements of the nucleotides. Thus, for the case of DNA we obtain
$$
{n_A + n_C + n_G + n_T \choose n_C + n_G}
\left(\frac{g}{2}\right)^{n_C+n_G}\left(\frac{1-g}{2}\right)^{n_A + n_T}
$$
You can check yourself that the difference due to the binomial factor is striking!


What's the difference between constitutional samples and tumor samples? I think the tumor samples have two copies of the chromosomes. But for constitutional samples, do they only have one copy of the chromosomes?

Constitutional samples do, as you surmised, refer to germ cells (sperm or ovum). Hence they have 1 copy of DNA instead of 2.

Tumours, as they acquire more mutations, often have aneuploidy, or different numbers of chromosomes, and can also have increased incidence of Xn chromosomes where X > 2. This is polyploidy for humans and organisms with normal 2n chromosomes.


Pavlovian Conditioning And Synesthesia I have been reading about Pavlovian brain conditioning and it seems that documented cases are mostly limited to motor reflexes (like conditioning an eyelid to close when hearing a tone) or taste aversion . Basically information flowing through Cerebellum and Hippocampus. Are there proofs or scientific studies about the limitations of such conditioning? Or studies about what can be associated and what not?

Let's imagine for example that a subject looks at a black neutral screen and whenever some tone is played, the screen turns bright red. After an intense conditioning would it be possible that this subject, when blindfolded would see some red when hearing that same tone?

This has been attempted, with some success, though on grapheme-color synesthesia, rather than sound-color synesthesia. Beyond conditioning, there have also been somewhat successful attempts to induce synesthesia through various psychoactive drugs. In both of these cases, however, the effects are temporary and generally weaker than genuine synesthetic perceptions.

There have been no studies (to my knowledge) about which associations can be induced and which cannot. I would say that sound-color might be a difficult association to generate, simply because no one would like to site and stare at a flashing screen while listening to various sounds, and it also predicates on the patients' ability to distinguish sounds, which can vary wildly from person to person. The grapheme-color experiment had the treatment group read materials with certain letters colored, which was much easier to implement.

This raises the question of whether synesthesia can be classified as a low-level interaction between typically non-interacting parts of the brain, or if it operates on a higher cognitive level (i.e. ideathesia).

See the article for details about the grapheme-color study:

"Pseudo-Synesthesia through Reading Books with Colored Letters"


Where does reverse transcriptase come from? I can't figure out whether the viruses provide reverse transcriptase, or their RNA has the code for it, or the host cell normally contains it.
Multiple sources just introduce the enzyme without explaining who provides it / where it comes from. Apparently, both the host cell and viruses have processes that are dependent on reverse transcriptase, so I guess the answer is all of above / case-dependent?

I was about to write an answer saying that all reverse transcriptases are viral genes/proteins, but then wikipedia reminded that the telomerase is technically also a reverse transcriptase.

To answer your (main?) question:

  I can't figure out whether the viruses provide reverse transcriptase or their RNA has the code for it

Retroviruses have (almost by definition) the code for a reverse transcriptase in their genome. However, they also have the enzyme (or rather an inactive pro-enzyme) packaged into the viral capsid. The reverse transcriptase is a part of the Pol gene.
There are some other viruses that also use reverse transcription, but aren't retroviruses - in these cases I'm not sure, but I would guess that they also have an RT in their genome.

Now going back to the telomerase and retro-transposon elemnts:

These are ancient genes/elements in the eukaryotic genome, that basically do the same thing as viral reverse transcriptases: they make DNA from RNA.
Retro-transposons are generally believed to be viral additions to the genome, collected over the course of evolution. However, also the Telomerase enzyme probably has one common origin with viral reverse transcriptases (Nakamura 1998, take a loot at figure 2 at the end), (Witzany 2008). The thing about these evolutionary events is that they go way back, up the point were eukaroytes just started evolving from ... something. The sources I cited argue that many "eukaroytic" features (e.g. nucleus, RNA processing, vesicular transport) were originally taken from viruses.


Why are Aardvarks capable of burrowing given their size? I was wondering if large animals could possibly dig extensive burrows for themselves to live in. The polar bear burrows, but snow is not dirt. The aardvark goes about 4' long, ~150 lbs: similar to a sheep. I think the aardvark might be the biggest dirt-burrowing animal, the only sheep-sized burrower.

I wonder why.

Is there anything special about the aardvark that at its size it burrows, while other burrowers are smaller?

The following paper examines the link between burrowing ability and the stress and strain resistance provided by increased endosteal tissue formation (specifically compacted coarse cancellous bone (CCCB)) in aardvarks:

Physiological constraints associated with digging, however, are known to be strongly influenced by body size, and larger burrowers are likely to exhibit a histological profile more conspicuously influenced by fossorial activity. Here, we describe for the first time the limb bone histology of the aardvark (Orycteropus afer), the largest extant burrowing mammal...
We hypothesize that the unusual histological profile of the aardvark is likely the outcome of physiological constraints due to both extensive digging behavior and strong metabolic restrictions. Adaptations to fossoriality are thus the result of a physiological compromise between limited food availability, an environment with high temperature variability, and the need for biomechanical resistance during digging. These results highlight the difficulties of deciphering all factors potentially involved in bone formation in fossorial mammals. Even though the formation and maintaining of CCCB through ontogeny in the aardvark cannot be unambiguously linked with its fossorial habits, a high amount of CCCB has been observed in the limb bones of other large burrowing mammals.

Digging the compromise: investigating the link between limb bone histology and fossoriality in the aardvark (Orycteropus afer), PeerJ Life & Environment (2018)

Further reading:

Ecosystem engineering through aardvark (Orycteropus afer) burrowing: Mechanisms and effects


Do larger unicellular eukaryotic organisms have larger organelles? It seems that many of the giant unicellular eukaryotic organisms (size 1mm and above) are multinucleate but there are some with a single nucleus as well (the genus of Acetabularia). My question is: do they have proportially larger organelles (mitochondria etc.)? If so, can they be seen by a person with sharp eyesight when removed from the cell?

The cell has the amount of organelles necessary to perform its function. If a cell requires a lot of protein, it must have multiple nuclei to produce this protein. If the cell performs many activities that require energy, it needs many mitochondria. So the size and quantity of the organelles will be proportional to their function, not their size. In relation to Acetabularia, it is a single-celled organism visible to the naked eye. The nucleus is visible, but other organelles are not.


How to determine whether changes of an allele's frequency are due to genetic drift or selection? Given that both natural/artifical selection and genetic drift are evolutionary mechanisms that influence how allele frequencies shift in a population:

Are there ways to determine whether a frequency shift for a specific gene/allele is due to genetic drift or selection? In other words: when we see an allele take over a population, is there a way to know whether it was selected or just 'got lucky'?

UPDATE: since apparently this issue is quite complex in experimental biology I want to clarify why I'm asking this and what I hope to learn.

I'm looking for a 'theoretical way' of determining whether the changes in allele frequencies in subsequent generations are the product of selection or mere drift.

I'm applying a genetic algorithm to the optimisation of websites, where each gene determines an aspect of the user experience of that website. The question is whether the alleles I see emerging in the fittest solutions (= the best user experience, rated by visitors) got there by chance or actually contribute to the fitness of the candidate solution (= make a difference in shaping the user experience).

Is there a way to disentangle selection from drift

Yes, there are actually many ways...so many so different ways that it is impossible to correctly answer this question. Hopefully, below answer will give you some appreciation of why there is such a diversity of methods and wil give you sources to further your knowledge on the question.

It depends upon the data you have

The answer very much depends on the data you have in mind. Are you looking at a

panmictic population
a structured population
are you comparing a large number of lineages along a phylogeny
do you have information about a proxy for fitness in this population
can you perform an evolution experiment (depends a lot on the generation time)
do you have genetic data that are temporally separated
...

Also, what type of selection are you thinking of?

balancing selection
Are you trying to find epistasis for selection
Are you looking at some form of balancing selection
Local selection
...

Also depends upon whether you have data about potentially correlated variables such as

phenotypic data
ecological data

There are tens (or even hundreds of methods esp. when having data about related lineages) under each bullet point above, so your question is definitely quite broad.

Source of information

Statistical tests that test to the null that there is no selection are often called "test of selective neutrality". You might want to read Nielsen 2001  and Nielsen 2005 to get an overview of tests of selective neutrality in panmictic populations.

You might want to have a look at this answer, this answer and especially this answer.

What does it take to understand the methods for disentangling selection from drift?

Understanding the tests of selective neutrality can be a bit demanding as it requires having good knowledge in classical statistics, bayesian statistics, MCMC, Approximate Bayesian Computation and even machine learning algorithms. It also requires good knowledge in population genetics (typically incl. coalescent theory) and statistical phylogenetic.

A specific example

Unfortunately, I can't think of any specific example of a test which is really easy to grasp without a priori knowledge. A classical, not too hard and historically example test for neutrality in panmictic population is the used of Tajima's D (which derivation require basic knowledge in branching processes). You might want to learn about it to have a specific example. I recommend Gillespie's book Population Genetics: A Concise Guide to learn about this test. More book recommendation can be found here.


GO terms for non-model organisms I have a list of differentially expressed genes from an RNA-Seq experiment in Xenopus laevis that I'm looking to functionally annotate with GO-terms. As X.laevis is not listed in DAVID it seems I have 2 options:

BLAST my DE genes against a database with GO terms (human/mouse) to look for orthologs
Use a program that assigns GO from BLAST results, such as Blast2GO

I've been trying with Blast2GO recently, but find if very slow and generally lacking - does anyone have any experience doing GO in Xenopus or other non-model organisms?

I've done a functional annotation of a non-model, and used Blast2Go with fine results.

Specifically, I took all of my proteins and queried again the NCBI non redundant (nr) protein database using mpiBLAST, then I analyzed this output using Blast2GO (B2G4PIPE) and a local B2G Database.


Bacteria resistance to natural antibiotics? It is a known fact that bacteria develop immunity to antibiotics. Why then did not all bacteria develop immunity to natural antibiotics like penicillin in the fungi?

It is for sure that fungi did not care to continue killing all bacteria so that them won't be able to develop immunity (as we're adviced today to use antibiotics carefully, in order not to develop a superinfection)..

Looking at all the time span that bacteria and fungi exist, it seems unlikely that there'd be any bacteria left not yet immune to penicillin at all. However, that's not the case, the antibiotic is still a rather successful one.

For a natural immunity to evolve, two things have to happen:

The immunity has to actually occur. That means all the necessary mutations will need to be there to grant this bacterium resistance to penicillin. For penicillin, for example, bacteria that evolved such a resistance evolved to produce the enzyme beta-lactamase.
The immunity has to grant an advantage. Penicillin is produced by Penicillium, which is a mold found in environments with lots of oxygen. Lots of bacterial species have never encountered penicillin and the vast majority (for example anaerobic bacteria that don't infect humans) never will. In the absence of this pressure, a resistance to penicillin, even if it evolves, will likely deteriorate within a few generations because the individuals with the resistance do not have an advantage in survival. Producing an enzyme such as beta-lactamase is not without its costs (protein synthesis).

While bacteria van exchange genetic material in the form of plasmids between different species, so not all species would need to evolve beta-lactamase de novo, this is also only "helpful" if the bacteria a) come in contact with resistant bacteria species, and b) if this resistance confers an advantage for the receiving species.

Origins and Evolution of Antibiotic Resistance

Mechanisms of Bacterial Resistance to Antibiotics


What is biological dark matter? I recently stumbled upon the Biological Dark Matter wiki page. Its pretty light on details, but it appears to be genetic material found in humans that doesn't fall into currently classifications.

But what do we know about it? Is it really a big black box that we know nothing about? The article claims that it can make 40% of the genetic material in our gut, and I find it hard to believe that we really know nothing about it.

There are multiple answers to this question depending on who you ask (meaning, what their field of expertise is).

The biological dark matter from the wikipedia article in question seems to mean sequence from metagenomic samples which was not assigned to any of our commonly known domains of life. That might not necessarily mean that it does not belong to them. Sometimes it is hard to decide where a small particle of sequence informations belongs to, because it does not match anything we know. Still, it might be from a perfectly "normal" bacterium. Or it might be a result of sequencing errors.

Additionally, depending on how you assign a taxonomy to the sequence, there might be cases where there are so many different possibilities for where this sequence came from (because it is very conserved in a lot of different organisms, even from different domains of life), that this sequence will not get any taxonomy assigned. Not because there is none, but because we cannot safely decide which it is.
Some people also speak of this information as "dark matter".
There is for example this project which specifically is designed to study the dark matter we can (or at least for some reason do) assign to be microbes, but not more specifically.

Basically, any decision of where to place potential dark matter sequence is guided by our previous knowledge about the domains of life and the genomes of all those organisms. This knowledge is very incomplete.

I am sorry this answer lacks some more nice sources. Most of the information is based on my knowledge as a person working with datasets that might include "dark matter", if I would call it that. (I call it "not assigned sequence".) I don't have the time right now to add more sources, but if needed I can maybe add some later.

Edit:
As a fast add-on after re-reading your question: How much of the sequence is unassigned for example if one would study your gut depends a lot on what is actually there in you gut that we know, how diverse the community in your gut is, what database is used for comparison and how old this database is, how the data is preprocessed and analysed, and so much more. But yes, there is still a lot of genomic information in nature that has not made it into any database.


What would happen if Carbon-14 was in a glucose molecule and decayed into Nitrogen? This interested me because of Melvin Calvin's experiment with photosynthesis where he used radioactive Carbon-14. If a plant used it as a reactant to make glucose, and that Carbon-14 decayed into nitrogen, what would happen to the molecule?

I am not experienced in the topic, and could not find any article related to these kind of reactions, but my guess is the following. During the nuclear transmutation the radiocarbon will lose an electron (beta particle), so the nitrogen product will have positive charge. After that there are 2 possible scenarios.

a.) less plausible scenario

The beta particle carries away the energy of the decay, so the molecule will have low energy and it will be able to rearrange.

The electron shells will collapse a little bit, since the nitrogen has smaller nuclear radius. The part after that depends on which carbon we are talking about in the glucose molecule. I would guess the following rearrangements:

${-CH2OH} \rightarrow {-NHOH} + H^+ $
${=CHOH} \rightarrow {=NH} + H^+ $
${-CHO} \rightarrow {-NO} + H^+ $

It is not easier to break an N-H bond compared to the N-C and N-O bonds according to this table, but I think what really matters here is the stability of the final product, and $H^+$ is way more stable than any $^+O*$, $^+C*$, etc. ion.

b.) what really happens

The beta particle carries away the energy of the decay only partially. So the nitrogen will have a lot of energy, which is more than enough to break all of the bonds. According to wikipedia the decay energy is 0.156476 MeV. Let's compare it with the bond energies:

$ 0.156476 MeV = 2.50702189 \cdot 10^{-17} kJ $

${2.51 \cdot 10^{-17} kJ} \cdot {6 \cdot 10^{23} \cdot 1/mol} = 1.51 \cdot 10^7 kJ/mol$

According to our table the covalent bonds have about a few hundred kJ/mol energy, e.g. a C-N bond has 305 kJ/mol energy. So it is very likely that the chemical bonds will break immediately after the decay and the molecule will fall apart.


Is the CMV promoter active in yeast? I wish to transfect yeast and want to control my efficiency. So I thought to use pEGFP-N1 as control. The EGFP is driven by a CMV promoter. Can yeast read CMV promoters.
Thanks
Hermann

Yes (reference)

While I found your question interesting this was pretty much the first hit when I typed "CMV yeast" in google scholar. You should really look there first before you ask!


Why does protein have 4 calories per gram? As I understand it, protien that isn't used for building and repairing the body is inefficiently converted into glucose in the liver (at a rate of roughly 3 grams of protein per gram of glucose produced). Glucose has 4 calories per gram. So does that mean that protien would provide 12 calories of energy if the body could convert it at a 1:1 ratio? If not, Where does the 4 calories per gram number come from?

Ultimately, the 4 kcal/g numbers come from calorimetry. That is, scientists take a small amount of glucose or protein, put it in a device which burns the material and figures out how much energy is released. Now, this doesn't account for certain factors which complicate matters, such as the fact that humans excrete waste nitrogen as urea and not fully oxidized nitrogen (as is produced in a bomb calorimeter). As such there's some corrections which are applied to account for those differences. When you do the math, you find that carbohydrates and proteins both have about 4 kcal/g energy. As such, most people these days don't actually bother to do the calorimetry to find the energy content, but instead take the content of carbohydrate/protein/fat/etc. and do the calories-per-gram calculation from there.

Now, you're correct that those numbers (from combustion calorimetry) don't match the number you got from the mass balance in gluconeogenesis. Part of the reason for this is that, like most processes, gluconeogenesis isn't 100% efficient. You get some loss as heat due to steps not being 100% reversible. The nutritional content is intended to be more of an estimate of the once-through energy content. (That is, the amount of energy you'll extract if you go directly from the input into a totally metabolized state.)

But perhaps a more important difference is that the mass/energy balance equations for gluconeogenesis from protein can be more complicated than your simple 3:1 analysis suggests -- there's various offshoots of ATP, NADH, etc. generated going from the raw amino acids to glucose. Each of these carries away some energy, and to get a true energy balance. You also need to account for these alternative offshoots of energy.

Which amino acids you're talking about also makes a difference. Alanine is probably the simplest amino acid to feed into gluconeogenesis. It's transformed at a 2:1 molar ratio, which works out to an approximately 1:1 mass ratio (as expected from the calorimetric ratios). Other amino acids like leucine are ketogenic, meaning that they cannot be converted in gluconeogenesis at all (at least in humans). The differences in how different amino acids metabolize can account for the discrepancy. The 3:1 ratio may refer to a "typical" amino acid distribution, which includes a mix of some 1:1 converted amino acids, some which are only partially converted, and some which aren't converted at all.


Relation of conformational entropy and protein folding I'm trying to figure out the relation between conformational entropy and protein folding.
I read the following in Lehninger, Principles of Biochemistry (6th edition):

  Most of the net change in free energy as weak interactions form within a protein is therefore derived from the increased entropy in the surrounding aqueous solution resulting from the burial of hydrophobic surfaces. This more than counterbalances the large loss of conformational entropy as a polypeptide is constrained into its folded conformation.

In this context the meaning of conformational entropy is that the higher the stability of the proteïn is the lower the conformational entropy is (I think).

Why does the surrounding entropy increases because of the burial of hydrophobic residues?

Why does the burial of those hydrophobic residus couterbalances the large loss of conformational entropy?

I think maybe because the unfolded protein has more conformation then the protein when it's folded because of the hydorphobic core, it lowers the possible conformation because the hydrophobic interaction restrict the possiblities. Am I right?

This question is an example of important general problem in chemical biology: “How does an ordered system arise without violating the second law of thermodynamics?” Berg et al. address this in the following manner:

  The Second Law of Thermodynamics states that the total entropy of a system and its surroundings always increases for a spontaneous process. At first glance, this law appears to contradict much common experience, particularly about biological systems. Many biological processes, such as the generation of a well-defined structure such as a leaf from carbon dioxide gas and other nutrients, clearly increase the level of order and hence decrease entropy. Entropy may be decreased locally in the formation of such ordered structures only if the entropy of other parts of the universe is increased by an equal or greater amount.

Your question is about the spontaneous folding of proteins. You ask:

  In this context the meaning of conformational entropy is that the higher the stability of the proteïn is the lower the conformational entropy is (I think).

  Why does the surrounding entropy increases because of the burial of
  hydrophobic residues?

Comments on your interpretation: Do not use the term ‘stability’ in this context. It is not a thermodynamic term and its meaning is imprecise. If we think of entropy as the degree of disorder or randomness, then we can see that Conformational entropy is used by the authors to mean the entropy of the protein as a random coil which can adopt many different structures. This has clearly a greater entropy than the folded protein with (to an approximation) a single structure. The adoption of the folded structure is thermodynamically favoured because it represents a state of lower energy (specifically Gibbs Free Energy) compared with the random coil structures, but entails a loss of entropy.

My answer: The surrounding entropy increases for the following reason. The surrounding entropy is that of the water molecules vibrating and interacting with other water molecules by means of the δ+ and δ– charges on H and O, respectively. In a system containing a protein with a random coil, the movement of these molecules is restricted by the hydrophobic side-chains they encounter, hence limiting the entropy, as it were. When the protein folds into a globule with polar residues on its surface, the vibrating water molecules are less restricted in their movement and hence have a higher entropy.

Further you ask:

  Why does the burial of those hydrophobic residus couterbalances the large loss of conformational entropy?

  I think maybe because the unfolded protein has more conformation then
  the protein when it's folded because of the hydorphobic core, it
  lowers the possible conformation because the hydrophobic interaction
  restrict the possiblities. Am I right?

My Answer: I have explained that in general terms above, in response to your first question. If you want a quantitative, mathematical justification you’ll be pushed to find one. Assuming that there are no other factors involved, we assume that it must be so because of the second law.

Comments on Your Answer: I don’t understand what you mean by “it lowers the possible conformation”. You can decrease the number of possible conformations — you cannot "lower possible conformation”. I assume English is your first language. You must try to use it more precisely if you are going to write about science (as well as checking your spelling, grammar and capitalization). If I were marking this paragraph as an exam answer I would put a line through it as unintelligible. The key thing is that you are comparing a single conformation of the lowest energy involving specific weak interactions and a polar surface, with a number of conformations which expose hydrophobic residues and restrict the free vibrations of the water molecules.

Further Clarification

The diagram below illustrates the problem:

The protein is changing from a disordered to an ordered state so, its entropy is decreasing:

  ΔSprotein = x ,  where x < 0

Whereas the water is changing from a more ordered to a less ordered state, so its entropy is increasing:

  ΔSwater = y ,   where y > 0

and

  ΔStotal = ΔSprotein + ΔSwater = x + y

If ΔSprotein + ΔSwater = 0 (x + y = 0), we would say that the increase in entropy of the water counterbalances the increase in entropy of the protein. For the folding to occur spontaneously, the total entropy must increase (ΔStotal > 0 , i.e. x + y > 0) and we would change the previous statement to  “more than counterbalances”.


Downloading specific yeast genes in an automated manner? I have 6 genes of Candida albicans yeast namely orf19.723, orf19.5908, orf19.610, orf19.2119, orf19.4998 and orf19.4056. And I have found the corresponding ortholog genes from Broad Institute website of other 16 species of yeast. So I have all gene names. Now how would I specifically download these genes and from where can I do this, preferably in an automated manner?

Also is there any standard naming convention? Because the ORF names given have other names too like BCR1, EFG1 and NDT80.

The list of gene names I have :

The orthologs of C. Albicans with S. cerevisiae
orf19.2119  YHR124W
orf19.4998  YBR033W YKL034W
orf19.5908  YBR083W
orf19.610   YMR016C YKL043W
orf19.723   NONE
orf19.4056  YMR136W

The orthologs of C. Albicans with S. paradoxus
orf19.2119  spar33-g1.1
orf19.4998  spar197-g23.1   spar324-g3.1
orf19.5908  spar200-g4.1
orf19.610   spar184-g1.1    spar324-g10.1
orf19.723   NONE
orf19.4056  spar165-g2.1

The orthologs of C. Albicans with S. mikatae
orf19.2119  NONE
orf19.4998  smik146-g12.1   smik109-g17.1
orf19.5908  smik83-g2.1
orf19.610   smik571-g2.1    smik109-g10.1
orf19.723   NONE
orf19.4056  smik1535-g1.1

The orthologs of C. Albicans with S. bayanus
orf19.2119  sbayc514-g9.1
orf19.4998  sbayc611-g22.1  sbayc652-g20.1
orf19.5908  sbayc678-g131.1
orf19.610   sbayc638-g23.1  sbayc652-g27.1
orf19.723   NONE
orf19.4056  sbayc657-g41.1

The orthologs of C. Albicans with S. castellii
orf19.2119  Scas697.24
orf19.4998  Scas625.4
orf19.5908  Scas718.27  Scas635.12
orf19.610   Scas106.1   Scas709.52  Scas625.8
orf19.723   NONE
orf19.4056  Scas680.22d

The orthologs of C. Albicans with C. glabrata
orf19.2119  CAGL0L13090g
orf19.4998  CAGL0L01947g
orf19.5908  CAGL0M01716g    CAGL0F04081g
orf19.610   CAGL0M07634g    CAGL0L01771g
orf19.723   NONE
orf19.4056  CAGL0I00902g    CAGL0L06776g

The orthologs of C. Albicans with S. kluyveri
orf19.2119  SAKL0E11330g
orf19.4998  SAKL0A09812g
orf19.5908  SAKL0B06578g
orf19.610   SAKL0D13442g
orf19.723   SAKL0A03476g
orf19.4056  SAKL0E04862g

The orthologs of C. Albicans with K. lactis
orf19.2119  KLLA0F24420g
orf19.4998  KLLA0F25674g
orf19.5908  KLLA0E12507g
orf19.610   KLLA0F04840g
orf19.723   NONE
orf19.4056  KLLA0F17116g

The orthologs of C. Albicans with A. gossypii
orf19.2119  AGR347W
orf19.4998  AFR275W
orf19.5908  AER177W
orf19.610   ABR055C
orf19.723   NONE
orf19.4056  ADR249W

The orthologs of C. Albicans with K. waltii
orf19.2119  Kwal33.14699
orf19.4998  Kwal26.8099
orf19.5908  Kwal27.12423
orf19.610   Kwal26.8176
orf19.723   NONE
orf19.4056  Kwal47.17849

The orthologs of C. Albicans with C. tropicalis
orf19.2119  CTRG01097.3
orf19.4998  CTRG03636.3
orf19.5908  CTRG02294.3
orf19.610   NONE
orf19.723   CTRG00608.3
orf19.4056  CTRG04523.3

The orthologs of C. Albicans with L. elongosporus
orf19.2119  LELG01178
orf19.4998  NONE
orf19.5908  LELG02666
orf19.610   LELG05390
orf19.723   LELG03123
orf19.4056  LELG01761

The orthologs of C. Albicans with C. parapsilosis
orf19.2119  CPAG04608
orf19.4998  NONE
orf19.5908  CPAG01691
orf19.610   CPAG00178
orf19.723   CPAG00564
orf19.4056  CPAG05034

The orthologs of C. Albicans with D. hansenii
orf19.2119  DEHA2A07282g
orf19.4998  NONE
orf19.5908  DEHA2G13794g
orf19.610   DEHA2E10978g
orf19.723   DEHA2E05984g
orf19.4056  DEHA2E07172g    DEHA2F25916g

The orthologs of C. Albicans with C. guilliermondii
orf19.2119  PGUG02096.1
orf19.4998  NONE
orf19.5908  PGUG04378.1
orf19.610   PGUG03651.1
orf19.723   PGUG05571.1
orf19.4056  PGUG05533.1

The orthologs of C. Albicans with C. lusitaniae
orf19.2119  CLUG00404
orf19.4998  NONE
orf19.5908  CLUG04694
orf19.610   CLUG02047
orf19.723   CLUG00627
orf19.4056  CLUG05535

These sequences do not have any standard i.d. The information in Saccharomyces Genome Database is also obsolete (2005) and does not have these identifiers.

These sequences can be found here (in the same site).

Each species has a short name:

ORGANISM        Short Name
S.cerevesiae    Scer
S. bayanus      Sbay
S. paradoxus    Spar
A. gossypii     Agos

.... and so on.

First letter of genus name in uppercase + first 3 letters of species name in lowercase.

The fasta file (for all ORFs) is:
 www.broadinstitute.org/regev/orthogroups/nt/<Shortname>.fasta

From there you can use grep to retrieve the sequence.

So, if you have saved shortnames and gene names two separate files you can do something like this:

for shortname in `cat shortname.txt`; do wget -O tmp.fa "http://www.broadinstitute.org/regev/orthogroups/nt/"$shortname.fasta; grep -A 1 -f ids.txt tmp.fa >> $shortname"_Select.fa"; done


Biology and dna samples to determine parental lineage How could you use nuclear and mitochondrial DNA samples run through electrophoresis to determine parental lineage.

Before DNA sequencing was widely available, some lineage information could be determined using restriction fragment length polymorphism, a kind of "DNA fingerprinting".
https://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism

Analyzing nuclear DNA would give information about both parents, while mitochondrial DNA would give information specifically about maternal lineage, as we inherit our mitochondrial DNA only from our mothers.


Why does olfactory sensation need lateral inhibition? Why does olfactory sensation need lateral inhibition? If it's not helping in spatial discrimination then why is it needed? Don't we just smell the odour which is more concentrated?

My attempt: It is said that lateral inhibition is an important part of olfaction as it aids in odour discrimination by decreasing firing in response to background odours and differentiating the responses of olfactory nerve inputs in the mitral cell layer. But we also know that sensory perception is based on the pattern of receptors activated by the stimulus. So following questions arise:

Why don't background odours laterally inhibit the target odour? Isn't there more chance of inhibition of target odour being inhibited since its concentration is less?

Here is the paper which directly answers your question.
Urban NN. Lateral inhibition in the olfactory bulb and in olfaction. Physiology & behavior. 2002 Dec 31;77(4):607-12.
A few salient points:

It is true that the spatial gradient of sensory attributes is not as clear in the olfactory bulb-neuronal topography as it is at other places with lateral inhibition, but lateral inhibition still seems to serve a similar purpose in all these cases, namely sharpening the perceived stimuli. It is not settled how is this "edge enhancement" brought about in a nontopographical system ( "...Specific inhibitory connections between groups of cells with similar receptive fields may allow for functional lateral inhibition in such nontopographic systems, but no evidence for such specificity has been provided in the olfactory system...").

Unlike say for example in the Retina, where lateral inhibition creates the on/off centres, the lateral inhibition in olfactory bulbs is more widespread. That is, the area inhibited is relatively more expansive. This fact, coupled with the highly localised excitation caused by odours, suggests that "....lateral inhibition will be most effective at suppressing signals with low spatial frequency, in other words, signals that involve activation of broad regions of the olfactory bulb...". This is what I assume was meant by your source while referring to background odours.

The overall neurological effects of lateral inhibition is not settled, and the evidence is scanty. To quote the aforementioned paper, "... A simple prediction for the effects of lateral
inhibition on olfactory behavior would be that impairment
of lateral inhibition should impair performance on olfactory
discrimination tasks, and perhaps that these effects should
be strongest for tasks involving discrimination of very
similar odorants. Such a result has been obtained in experiments
in the honeybee in which inhibition is blocked by
picrotoxin. However, in these experiments, the blockade
of inhibition did not affect the odor-evoked firing rate of
the cells recorded, suggesting that the impairment of discrimination
ability was independent of a broadening of
tuning curves..."

Have a look at the cited paper, and the papers quoted therein, for further information.


What is the name of this whorled-leaf tree in India? Location: South India

Month: June

Season: Rainy

Branch Distribution:

Leaf of the tree:

Bucida molineti also called geometry tree


How are chemical reactions organized in prokaryotic and eukaryotic cells? I realized I only have a vague understanding based on what remember from high school and I don't know if they ever really broke it down for us but:

In general how do both prokaryotic and eukaryotic cells organize their chemical reactions? In prokaryotic cells I thought there were no organelles so does that mean that every reaction depends on the diffusion of the reactants throughout the cell and that any reaction could happen anywhere in the cell? And in eukaryotic cells, are organelles always used to compartmentalize stages in chemical synthesis?

What I'm getting at is that if everything is just floating around freely within a cell, wouldn't a lot of reactions interfere with each other? I'm wondering how these two types of cells approach this problem.

Okay, this is my first post on this site so please bear with me when it comes to the format of my response!

To begin with I'm going to try and answer your question by clarifying some things.

  In prokaryotic cells I thought there were no
  organelles so does that mean that every reaction depends on the
  diffusion of the reactants throughout the cell and that any reaction
  could happen anywhere in the cell?

Yes and no, the fact that there are no membrane bound organelles in prokaryotic cells means a majority of the reactions occur in the cell's cytoplasm via diffusion but something to keep in mind is the selectiveness of the cell's membrane will regulate the substances entering the cell in turn controlling that reactions that occur within it.

  What I'm getting at is that if everything is just floating around
  freely within a cell, wouldn't a lot of reactions interfere with each
  other?

When it comes to  eukaryotic cells structures do not float around freely like soup, there is cytoskeleton composed tubules and filaments that is used for  intracellular transport, this skeleton acts like a road system to move substances between static organelles. Prokaryotic cells do not require this since they do not have membrane bound organelles and the diffusion of substances into the cell is controlled by the cellular membrane.

  in eukaryotic cells, are organelles always used to compartmentalize
  stages in chemical synthesis?

Not always, you can look at things like cellular respiration to see glycolysis occurring in the cytoplasm.

I hope this helped out some!


Sodium concentration during action potential generation At the peak of the graph, is the concentration of Na+ outside the cell more than inside? That must be to overcome the electrical force in the opposite direction.

When is the concentration of Na+ greatest inside the cell? At the peak assuming the Na+ channel close immediately at it then it is also greatest at 3. If there is still passage of Na+ then 3 is the maximum. Is this true or false?

One last question: is the inside of membrane actually negative, or only negative relative to the outside? In a galvanic cell for example, a given rod isn't actually negative, but it is negative relative to another.

Below is a schoolbook example of the membrane potential combined with the individual conductivities of Na+ and K+ during an action potential (AP) (Fig. 1);

Fig. 1. Membrane potential and conductivities of the two most important ions in AP generation. source: Physiology Web

And in Fig. 2 is an example of the currents of Na+ and K+ during an action potential (AP) (Fig. 1). Note that K+ stays high due to amanipulation of ion concetrations.

Fig. 2. Sodium and potassium currents during AP generation.

However, you ask about the concentrations of Na+ in the cell. As far as I know, this has not been investigated directly. Intracellular Ca2+ concentrations, for example, can be imaged with various imaging techniques, but absolute Na+ and K+ concentrations have to be measured with intracellular electrodes. So while the conductivities and the currents are depicted quite clearly in the above figures, they do not show the absolute concentrations of Na+ or K+ and I doubt it can be found anywhere in the literature. It can of course be mathematically deduced, by calculating the number of ions entering the cell using the Nernst equation and correcting that for the background effect of the sodium-potassium pump and other factors that alter Na+ concentration in the cell (protein transporters and what not). It will at least give an approximation of [Na+]i.


what is the function of satellite in a chromosome? What is the specific function of a satellite in a chromosome ? How are sat-chromosomes different from others ? On molecular basis, what are the functional advantages of it ?

There are at least 2 SAT chromosomes in each diploid nucleus. They
  play a vital role in the formation of the nucleolus after cell
  division is completed.

  In humans, chromosomes number 13, 14, 15, 21 and 22 are examples of
  SAT chromosomes.

cuted from http://en.wikipedia.org/wiki/Satellite_chromosome


Is the PCT of the nephrons of the kidneys of marine vertebrates to minimize the natural tendency for exosmosis? For marine vertebrates, the concentration of salts outside their body (in the water, that is) is more than that inside their body. So, there is a natural tendency for exosmosis to occur.

To minimise this natural tendency for exosmosis to occur, these vertebrates would need to retain more salts inside their body.

I understand that the Proximal Convoluted Tubule (PCT) of the nephrons of the kidneys is involved in selective reabsorption of salts. So, making the PCT more coiled would increase the surface area of absorption, thus increasing the absorption, and therefore retention of salts in the body.

So, my question is: is the PCT of the nephrons of the kidneys of marine vertebrates more coiled than that of terrestrial vertebrates?

First off, I agree with @WYSIWYG - marine life has adapted to conserve water, not electrolytes. Osmosis in sea water draws water from the body and hence their problem is to keep the water in, not the salts.

Osmoregulation in marine mammals is accomplished mainly via differences in hormonal regulation of the kidneys. The histology and morphology of the kidneys are different, but the adaptations have more to do with adaptations to diving/pressure than anything else. Instead, most marine mammals take care not to drink too much sea water and obtain their water from metabolism and foods (Ortiz, 2001).

Reference
- Ortiz, J Exp Biol (2001); 204: 1831-44


Relation/difference between metabolism and cellular organisation In the highlighted paragraph from NCERT textbook, they mention that cellular organisation is the defining property of life forms while metabolism without exception is also the defining property of life forms. My doubt is whether the term 'metabolism' also includes the metabolism reaction in vitro condition too or metabolism only means all the chemical reactions occuring in the cell excluding in vitro condition. If what I mean is true, does cellular organisation and metabolism both mean the same thing? But then again if both are the same thing, metabolism also should be the defining property of life forms, but it is not the case as mentioned by my textbook. So that means both metabolism and cellular organisation are different things. Is this right?

This paragraph appears to draw a distinction between "the sum total of all reactions in cells" and "some isolated reactions that occur in cells". The former is "metabolism" and one defining trait of life; the latter are "metabolic reactions" and can occur in a test tube, and if so they do not fit tidily in a living/nonliving distinction (the paragraph talks about "not living things" but "surely living reactions", which is one way of illustrating the confusion I guess).
As to whether "metabolism" and "cellular structure" are the same thing, I think it's not so much that they're literally the same thing but they're not really separable, are they. The cellular structure is made by "all the chemical reactions in the cell", and "all the chemical reactions in the cell" are mediated by the cellular structure. It's a bit like trying to separate out "a race" from "the people running in the race". You can have one or two metabolic reactions happening in vitro, but if you had all of them in your test tube, happening the same way they do in the cell, you'd have a cell.
The reality of course is that there isn't a single all-encompassing definition of "life", so don't try and nitpick things too much. Metabolism is important because it's what allows living things to do what living things do, thermodynamically speaking. Cellular structure is important because it happens to be the way all living things implement their metabolism, and arguably it is a necessary requirement for metabolism to occur (there are arguments for why you need a small space enclosed by a membrane for example). Other things are also important like reproduction (and other near-universal feature of life that is a basic thing living things do, and allows Darwinian evolution), being subject to Darwinian evolution (because that is the process that leads life to being optimized in the way it is, and able to do the things it does to begin with), sensing and reacting to its environment (all this stuff about "what life does", well, those are universal things life does)... That means you can have arguable examples like viruses, which I would expect your textbook to call "nonliving" because they do not have metabolism or a cellular structure, but some others might call "living" because they have genetic information, replicate, are subject to Darwinian evolution and share a common ancestor with all other known life. The labels are less important than the features one is discussing at any one time. I expect your textbook probably says something like this at some point.


How can E. coli affect C. elegans expression? Plasmids can be transferred to E. coli. These transformed E. coli can be fed to C. elegans to silence its gene expression by RNAi.

How can E.coli release RNAi to C. elegans? Even if we assume E. coli could enter cells of C. elegans for being intracellular Bacteria, it is hard to imagine that RNAi will exit E.coli directly and enter C.elegan's cells? Normally, no cells or bacteria will release RNA or genomic material outside of their cells?

Yes, as bizarre as it may seem, that is what happens. The E. coli express a double-stranded RNA hairpin (under the regulation of an inducible promoter), and the RNA contains a sequence derived from a C. elegans gene.  When the worms eat the bacteria they grind them up in their pharynx, and release the cell contents (including the induced RNA) into the worms' gut. The gut cells are able to absorb the dsRNA  and transport it to other cells as well. The RNAi pathway processes the inhibitory RNAs to down regulate the target gene.


Why is the species-diversity of deadly parasites greatest in the tropics? There are so many parasites living in tropical regions of Africa, South America, or Asia, but very few in Europe or North America.

Is this due to climate, or are there other reasons?

Many of the tropical diseases and parasites are transmitted by insects, such as flies and mosquitoes. Well there are flies and mosquitoes in Europe as well.

There might be malaria-transmitting mosquitoes in the very south of Europe, and there is encephalitis transmitted by ticks. But that's it. Why don't the hundreds of different parasitic species from Africa spread to Europe ?

The diversity of parasites shows a gradient with increasing diversity from the poles to the equator. Several reasons have been brought forth to explain the latitude-dependency of parasite diversity:

An increased diversity overall around the equator; species diversity in general is greater in the rain forests and hence more hosts are available and thus more parasitic species can develop that target specific hosts;
Larger amounts of precipitation and higher temperatures around the equator may favor the development and transmission of parasites (Nunn et al., 2005);
Increased available energy overall around the equator (Guernier et al., 2004).

References
- Guernier et al., PLOSone (2004): 0020141
- Nunn et al., Diversity and Distrib (2005); 11: 249–56


Does an organism have only certain antibodies for life? Before birth, in the bone marrow millions of different B-cells are formed. These cells are differentiated and express different antibodies.

Are these the only B-cell types you will ever have? Or can the body generate new types of B cells, with new antibodies to deal with newly encountered threats?

Are these the only B-cell types you will ever have? Or can the body generate new types of B cells, with new antibodies to deal with newly encountered threats?

New B cells are constantly formed throughout one's life; the B cells that are present in the newborn are constantly supplemented by newly formed B cells.

  ... there is no statistical difference in the rate of production of new immature B cells in the marrow of young and old animals. In total, our results confirm previous work showing that mature B cells in old mice have a slower turnover, but more importantly suggest that the defect in mature B cell turnover is not due to a decline in B lymphopoiesis, but rather an inability of the newly made cells to replenish the peripheral compartments.

--Aging and developmental transitions in the B cell lineage.

But the second part of your question seems to have a misconception.  The newly-formed B cells have no relationship to newly-encountered threats.  No matter what new pathogens you encounter, your newly-formed B cells don't reflect them; they are formed randomly, and it is only by chance that any particular B cell might be able to react with a new threat.  Fortunately, there are so many B cells that the chance of at least a few reacting is very high, even though only a tiny fraction of the whole B cell population can do so.

Although new threats (mainly) require new B cells, repeated threats don't -- once a B cell is stimulated the first time, it undergoes a pathway that functionally makes it longer lived and more effective, so that on repeat exposure these optimized B cells are called in and there's much less need for the new naive B cells.


simple explanation of a crispr screen vs pooled crispr screen? I'm familiar with how CRISPR works to make either knockdown or amplification effects for a single gene because you can make precision cuts.

What exactly does a pooled crispr screen do & how does it work?

In the context of pooled CRISPR screen, you first design a library of gRNAs against a certain set of targets (instead of just one target).

The library can have the size you want, most commonly it is either targeting the kinome, or the whole genome (genome-wide).
In this context, you would add the full library on your cell of interest in which you want to make the perturbations.

Depending on how the screen is set-up you try to select the perturbations which either allow you to pass a selection process (toxicity, fluorescent readout, etc). Usually an elegant way is to have either a label also code barcode which helps you to identify the gRNA which generated the surviving/selected phenotype. With the barcode/gRNA you can track back which gene was likely perturbed in the screening process.

Hope that helps and that answers you question, please don't hesitate to further refine it if this is not clear to you.


Are there functional examples of parallel DNA double helices? The anti-parallel structure of the DNA double helix is well studied, but I am curious if there are any examples of parallel DNA double helices. There are reports of synthetic such structures; see this paper, for example. However, my question is: are there functional examples of parallel DNA double helices? Here are some implicit/additional/guiding criteria:

It should be double stranded. This excludes structures such as G-quadraplexes, which do have some parallel strands.
It does not have to be an extended helix. I don't have any specific length restrictions, but don't assume it needs to be hundreds or even tens of base pairs long.
The structure need not be solely composed of DNA. If a parallel helix is induced by, say, protein or small molecule binding, so be it.
By "functional examples", I mean that the parallel structure should have some effect on cellular processes. The structure can be studied in vitro, even using synthetic constructs, but it should have some functional significance in vivo (or, at least a proposed significance).

Note that although I only mention DNA above, papers discussing parallel RNA double helices in the same spirit would also be welcome.

Related question: why is DNA antiparallel? Can it be parallel?

Surprisingly, a parallel DNA duplex has been reported! In a paper, Tchurikov et al have reported the presence of parallel complementary DNA in the non-coding region of alcohol dehydrogenase gene as well as between two Drosophila DNA sequences. The region, which is ~40 bp long, has 76% bases in same polarity along with complementarity. However, its presence in vivo and its significance are not known (they observed its existwnce in vitro).

Tchurikov et al, in another paper, have reported that parallel complementary RNA in E. coli plays some role in RNA interference and is indeed more effective than antisense RNA in silencing mRNA for gene expression regulation. They also propose the presence of such a system in vivo in E. coli cells. (Seemingly, this paper alone is enough to answer your question since it fulfills all your criteria).

In another paper, Szabat et al have shown that DNA, 2'-O-MeRNA and RNA oligonucleotides can adopt parallel duplex configuration at pH 5 and lower. Also, presence of LNA stabilizes parallel duplex configuration. This might seem helpful in processes such as RNA interference, though this study too was in vitro (obviously, in vivo LNA is not known).

Many such papers, like Westhof et al, Mohammadi et al, etc. have reported the presence of parallel duplex DNA.

References:

 1. Tchurikov NA, Chernov BK, Golova YB, Nechipurenko YD. Parallel DNA: generation of a duplex between two Drosophila sequences in vitro. FEBS letters. 1989;257(2):415–8. pmid:2479581

 2. Tchurikov, N. A., L. G. Chistyakova, G. B. Zavilgelsky, I. V. Manukhov, B. K. Chernov, and Y. B. Golova. 2000. Gene-specific silencing by expression of parallel complementary RNA in Escherichia coli. J. Biol. Chem. 275:26523–26529

 3. Szabat M, Pedzinski T, Czapik T, Kierzek E, Kierzek R (2015) Structural Aspects of the Antiparallel and Parallel Duplexes Formed by DNA, 2’-O-Methyl RNA and RNA Oligonucleotides. PLoS ONE 10(11): e0143354. doi:10.1371/journal.pone.0143354

 4. Westhof, E., and M. Sundaralingam. 1980. X-ray structure of a cytidylyl-3′,5′-adenosine-proflavine complex: a self-paired parallel-chain double helical dimer with an intercalated acridine dye. Proc. Natl. Acad. Sci. USA. 77:1852–1856.

 5. Mohammadi, S., R. Klement, A. K. Shchyolkina, J. Liquier, T. M. Jovin, and E. Taillandier. 1998. FTIR and UV spectroscopy of parallel-stranded DNAs with mixed A-T/G-C sequences and their A-T/I-C analogues. Biochemistry. 37:16529–16537.


What is the depression between bridge of nose and brow called? In a human being, what is the depression often found between the bridge of the nose and the brow called?

Nasion [New Latin nāsion : nas(o)- + Greek -ion, diminutive suff.] is the region below glabella , also known as the bridge of the nose.

  The nasion is the midline bony depression between eyes where the frontal and two nasal bones meet, just below the glabella.It is one of the skull landmarks, craniometric points for radiological or anthropological skull measurement.

Source:https://radiopaedia.org/articles/nasion


Bacterial Growth Formula What are the units of $N$: the colonies of bacteria or the viable cell count?

This is in regards to the bacterial growth formula used during serial dilutions,

$$
N =N(0) e^{kt} \quad .
$$

Either; they're identical to the units of $N(0)$.  In $N =N(0) e^{kt}$,

$t$ has units of time (days, minutes, whatever you have chosen)
$k$ has units of (1/time) (inverse of $t$'s units)
$kt$ is thus unitless, as is $e^{kt}$
$N$ and $N(0)$ have the same units.


Why is the outer circle of human mitochondrial DNA ‘heavy’, whereas the inner circle is ‘light’? Why is the outer circle of human mitochondrial DNA "heavy" whereas the inner circle is "light"?

The heavy strand is literally heavier than the light strand. The first, or at least one of the first, observations of this phenomenon was in this paper:

Corneo G, Zardi L, Polli E. 1968. Human Mitochondrial DNA. J Mol Biol 36(3):419-423.

They showed that alkaline denatured mitochondrial DNA separates into two bands upon ultracentrifugation in a cesium chloride gradient:

  Human mitochondrial DNA when centrifuged in alkaline CsCl in the analytical ultracentrifuge splits into two bands displaying densities of 1.727 g/cm3 and 1.766 g/cm3, respectively. The two bands appearing in the alkaline gradient correspond to the complementary strands of human mitochondrial DNA with a different GT/CA ratio... However, when an equimolar mixture of them is renatured by heating at 65°C for five hours in 2X SSC, a single band with a density very close to that of the native DNA is obtained. The latter experiment clearly indicates that the two bands correspond to the complementary strands displaying a bias in base composition.

The difference in molar mass (M) is due to a higher purine content (Pu) in the heavy strand (which are heavier than pyrimidines). This can be seen by tabulating the base composition of the RefSeq sequence of human mitochondrial DNA:

               A      T      G      C      Pu(%)   M(kDa)
Light Strand   5124   4094   2169   5181   44      5063
Heavy Strand   4094   5124   5181   2169   56      5174

R script if anyone is interested:

#uses Biostrings
light = readDNAStringSet("mtDNA.fasta")
heavy = complement(light)

comp = function(seq) {
  ll = as.list(alphabetFrequency(seq)[1, c("A", "T", "G", "C")])
  ll["%Pu"] = with(ll, (A + G) / (A + T + G + C)) * 100
  ll["M(kDa)"] = with(ll, (A * 313.2) + (T * 304.2) + (G * 329.2) + (C * 289.2) + 79.0) / 1000
  return(ll)
}

comp(light)
comp(heavy)


Can one conduct “novel” research without an advanced laboratory? Has it been done by school pupils? I want to conduct an experiment but as a secondary school pupil I will be using my school’s laboratory and to make novel or interesting discoveries, wouldn’t one need advanced equipment, a prospect which is not feasible for one of my station in life? I want to know if anybody has done a simple experiment and discovered anything new? Thanks.

I can point to two published papers in which students performed useful experiments.

The present study (on the vision of bumble-bees) goes even further, since it was not only performed outside my laboratory (in a Norman church in the southwest of England), but the ‘games’ were themselves devised in collaboration with 25 8- to 10-year-old children. ... They also drew the figures (in coloured pencil) and wrote the paper.
Principal finding ‘We discovered that bumble-bees can use a combination of colour and spatial relationships in deciding which colour of flower to forage from. We also discovered that science is cool and fun because you get to do stuff that no one has ever done before. (Children from Blackawton)’.

--Blackawton bees

As part of a high school class project, influenza sequences with possible errors were identified in the public databases based on the size of the gene being longer than expected, with the hypothesis that these sequences would have an error. Students contacted sequence submitters alerting them of the possible sequence issue(s) and requested they the suspect sequence(s) be correct as appropriate.

--Sequencing artifacts in the type A influenza databases and attempts to correct them
You'll notice that both of these projects were guided by "professional" scientists. The biggest problem with doing your own experiments is that you're very likely to simply repeat something that's already done, or else do something that's not useful or is trivial. It's very difficult even for professional scientists to have a reasonable grasp of even a very focused field of science, and for someone outside the field to try to understand what has and hasn't been done, and what is and isn't considered interesting, is nearly impossible.


Can epigenetic changes affect reproductive success? This is prompted by niallhaslam's answer to this question [Since Darwinian times, has there been any striking/notable effects of evolution on humans?]. A comment by Alan Boyd asks whether epigenetic changes count as evolution.

Transgenerational epigenetic inheritance can occur, and does increase the natural variation of a species (although this review is more about plants, this does apply to animals too) [1]. Based on this alone I'm inclined to say that epigenetics can affect the fitness of a species, and thus could contribute to evolution.

I am interested to know if, in practise, this does occur, and whether epigenetics have been shown to affect the reproductive success of a species? Because the changes are not permanent I could imagine that they actually have very little impact "species-wide", as environmental effects (infections, toxic exposures) also affect epigenetics. So, is there any evidence for epigenetics affecting the reproductive success of a species? This also includes whether epigenetics can influence traits enough to create a new sub-species.

Becker, C., & Weigel, D. (2012). Epigenetic variation: origin and transgenerational inheritance. Current opinion in plant biology. doi:10.1016/j.pbi.2012.08.004.

This article deals with the effect of phenotypic variation brought on by epigenetic patterns, and how these are inherited to the next generation. Their conclusions?

Our results show that epigenetic variation is inherited in chickens, and we suggest that selection of
favourable epigenomes, either by selection of genotypes affecting epigenetic states, or by selection of methylation
states which are inherited independently of sequence differences, may have been an important aspect of chicken
domestication.

However, I personally prefer this article, as it has a more profound implication on reproductive success and addresses your question specifically. They found the there is a species-level difference in DNA methylation between humans and chimps, but more importantly that this difference is responsible for the causation of numerous lethal diseases/conditions, which has a direct impact of the fitness of the species as a whole.

Finally, we found that differentially methylated genes are strikingly enriched with loci associated with neurological disorders, psychological disorders, and cancers. Our results demonstrate that differential DNA methylation might be an important molecular mechanism driving gene-expression divergence between human and chimpanzee brains and might potentially contribute to the evolution of disease vulnerabilities. Thus, comparative studies of humans and chimpanzees stand to identify key epigenomic modifications underlying the evolution of human-specific traits.

In summary, evidence has shown that epigenetics does seem to play an active role in the evolution of species, although the exact mode of inheritance of DNA methylation from generation to generation is unknown.

References

Nätt, Daniel, Carl-Johan Rubin, Dominic Wright, Martin Johnsson, Johan Beltéky, Leif Andersson, and Per Jensen. “Heritable Genome-wide Variation of Gene Expression and Promoter Methylation Between Wild and Domesticated Chickens.” BMC Genomics 13, no. 1 (February 4, 2012): 59.

Zeng, Jia, Genevieve Konopka, Brendan G. Hunt, Todd M. Preuss, Dan Geschwind, and Soojin V. Yi. “Divergent Whole-Genome Methylation Maps of Human and Chimpanzee Brains Reveal Epigenetic Basis of Human Regulatory Evolution.” The American Journal of Human Genetics 91, no. 3 (September 7, 2012): 455–465.


How closely related will your descendants be to you? I wonder how similar my DNA will be to that of my great-grand-children. If a new person enters my family tree every new generation, he/she will bring in half of his/her DNA, therefore decreasing the amount of DNA that each new generation shares with me. I assume, then, that after several generations, my descendants are going to be no more closely related (genetically) to me than to random people on the streets?

I also once heard that even though the share of my genes will be descreasing, the mutations unique to me will stay. Is that true, and, if so, how is that possible?

And what about all-males descendants? For example, if I have a son and he has XY, then if there always will be a son down the line then will the Y chromosome stay the same through each generation? More specifically, will it still be the Y chromosome from me?

For how genetically related to you your  my grand-grand-children will be....

Well on the surface the answer is simple. Your grand grand children will 12.5% of your DNA.

Dig a little deeper... the question becomes a bit more difficult to answer.

(1) Humans do cheat a small but significantly amount of time. On average about 0.7-3% of all children are unknowingly raised by men who are not their biological father http://theconversation.com/what-are-the-chances-that-your-dad-isnt-your-father-24802. This is less than the 9-30% which has been reported. The reason appears to be that the data was derived from paternity clinics where  there was already suspicion on paternity of the child. Not the best data set to represent the population, even if the data set was large and mostly free to researchers.

So which that factored in... it depend on what gender you are, and how said grand grand child is related to you. Are you a woman? Is that grand grand child, the child of your daughter's daughter. A pure maternal descended would guarantee a 12.5% genetic relatedness.

But if you are a man, and the grand grand child, is the child of your son's, son... on average genetic relatedness falls to 11-12% (on average). But since a person is related to your or not, there is a 3%-10% that your grand grand child is not related to you if that child is your son's son's child.

(2)Rural (old world) populations tend to share more genetic material since they have had less outside influence into the genepool. This is a reflection of history, where mobility was limited and families tend to stay for generations. In these places, a random stranger isn't that random after all. In which case genetic relatedness calculations become more complicated. Terms to look up are founder effect, population structure. Large cities, with massive influx of people moving in and out tend to be more mixed. Also note isolation, can also because by social stratification. The nobility is a great example where two random nobles are not as random as you think.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1685612/pdf/ajhg00202-0030.pdf
http://link.springer.com/article/10.1007/BF02442864
http://www.nytimes.com/2004/07/31/us/by-accident-utah-is-proving-an-ideal-genetic-laboratory.html rare american example.
https://en.wikipedia.org/wiki/Stoccareddo
http://gizmodo.com/5882644/iceland-is-so-inbred-it-needs-a-website-to-avoid-incest

  And I also once heard that even though the share of my genes will be
  descreasing, the mutations unique to me will stay. Is that so and how
  is that possible?

Not quite. A mutation unique to you has only 50% chance of passing on to a child. (Or a 50% chance of not passing to a child.) So if you have 2 children, that mutation will have a (0.5*0.5=0.25) 25% chance of failing to pass to the next generation. In fact unless that mutation has some sort of selective advantage (awesome X-men powers), or your family has really big families for several generation or you and your families becomes a founder of a new colony/town (founder effect), your unique mutation will likely fallout after a few generations.

  And what about all-males descendants? Like, if I have a son and he has
  XY, then if there always will be a son down the line then Y chromosome
  is going to stay the same, being the one from me?

yeah they will inherit your Y chromosome.. which will change very little over the generations. It will accumulate a few mutations but that is over thousands of years.


Oxygen mask to patients Why are oxygen masks given to patients? Can't they take in the  atmospheric oxygen? Also, why do they die if the oxygen mask stops providing oxygen?

Oxygen masks can provide up to near 100% oxygen, whereas the atmosphere contains only ~20%. Typically, oxygen is provided in cases where patients' blood oxygen saturation is low or is likely to be low.

Giving a patient supplemental oxygen helps them to achieve oxygen saturation even if their breathing or circulation is impaired, and allows slightly more oxygen to be dissolved in the blood, which can be helpful in cases of blood loss or other traumatic insults.

I'm not sure of any cases where patients simply die immediately if their oxygen mask fails, outside of movies/TV; it's more of an issue of trying to provide the best outcome possible in a difficult situation.

There are also some negative side effects of oxygen supplementation. Overall, Wikipedia has a reasonable overview of these, as well as the indications for oxygen supplementation.


How much DNA do humans have? A normal human body has approximately 3 billion base pairs. Given that humans have 10 trillion cells, how is that the number of base pairs of DNA is less than the number of cells? It can happen only if most of these cells don't have DNA, or have I misunderstand the topic?

Can you give an account of why the number of cells exceeds the number of DNA base pairs significantly? Isn't it logical to have more DNA base pairs than the number of cells?

Answer to the question
How much DNA is there in our cell nuclei?
In humans, there are about 6 billion base pairs in the nucleus of each cell. Why 6 billions and not 3? There are 3 billions base pairs per haploid genome (see ploidy) and therefore 6 billions base pairs for the whole genome. This number may actually further double during specific phases of the cell cycle. Each single cell contains a copy of the whole genome (with a few exception such as red blood cells for example).
So the total number of base pairs in a 10 trillion cells individuals is about $6\cdot 10^9 \cdot 10^{13} = 6\cdot 10^{22}$ base pairs.
Further information for fun
How much DNA in our cells outside of nuclei
Now, in cells there is DNA outside of nuclei. In animals (incl. humans), we have DNA in mitochondria as well. there is of the order of 104104 base pairs per mitochondria (16,569 sites to be accurate) and there are of the order of 104104 mitochondria per cell, that is 108108 base pairs total per cell which is only one order of magnitude below the number of base pairs in the nucleus per cell.
There is therefore an extra $3\cdot 10^8 \cdot 10^{13} = 3\cdot 10^{21}$ base pairs in cells outside the nucleus.
How much DNA in bacteria living in the human body?
Note that by "in the human body", I also include "in the gut" even though the inside of the guts are typically considered as being the outside our body.
There are about 100 trillions of bacteria in every one of us (this number is a vague approximation; see wiki > Human microbiota). Yes, most of the cells living in us are not our cells but are bacterial cells!
Bacterial genome vary widely but as a gross and almost insulting approximation, let's consider that the average bacterial genome from our microbiome has a genome size of $10^6$ base pairs (note bacteria don't have nuclei or mitochondria).
That means that in our body we have to add to the above numbers $10^6 \cdot 10^{14} = 10^{20}$ base pairs (which is only a hundredth of $10^{22}$).
How much DNA in the viruses in our body?
Let's not forget our virome. Unfortunately, I could not find estimates of the number of viruses (and viroids) in our body.
How much DNA is outside cells and viruses in our body?
Of course, there's plenty of DNA in our body. There's DNA in everything we eat and this DNA end up in our blood stream and in our cells. I failed to find an estimate of how much DNA does that represent.


Construct Phylogeny form Edgelist I am working on large scale biodiversity simulations and have collected a lot of data on simulated phylogenies. I have a list of child-parent edgelist species in the form:

list = [1, 1, 2, 2]

      /-- 3
1 -- 2
      \-- 4

children = [1, 2, 3, 4]
parents = [1, 1, 2, 2]

Where the index is the child and the value is the parent. 1 is it's own parent (the root).

I have such a tree for a large dataset upwards of 1000 individuals. I can build the tree programmatically in igraph or networkx easily and visualise it. However, I cannot find a way to convert the tree into a format for phylogenetic analysis. There are function to convert dendropy and ete trees from igraph/networkx into their own formats but no way to re-import the igraph/networkx trees. There also appear to be no way to write the igraph/networkx trees into phylo formats (newick).

There also seems to be no support in dendropy or ete to programmatically build trees and it would be infeasible to manually build all the trees I have.

Is there a way to build the trees so I can analyse and visualise them as phylogenies?

Tried approach

library(ape)
p <- c(NA, 1, 1, 3, 3, 4, 4)
x<-data.frame(name=as.character(c(1:7)) , id=1:7,  parent = c(NA, 1,   1, 3, 3, 4, 4))
x1<-na.omit(x)[,3:2]
n <- c(c(1, 3, 4), c(2, 5, 6, 7))
edges <- matrix(c( x1$parent, x1$id), ncol=2)

tree<-list(edge=edges, Nnode = 3, tip.label = as.character(x$name[c(2, 5, 6, 7)]), node.label = as.character(x$name[c(1, 3, 4)]))

class(tree)<-"phylo"

#plot.phylo(tree, show.node.label=TRUE)

The plot command just causes R to crash and the tree object has an invalid structure.

This will be a complete answer, but it's got code, so it won't work as a comment. Working backwards from rtree(3), here's a way to build a phylo object from component parts, which might be helpful:

children <- c(5, 1, 2, 3)
parents <- c(4, 5, 5, 4)
x <- matrix(c(parents, children), ncol = 2)
tr <- list(edge = x, tip.label = 1:3, Nnode = 2)
class(tr) <- "phylo"
plot(tr)

Doing the same with your children and parents, doesn't work, however.

children <- c(1, 2, 3, 4)
parents <- c(1, 1, 2, 2)
x <- matrix(c(parents, children), ncol = 2)
tr <- list(edge = x, tip.label = 1:3, Nnode = 2)
class(tr) <- "phylo"
tr

Gives

Error in if (tabulate(phy$edge[, 1])[length(phy$tip.label) + 1] > 2) FALSE else TRUE : missing value where TRUE/FALSE needed

I don't know hot to make the edge list conform to the expected order for a phylo.


Colloids in digestion I am looking for examples of colloids involved in digestion for a cross-curricular (bio-chem-physics) lesson plan.  Although I have found references implicating colloids in both lipid and protein digestion, I haven't been able to identify which colloids they are speaking of.  Can someone provide specific examples?

Fat released from food will form macroscopic lipid droplets in the aqueous environment of the gut. In the small intestine, bile synthesised by the liver is secreted into the lumen via the bile duct. Bile contains bile salts which act as detergents to disperse the lipid droplets by forming micelles. I think this dispersion of micelles could be described as a colloid.

I have no idea what the reference to protein digestion could mean, although some hydrophobic proteins might become associated with the micelles that I've already described, and I imagine that bile salts might help to solubilise protein aggregates in the gut lumen by direct interaction - they, or their derivatives, are sometimes used by protein biochemists as detergents for protein solubilisation (e.g sodium deoxycholate.


How are synaptic vesicles brought to the synapse? I'm reading about how synaptobrevin is used to identify synaptic vesicles for tethering near the synaptic cleft. Since neurons have a synapse and dendrites, I'd like to know how exactly  the vesicles get moved from the Golgi to the synapse.

As far as I can tell, they are transported along microtubules by dynamins as opposed to floating freely in the cytosol (correct?). If so how do the dynenins identify synaptic vesicles - would they form a SNARE complex that gets released near the synapse or by some other means?

You are looking for a review on vesicle cargoing along the cytoskeleton. This open access article is the most recent I found on the subject.

From the abstract:

  How synaptic cargos achieve specificity, directionality and timing of transport is a developing area of investigation. Recent studies demonstrate that the docking of motors to their cargos is a key control point. Moreover, precise spatial and temporal regulation of motor-cargo interactions is important for transport specificity and cargo recruitment. Local signaling pathways Ca2+ influx, CaMKII signaling and Rab GTPase activity regulate motor activity and cargo release at synaptic locations.

M. A. Schlager, C. C. Hoogenraad: Basic mechanisms for recognition and transport of synaptic cargos. In: Molecular brain. Vol. 2, 2009, p. 25. DOI:10.1186/1756-6606-2-25. PMID 19653898. PMC 2732917.


How to create a phylogenetic tree (using Maximum Likelihood method) in newick format for a Multiple Sequence Alignment file in FASTA format? The file size is really big (26.7 MB). So, I am unable to use the online web tools, as they cannot handle such large input data.

RAxML (Stamatakis, 2014) would be a good place to start.


How long does it take for a hard clam (Mercenaria mercenaria) to reach sexual maturity? How long does it take for a wild hard clam (Mercenaria mercenaria) to reach an age where they are reproductive? How does fecundity depend on age and size? I've looked at several hard clam life cycles and none of them have this information. They tend to agree that hard clams are long lived and take multiple years to reach a size suitable for harvest. While I am more interested in wild hard clam, please do also share information on farmed hard clam if you have it?

According to Ebersole 1987, Mercenaria mercenaria reaches sexual maturity at two years of age although some individuals can reach maturity at 1 year of age under certain growing conditions.  The mean size of individuals reaching sexual maturity is 33 mm with males somewhat smaller than females.

Ebersole cited a few studies that estimated fecundity of M. mercenaria. The results were highly variable. Individuals of about 60 mm in size released between 2 million and 6 million eggs.  Other estimates were as high as 25 million eggs.  Ebersole also cited a paper by Bricelj and Malouf (1980) where they found a general association of increasing fecundity with increasing clam size.  I don't have access to that paper but a book called The Great South Bay edited by Schubel et al. 1991 discussed the results of Bricelj and Malouf. Scroll to page 45 of the Google Books preview.  They show the mean fecundity and size as follows:

Seed (<48mm): 1.6 million eggs / individual
Little Necks (48-70mm): 2.9 million
Cherrystones (70-79mm): 5.9 million
Chowders (>79mm): 6.3 million

However, the figure on page 45 of Schubel et al., and taken from the Bricelj and Malout (1980) paper, shows a lot of variability in fecundity at different size classes.  Hopefully, the citations in the Ebersole paper will point you to other useful studies. If you don't have ready access to the book, your local library may be able to get it for you on loan.

Literature Cited

Bricelj, V.M. and R.E. Malout. 1980. Aspects of reproduction of hard clams (Mercenaria mercenaria) in Great South Bay, New York. Proceedings of the National Shellfish Association 70: 216-229.

Ebersole, 1987. Species profiles: Life histories and environmental requirements of coastal fishes and invertebrates (South Atlantic). Hard clams. US Fish and Wildlife Service Biological Report 82 (11.75).

Schubel, J.R. et al. (editors) 1991. The Great South Bay.  State University of New York Press, Albany, New York, USA.


Regarding the NCBI FTP site I am trying to extract information about SNP data from the FTP server of NCBI. Could someone please explain to me how the directory is organised? There are many many files and folders and I can't figure which contains what. Is there one file which explains the organisation of the ftp site properly? The NCBI help manual did not give much help beyond helping me find species of interest.

Getting SNP data from FTP Site of NCBI SNP:

It's actually simple to download the data from the NCBI, if you follow the method given by FAQ( as given by @WYSIWYG).

Step 1:

Goto organism FTP: ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/

Step 2

Open your required organism folder:

From here you can download any file you wanted. If you trying to study the whole organism please download any one of the whole folders(ASN.1, rs_fasta, XML(recommended)).

Now,

It's not about the downloading it's about understanding the files which are provided.

files types:

XML files
ASN.1 or Abstract Syntax Notation One
rs_fasta

All of them contents almost the same data, just in different format. It's up to you how your script(preferably Python or Perl) works to get out the import information.

Other way of Download from NCBI FTP:

You can always use filezilla:

Put Host as : ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/
rest Username and Password, etc empty


How do fully dioecious plants determine sex? I know that a minority of plants are fully dioecious, with adult plants producing either only male or only female flowers. When is this sexual differentiation determined? Is the seed of such a plant already male or female? Is it a simple genetic difference?

The short answer is that in dioecious plants the sex of an individual plant is determined by its chromosomes.

Several familiar crop plants are dioecious: asparagus, kiwi, hop, papaya, spinach and yam. The evidence indicates that dioecy has evolved independently in different plant families. I refer you to

  Matsunuga & Kawano (2001) Sex determination by sex chromosomes in dioecius plants. Plant Biol 3: 481-488.

I have summarised below some of the introductory information in this review.

First some background for context: In mammals there is an XY system in which maleness is determined by an active Y chromosome i.e. the Y chromosome carries male sex determination gene(s). Males are said to be heterogametic. In Drosophila there is also an XY system, with heterogametic males, but in this case what determines sex is the ratio of X chromosomes to autosomes. This ratio exerts its effects through the Sxl gene. In this system the Y chromosome does not carry male-determining genes.

In flowering plants, in dioecious species, the usual situation is that males are heterogametic. However, there is variability in the underlying mechanism of sex determination.  So for example in hop (Humulus lupulus) there is a pair of sex chromosomes that can be distinguished by their appearance. However there is no active male determination but rather the X to autosomal ratio determines sex (as in Drosophila). Conversely, in asparagus (Asparagus officinalis), sex is determined by a pair of chromosomes designated pair 5. The two chromosomes are morphologically indistinguishable but genetic evidence indicates that there is active sex determination in this species - one member of pair 5 acts like the mammalian Y chromosome.


What triggers DNA to produce proteins? What is the trigger for DNA to produce proteins or RNA?

I have found enough material to study the inner workings of the cell and DNA; but, I can't find an explanation of the mechanics the cell uses to react to its inner state or external events and in turn initiate transcription.

This question is not easily answered as there are a multitude of factors involved in the production of proteins.  DNA - the molecule - does not "determine" when proteins will be produced.  The environment (truly environmental, extracellular, intracellular, etc.) of the organism governs this.  If you have not found enough material to satisfy your inquiries I recommend Jim Watson et. al. Molecular Biology of the Gene.  A classic.