Why are there ecosystems? Why would things self-organize in such a manner? I'm a mathematician and I have no baggage in ecology or biology. If the question is too broad maybe someone can point me to formal sources where this type of issues are tackled.

Basically, they don't. Ecosystems are pretty much either de facto, delimited by geographical boundaries, or defined by us. For example, an underground lake would be an ecosystem and it is organized in such a way for the simple reason that there is no communication between it and any other system.

Most ecosystems however, do communicate. For example, we call a desert an ecosystem but what of creatures living in the borders? That can survive both the harsh desert and the milder outskirts. Do they belong to the desert ecosystem? To the surrounding one? To both?

Basically, we divide nature into ecosystems because we can study them better that way. Species that form part of the same ecosystem tend to interact in one way or another and species from completely separate ecosystems tend not to. This is not some kind of rule however, it is simply the way we categorize things.

To take a different example, how would you define a city? Where does a city end and the countryside begin? Ecosystems are similar, there are seldom very clear cut lines separating them, they sort of bleed into one another.

In other words, your question is moot, ecosystems don't really self organize as such. The organization that does exist is between the different species and is an emergent quality of the complex system that is the ecosystem. Thinking of ecosystems, however, as distinct and well defined entities is generally wrong.


What are treatable foetal conditions during pregnancy? What are different foetal conditions during pregnancy that could be treated with appropriate prenatal genetic testing?

I only know that pregnant women are encouraged to take certain supplements to make sure certain conditions won't develop in the foetus, and which are apparently also the case for deficiencies in human growth hormone, but I imagine there must be other specific cases that are treatable for specific conditions diagnosed to only a small number of cases?

Your question probably expresses a subtle confusion about the prenatal diagnostics and genetic testing.

So, genetic testing is one of the diagnostic methods in prenatal diagnostics (among with the other methods, see the list) which is used to diagnose genetic disorders of the foetus, whereas the disorders that are diagnosed on this stage are mostly genetic anomalies with dramatic impact on the feotus development, for example chromosome aberrations (like Down or Turner Syndromes). Should these conditions be diagnosed, the woman is given a choice to interrupt the pregnancy prematurely.

Less dramatic conditions (like sickle-cell disease) can be diagnosed at this time too, but are not treated before the birth.

The genetic disorders that are amenable to the dietary or medical treatment (like phenylketonuria or congenital hypothyroidism) are usually diagnosed in the newborn screening tests (newborn heel prickle test), because these screening is more precise and less dangerous compared to the pre-born diagnostics.


Karyotypes Appearance Most actual karyotypes online appear as single chromosomes (unreplicated). I was under the impression that a micrograph of the replicated chromosomes was taken during metaphase of mitosis and thus should show up as duplicated sister chromatids instead of single chromatids post anaphase.  Are the arms of the chromatids just so close to each other that they are hard to distinguish?

Many karyotype images, especially those used for introductory educational purposes, have been edited to show a regular human 2n. For example this image has been edited to depict a regular 2n (46) compliment of human chromosomes.

While this image is unedited and shows the replicated homologous pairs in metaphase:


Identify this insect - unknown location Please help identify this insect - genus, species and anything interesting about it.

(Part of this old thread.)

It is a beetle of the genus Eudicella.
There are several species and some look quite similar, they are from tropical Africa.


How do you remove DNA/RNA from plastics? I want to know how to make plastic containers free of DNA & RNA? this is just for knowledge

Lab cleaning solutions can be bought which remove/destroy nucleic acids such as this one. UV is another technique for destroying DNA. And bleach is used to remove contaminant DNA in ancient DNA studies.

Searching for a DNA/RNA lab cleaning protocol would be a good idea to - something like this.


How are single cells sorted in an scRNA-Seq protocol by FACS? I am computational guy trying to understand how FACS sorting works in an scRNA-Seq protocol. About sorting single cells in each well of a 384-well plate, I have a question that would be grateful if you could answer it.

The protocol reads that cells are sorted in the wells based on their marker levels. For example it says:

  NK single cells were collected from the CD19-/TCR-β- events by gating
  for NK-1.1+ events in NK-1.1 vs. Gr1.

The part that I don't understand is that how it is possible to know positive/negative events or even to gate on events beforehand? I know that FACS first examines markers and then sorts them into positive, negative or waste collections. Here is my question:

  But how do we know what an expression level is acceptable for calling
  a cell positive, and also in more complicated case, how do we to gate
  on a subpopulation of cells (like top right quadrant) when no events
  have yet crossed the laser beam because we don't know the baseline of
  CD markers' expression levels yet?

For instance, It could be possible that in my panel setup a CD marker can never reach a value more than X, but in your setup it can never reach a value more than X/2.

N.B. As protocol says, subsampling of the main sample for FACS is not possible to infer these values beforehand because it is very likely that the populations of different cell types is not conserved in the subsample.

I will append the previous sentence in your protocol, and put what might help you in bold:

  To  obtain  B  cells,  NK  cells  and  monocytes,  a  splenocyte  suspension  was  stained  with PE-Cy7-conjugated  CD19,  eFluor  450-conjugated  NK-1.1,  PerCP  Cy5.5  Gr1,  FITC TCR-β,  APC  CD11b  and  PE  B220  (CD45R).  B220+ and  B220neg (germinal  center)  B cells  were  collected  by  gating  for  CD19+(TCR-βneg)  cells  and  then  by  B220  against  theCD19  marker.  NK  single  cells  were  collected  from  the  CD19neg/TCR-βneg events  by gating  for  NK-1.1  positive  events  in  NK-1.1  vs.  Gr1.

The cell types in question have unique properties that can be stained for using (immuno)histochemistry, i.e. chemicals and/or antibodies. The antibodies themselves tend to be conjugated, i.e. they are covalently bound to fluorophores typically which are fluorescent. That means a cell type can be labeled by fluorescence, and the FACS machine can sort fluorescent cells from non-fluorescent cells.

They stained the different cell types with different markers. The markers are sufficiently different from each other to be able to use them together in some cases. For instance, whatever FITC is could be used simultaneously with PE-Cy7-conjugated antibody.

First, they collect two subsets of B cells (the B220 positive and negative cells) by using the CD19 marker (PE-Cy7-conjugated antibody that binds CD19).
Then, from one of the subsets, the B220 positive one, they sort another subset which is positive for eFluor 450 (which is conjugated with an NK-1.1 antibody). This collected subset fulfills their criteria for being NK cells.
This subset is used for single cell capture on a plate (e.g. for SMART-seq2) or using microfluidics (e.g. for 10X Chromium).

For a FACS machine, you can select the threshold level of e.g. florescence that will be used as a cutoff between positive and negative events (cells). This is arbitrary and is usually subject to trials.


Do mitochondria use ATP in order make another ATP from glucose? Do mitochondria use ATP in order make another ATP from glucose, or does it use another source of energy to convert glucose to ATP?

During ATP production through the citric acid cycle, some ATP is used to transport necessary molecules for the reactions.

piruvate molecules are actively transported into the mitochondrial matrix [2]
two NADH equivalents from glycolisis are transported into the mitochondrion and consume two molar equivalents ATP [1]
protons leakage across the mitochondrial membrane leads to reduced ATP from NADH and FADH2 [1]

In theory, one molar equivalent of glucose can generate 38 equivalents of ATP. The actual number is only 25 [1].

References:

Wikipedia contributors, "Citric acid cycle," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Citric_acid_cycle&oldid=610117265 (accessed June 26, 2014).
Wikipedia contributors, "Mitochondrion," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Mitochondrion&oldid=614223751 (accessed June 26, 2014).


How can the number of genes increase through evolution? I am aware of the basics of evolutionary theory, however I don't understand how mutations can add genes over time.

Am I correct in thinking that creatures within the same species who mutate to have an additional gene in their genome would normally be infertile?  Or am I misunderstanding that?

Can someone explain the process of the creation of genetic material through evolution?  Citation to a decent academic paper or book on the matter would be appreciated too.

Mutations can have all sorts of impacts on genetic architecture. A mutation can have a small impact on a genetic architecture such as

Substitution
Insertion
Deletion

or can have a much bigger impact on a genetic architecture such as

Amplification (incl. gene duplication)
Deletions
Chromosomal translocations
Interstitial deletions
Chromosomal inversions
Chromosome duplication
Change in ploidy number

Some of these mutations (gene duplication, Chromosome duplication, change in ploidy number) typically allows duplicating DNA segments. After duplication, the two copies of a gene can diverge through neofunctionalization or subfunctionalization. Have a look at wikipedia > gene duplication to understand what biochemical processes can cause such mutations (e.g. ectopic recombination, retrotransposition event, replication slippage).

  Am I correct in thinking that creatures within the same species who mutate to have an additional gene in their genome would normally be infertile?

You are being mistaken. I understand the naive intuition that a change in copy number of a given gene would be extremely deleterious but in reality, living organisms seem much more resilient to such Copy-Number Variation (CNV) than you would think. Of course, some CNV are associated with diseases but it is not the case of all (McCarroll and Altshuler 2007).

Gene duplications are actually quite common whether in C. elegans (Lipinski et al. 2011) or in humans (Cotton and Page 2005). Chromosomal duplications are also common (Bowers et al. 2002). Even whole-genome duplications (see a classical example in Wolfe 2015) have played major roles in the evolution of many lineages (Whitton and Otto 2010) including vertebrates (Dehal and Boore 2005).

Below is a phylogenetic tree of sequenced green plant genomes highlighting some of the main events of whole-genome duplication.

For the record, some species of strawberries are decaploid (10 copies) (Hummer 2012). Then there are the extremes. In Entamoeba populations, there can be variation in ploidy level among individuals ranging from diploid (2 copies) to tetracontaploid (40 copies) (Mukherjee et al. 2008)!


Can I ask tip for tissue measuring(especially for RNA preparation)? I extracted RNA at mouse liver and human blood, but degradation occurs. I think, at mouse liver, too hard to measuring 50mg liver(I am newbie for animal tissue preparation) so spend several minutes. liver is soft but very small, and too hard to keep the weight. (human blood spend time for defreeze, but It degraded, too.)

for example, I want to weight 20mg mouse liver,
1. cut liver by scissors about 10mg after set zero point of scales with ep-tube.
2. cut liver almost 10mg, but it's exceed weight 2~3mg, so I have to cut it 2~3mg.
3. this scale is too small... so I spend for keep the weight for 20mg, like this: 10->23->19->19.3->19.8->21->19.8->20.

I want to ask for advice about how it faster animal tissue measuring and preparation. When preparation genomic DNA, is it OK so DNA is stable than RNA. but, when extract RNA, keep the weight fast and incubate sample at ice for prevent RNA degradation.

I do not have specific experience with liver tissue, but here I would do a couple of things. First, to get around your issues with weighing tissue, set an acceptable range around 20 (say, plus or minus 5mg, so ranging from 15 to 25mg) and then normalize your RNA yield to that starting weight. Second, look into ways to preserve the RNA in your tissue as you're processing it. You could try RNAlater solutions or other chemical means of stopping RNA degradation, or just snap freeze your tissue in liquid nitrogen. Good luck!


Clarification of the procedures to amplify cDNA needed The typical procedure to obtain cDNA from genomic extracted DNA is the following:

RNA is extracted from desired tissue, RNA/DNA hybrid is obtained by virtue of reverse transcriptase RNA dependent DNA polymerase, H RNAse creates gaps in RNA of DNA/RNA hybrid and with the aid of a typical DNA polymerase dsDNA is transcribed, right?

Then, the newly synthesized cDNA is linear (like a "small chromosome")?
How is it protected from the nucleolytic activity?
Is the procedure really like I described or does the reverse transcriptase already give a dsDNA from single stranded mRNA?

Here is the rough procedure that I've used to prepare cDNA before

Extract RNA from desired tissue (select for mRNA using the polyA tail of mRNA)
Conduct reverse transcription. This requires a primer complementary to the polyA tail to get the reverse transcriptase started (Edit:You could also use random primers to prime reverse transcription. This eliminates the redundant polyT sequence from the cDNA. This is the method used in the Illumina TruSeq high throughput sequencing library prep kit). Now you have a collection hybrid RNA/DNA double strands
Digest the RNA strand specifically. This can be accomplished with RNAse H as you mention, or by introducing basic conditions, which degrade RNA much more rapidly than DNA due to the 2'OH of RNA. Now you have linear ssDNA complementary to the inital mRNA templates.
From this point your applications may differ. If you are doing microarrays, all you need is ssDNA, since you want to hybridize the cDNA to the array. If your downstream use of the cDNA requires dsDNA, then you need to synthesize a complementary strand to the cDNA (and potentially amplify the product). This can be accomplished through PCR random primers, or some more complicated PCR that will incorporate extra sequences on either side of your cDNA (e.g. bar-codes and adapters in RNA-Seq).

  How is [the cDNA] protected from the nucleolytic activity?

If you are digesting the product of reverse transcription with RNAse H, that enzyme digests RNA specifically, so your DNA is unharmed. If you are going with an alkaline conditions treatment, then the RNA will be degraded in those conditions much more quickly than the DNA due to the presence of the 2' OH group in RNA which can act as a nucleophile for a self-cleavage reaction.


How do plants intake minerals through their leaves? How do plants intake the fertilizer when it is sprayed all over the leaf surface as a foliar feed?

They absorb minerals through pores in the leaves known as stomata, this is some what similar to the way a medicine patch is absorbed on human skin except for the fact that the human skin has sweat pores instead of stomata.

Here is a animation of them opening and closing on a tomato plant provided by Wikipedia:

sources:

  A nice review by Wocjik (2004) (from the comments)

  http://www.wisegeek.com/what-is-foliar-feeding.htm

  http://en.wikipedia.org/wiki/Foliar_feeding

  http://cronodon.com/BioTech/Plant_Transport.html


Does osmosis occur when we have two different substances? Assume that we have a semi-permeable membrane with water on both sides. First, straightforward, case: On the right side, we have a concentration of the substance A, and on the left side, we have pure water. Obvious effect: water flows from left to right.

Now, imagine we have a second case. We have the same membrane, and a water solution of A to the right. To the left, we have a water solution of a different substance, let's call it B. Now, what happens? I can imagine a few possibilities:

the system behaves exactly as in the first case, because the substances have no influence on each other
the system behaves as if it was a solution of A on both sides, with water flowing in the direction of higher concentration (because it only matters if there is something dispersed between the water molecules, but it does not matter what)
some interesting cross-influence effect happens
either one of the three things above can happen, depending on the particular combination of substances A and B

Which one is the true effect? What happens, and why?

If you need an example of the actual substances, let B be thiamine and A be plain sodium chloride, but I am interested in the general case.

If A and B are at the same concentration there will be no net movement of water.

Everything is down to diffusion. In your example of solution A/pure water, water molecules on both sides of the membrane are diffusing through the membrane to the other compartment. However the "concentration" of water is less in solution A, so the rate of movement is less from solution A to water than it is from water to solution A. Water will continue to move into the solution until another force, such as hydrostatic pressure, counteracts the "osmotic pressure".

If solution A and solution B have solute at the same concentration then the rate of movement of water will be the same in both directions, so no net movement will occur.

(In a typical experimental set up using dialysis membrane none of this would apply with the solutes that you mention since they would also be able to move through the pores and you would end up with perfect mixing. You would have to use macromolecular solutes.)


Molds and fungi usually found on book pages: identifying and preventing further spread I know I can use bleach to kill most of the spores that live on my walls. I know I have to keep humidity below a certain level and temperature above another to prevent the spread of mold. I have read tons of websites on how to treat 'wall infestations'.

It's the mold that affects my books that worries me the most.
Especially now that I've discovered a very enticing market for used books. You can find bargains but sometimes the books smell "of mold".

I would like to know more about the kind of molds (and/or fungi or other bio-monsters) that usually feast on paper. The paper that makes the pages of a book.

Can someone point me to any kind of resource with answers to the following questions?

What are the most common biological causes of page deterioration?
1b. Can they be identified without lab instrumentation?
Can they spread from one book to another, and if yes how and how fast?
Can they be neutralized in some way (stopping the spread), or should one just burn the moldy books to avoid contagion?

I seek knowledge to protect knowledge.

Mold can grow in Extreme environments: they can live in very low water activity level, sometimes as lower as 0.71, live in refrigerator temperatures, these characteristics make it difficult to kill them thoroughly.
You can search "paper deterioration" in Google or library, then you can find lots article about this.

1) Causes

Foxing and other white, fluffy coating or light yellow powder on paper caused by: Eurotium rubrum, E. repens, Aspergillus versicolor, Penicillium solitum, and Penicillium decumbens. (Karbowska-Berent, Joanna, Joanna Jarmiłko, and Jolanta Czuczko.
Source: "Fungi in Fox Spots of a Drawing by Leon Wyczółkowski." Restaurator. International Journal for the Preservation of Library and Archival Material 35.2 (2014): 159-179.)

Black spots: Monilia, Aspergillus, Penicillium, Mucor, Stemphylium, Hormodendrum, Fusarium, Chaetomium, Byssochlamys
Source: Beckwith, Theodore Day, Wilbur Harold Swanson, and Thomas Marion Iiams. "Deterioration of paper: the cause and effect of foxing." Publ. Univ. Calif., biol Sci. 1.13 (1940): 299-356.

2) Spreading

For their spread, I think the mold can spread everywhere, but i did not find any resource about it.

3) Method that kill the mold

Drying the affected paper objects and applying 70% ethanol are the most preferred options to stop active fungal growth.
Source: Sequeira, Sílvia O., Eurico J. Cabrita, and Maria F. Macedo. "Fungal Biodeterioration of Paper: How are Paper and Book Conservators Dealing with it? An International Survey." Restaurator. International Journal for the Preservation of Library and Archival Material 35.2 (2014): 181-199.


Is it possible to obtain single strands of DNA in solution? Being that it is relatively simple to extract DNA from a variety of sources, what further technique can be used to separate the two complementary strands in solution?

There is usually a denaturation step in a typical PCR protocol, see e.g. here, which serves exactly this purpose: the strands are thermally divided (typically at 95 °C for a few seconds). As you can see, this is a very common process, but the strands only remain denatured if kept at high temperatures.

Room-temperature strand separation in regular buffer solutions will be very hard, because annealing (the opposite process, where two complementary strands pair up) is thermodynamically favourable.
More permanent separation might be obtained by dissolving DNA in particular solutions, as described here, where DMSO seems particularly effective.
This results in separated strands at room temperature, but both strands will clearly still be present. One might think about separating the two with various methods (e.g. HPLC), but I doubt these solutions are compatible with regular HPLC columns.


Prediction of transmembrane beta barrels? I studied that prediction of transmembrane alpha helices is more easy and accurate and also good algorithms are available for their prediction. But when we move towards prediction of transmembrane beta barrels (cylindrical structure composed of anti parallel beta-sheets) then for their prediction only a small number of algorithms are present which also don't give reliable results.

My query is that Why it so? Why the prediction of transmembrane beta barrels is difficult and why developers can't develop reliable algorithms for this purpose?

I could tell only from my pretty poor experience.
I had all PDB entries processed with DSSP and then I've tried to find any trends in amino acid preferences. I did not find any except the pretty obvious absence of proline in double (i.e. with two neighbours) strands. Also, negative charged amino acids (I, L, V) were slightly more frequent in parallel strands. After that, I tried a sort of naive Bayes classifier for the amino acid and it's neighbours in two neighbour strands and +/-2 amino acids up/downstream. For single\double parallel\antiparallel strands, the prediction precision was about 60%.


Why does cutting onions cause tears? Why does cutting onions cause tears? From a couple of sites, I found that it is because of sulfuric acid produced by onions. But I could not find more details. What is the biochemical pathway by which onions cause tears? Also, which compound is responsible for it? If it is enzyme-catalyzed reaction, can we just stop the production of this enzyme without causing any side-effects?

Interesting question! The cause of tears and itching is the chemicals produced by onion (Allium cepa). Lets go into some details.

Onions, coming from the family Liliaceae (also containing garlic, chives, scallions and leeks) store compounds known as amino acid sulfoxides, and the one we are talking about here is S-1-propenyl-L-cysteine sulfoxide (abbreviated as PRENCSO), also calles isoalliin (due to its similarity with alliin found in garlic). When onion is damaged (cut, chewed, etc.), an enzyme alliinase converts PRENCSO into 1-propenyl sulfenic acid. This compound is then converted into propanethial-S-oxide by an enzyme lachrymatory factor synthase (earlier this reaction was considered spontaneous). The reaction looks like this:

Propanethial-S-oxide is the major cause of the flavor and aroma of onion. However, it is a volatile compound i.e. vaporizes very quickly. When its vapors reach the eye, it causes tears because of being a lachrymator (aka tear gas) i.e. as soon as it comes in contact with cornea, it triggers a nervous response which leads to activation of lachrymal (tear) glands.

PS: when propanethial-S-oxide comes in contact with cornea, a small amount of it reacts with water to form sulfuric acid. This sulfuric acid is the cause of itching and irritation in eyes due to onion. Also, scientists are now trying to genetically either modify or stop the production of lachrymatory factor synthase enzyme to produce tearless onions. This (modification) has even been achieved to a high efficiency, as another answer discusses. However, making tearless onions could prove harmful to the crop in several ways, as discussed here.

EDIT: As asked in comments, I will add some details about how the sulfuric acid is produced from the reaction between propanethial-S-oxide and water.

The only resource I could find giving some details about this was Marta Corzo-Martínez, 2014. They summarize the complete pathway in the following diagram:

After applying some common chemistry principles, the concerned reaction turns out to be:

$\ce{4~C_3H_6SO~+~4~H_2O \rightarrow 4~C_3H_6O~+~H_2SO_4~+~3~H_2S}$

As you see, one of the products of hydrolysis of propanethial-S-oxide is hydrogen sulfide ($\ce{H_2S}$). Just like $\ce{H_2SO_4}$, $\ce{H_2S}$ also causes irritation in the eyes (its effect on eyes has been well documented, see Lambert et al, 2006 as an example). Thus, the produced $\ce{H_2S}$ only increases the irritation and itching in the eyes caused due to $\ce{H_2SO_4}$.

BONUS: Another interesting point here is runny nose. propanethial-S-oxide is actually the compound responsible for the smell and flavor of onions. But, it causes tears by exciting the lachrymal glands i.e. reflexive lachrymation. propanethial-S-oxide excites the trigeminal nerve (the fifth cranial nerve) causing activation of lachrymal glands. Interestingly, the nerve endings of trigeminal nerve are also present in the nose, along with the eyes. So, this compound can also activate the lachrymal glands from your nose, and since the lachrymal duct is joined from eyes to nose, you can also experience runny nose along with tears and irritation in eyes.

References:

Propanethial-S-oxide | University of Bristol
Alliin | Wikipedia
Tear Gas | Wikipedia
Timothy William Lambert, Verona Marie Goodwin, Dennis Stefani, Lisa Strosher, Hydrogen sulfide ($\ce{H_2S}$) and sour gas effects on the eye. A historical perspective, Science of The Total Environment, Volume 367, Issue 1, 15 August 2006, Pages 1-22, ISSN 0048-9697, https://doi.org/10.1016/j.scitotenv.2006.01.034
Encyclopedia of Perception, Volume 1 -
E. Bruce Goldstein,
SAGE, 2010
The Neurology of Lacrimation – How an Ear Infection Can Cause Dry Eye -
by Noelle La Croix, DVM, Dip. ACVO


What is the difference between meristem and bud? Keep reading both terms quite frequently while studying plant physiology. I did some research trying to establish their differences and I learnt that meristems are undifferentiated cells that can generate more cells that eventually could grow to form any part of the plant. But I really mess up both concepts, so I would really appreciate a comprehensive explanation of both of them separately. Thank you in advance for your help!

I looked in Taiz and Zeiger. Plant Physiology 5th ed and this is what I found:

Plant growth is concentrated in localized regions of cell division called
meristems. Nearly all nuclear divisions (mitosis) and cell divisions
(cytokinesis) occur in these meristematic regions. In a young plant, the
most active meristems are called apical meristems; they are located at the
tips of the stem and the root (see Figure 1.1). At the nodes, axillary buds
contain the apical meristems for branch shoots.
The root and shoot apical meristems formed during embryogenesis are called
primary meristems. After germination, the activity of these primary
meristems generates the primary tissues and organs that constitute the
primary plant body.
Most plants also develop a variety of secondary meristems during
postembryonic development. Secondary meristems can have a structure similar
to that of primary meristems, but some secondary meristems have a quite
different structure. These include axillary meristems, inflorescence
meristems, floral meristems, intercalary meristems, and lateral meristems.
Axillary buds are secondary meristems; if they are also vegetative meristems, they will have a structure and developmental potential similar to that of the apical meristem.

So, briefly, I could say that meristems are localized regions where undifferentiated cells reproduce themselves and originate new plant tissue. Axillary buds contain secondary (formed after embryogenesis) meristems. This meristem can behave like an apical meristem if it becomes vegetative i.e. either apical dominance disappears or it is excised and subcultured elsewhere.


Is there any evidence that any other species are "pre-intelligence"? Is there any evidence regarding whether other species might, given time, evolve intelligence as humans have?

I realize "intelligence" is a vague word here, but I'm interested in throwing a wide net, since I imagine the small sample size of positive cases makes finding any evidence at all extremely difficult.

The only information I've been able to find so far seems vague and unscientific, but I'm expecting that is the best I'm going to be able to find.

I don't exactly know, what the intelligence is, but i've got an idea what it can be.
I've read about smth similar before. I suppose, we can measure intelligence with working memory (don't mix with shott-term-mempory)  term (like registers of processor).
There were many experiments that was provided to check how big a working memory of humans and apes.

According to information people got from these experimence, average WM of humans equal to 7, apes - equal to 4 (count of terms subject can manipulate without any significant mistakes). So, apes can be considered as pre-intelligence this way. But anyway it is still controversial question.

You can also google articles like this:  http://www.pnas.org/content/110/Supplement_2/10371.full.pdf


Protein electrophoresis Three proteins A, B and C of equal molecular weight are being investigated in a study. They contain six, four and four cysteine residues respectively. Only Proteins A and B were treated with β-mercaptoethanol (which reduces disulphide bond) and heated in boiling water bath for a few minutes. Which of the following is expected in the SDS PAGE gel run?

a. Protein C will move fastest.

b. Protein B will move fastest.

c. Proteins A and B will move at the same speed but faster than C.

d. Proteins B and C will move at the same speed.

Before knowing the answer the I thought the answer would be b. Because as Protein A has the most no. of amino acids so it will be behind Protein B and C for sure. And for protein B and C, as Protein B has been in a reducing environment it will not form disulfide bridges but Protein C will, so it will be billore and hence will be behind Protein B. So B will be fastest?

But the answer key says C, I am not really sure how?

So the answer is C . Before knowing the answer I thought the answer would be b. Because as Protein A has the most no. of amino acids so it will be behind Protein B and C for sure. And for protein b and c as Protein B has been in a reducing environment it will not form disulfide bridges but Protein C will so it will be billore and hence will be behind Protein B. So B will be fastest? But the answer key says C

The problem statement says all the proteins have the same molecular weight but does not say how many amino acids they have.  It does say how many cysteine amino acids each has, but not how many other kinds they have.  Cysteine forms disulfide bonds, holding bends in the protein structure.

BiteSizeBio says:

  SDS is a detergent that is present in the SDS-PAGE sample buffer where, along with a bit of boiling, and a reducing agent (normally DTT or B-ME to break down protein-protein disulphide bonds), it disrupts the tertiary structure of proteins. This brings the folded proteins down to linear molecules. SDS also coats the protein with a uniform negative charge, which masks the intrinsic charges on the R-groups.

So the point to SDS-PAGE is to have proteins migrate in the gel according to molecular weight without regard to the natural charges carried by the various component amino acids.  The three proteins should thus migrate at the same rates in SDS-PAGE (not A being slower than B and C, as OP thought).

However, protein C is not treated with β-mercaptoethanol (B-ME) which is an important part of SDS-PAGE, so it retains the disulfide cross-links and thus is not a linear string of amino acids.  Hence C will migrate more slowly than A and B, and the expected result is as stated in choice (c.).


Can two proteins sharing a few domains be considered homologous? I wonder when to say two proteins are homolog. In the current example I checked the sequence of these two proteins in pfam and as you see they have some shared domains but all domains are not shared. Can I say that these proteins are homolog? How can I be confident about my decision?

Homology means shared evolutionary ancestry. Sequence similarity is often used as a proxy for homology but inferences should be made with care.

The similarity between two genes/proteins should not just be good but has to be statistically significant (metrics like E-value) for the two genes/proteins to be considered homologous.

  INFERRING HOMOLOGY FROM SIMILARITY

  The concept of homology – common evolutionary ancestry – is central to
  computational analyses of protein and DNA sequences, but the link
  between similarity and homology is often misunderstood. We infer
  homology when two sequences or structures share more similarity than
  would be expected by chance; when excess similarity is observed, the
  simplest explanation for that excess is that the two sequences did not
  arise independently, they arose from a common ancestor. Common
  ancestry explains excess similarity (other explanations require
  similar structures to arise independently); thus excess similarity
  implies common ancestry.

  However, homologous sequences do not always share significant sequence
  similarity; there are thousands of homologous protein alignments that
  are not significant, but are clearly homologous based on statistically
  significant structural similarity or strong sequence similarity to an
  intermediate sequence. Thus, when a similarity search finds a
  statistically significant match, we can confidently infer that the two
  sequences are homologous; but if no statistically significant match is
  found in a database, we cannot be certain that no homologs are
  present.

  Pearson, 2013

Members of a protein family are descendants of a common ancestor and are hence homologous. However, in the course of evolution they would have acquired new domains or reshuffled their domains such that their sequences are no longer similar. Proteins that have full length sequence similarity are called homeomorphic (Wu et al., 2004). Therefore, members of a protein family may be homologous but not homeomorphic. However, homeomorphic proteins can evolve independently and therefore may not be considered homologous.

Identifying homologous proteins is, therefore, not a simple task. Machine learning algorithms are used for better identification of homologous proteins. Some of these algorithms are mentioned in the linked papers.

In general, global similarity, rather than local similarity should be considered for identifying homeomorphs. See What is the difference between local and global sequence alignments?


Is it impossible for a retrovirus to be lysogenic? Is it impossible for retroviruses to be lysogenic? In the lysogenic cycle, the viral genetic material is incorporated into the host cell's DNA. Because retroviruses have RNA, it would be impossible for their genetic material to be incorporated into the host cell's DNA, unless the RNA is reverse-transcribed or something.

Is this the case? How does this work?

Thanks!

evamvid

Both things are not exclusive of each other. Retroviruses are RNA-based viruses which need to reverse transcribe their RNA genome into DNA before they can multiply. This is done by the reverse transcriptase enzyme, which is part of the virus and is incorporated into the cell.

Once the reverse transcriptase has been active and made the DNA, this DNA can also be incorporated into the hosts genome. If you look into the Wikipedia article on Bacteriophages, you will find a list of different bacteriophages, with all kind of genomes, among them as well a number of RNA-based viruses.

RNA-based viruses which enter the lysogenic pathway are obviously either pretty rare or they haven't been discovered yet in bigger numbers. Two examples are the phages F2 and MS2 (which are closely related).


Gene perturbation, what is it used for, explain to computer scientists? I am trying to build a gene regulation network, and I need some basic knowledge of it.

So, in gene research, we perturb genes. Such as knock down them?

Can people tell 2 or 3 experiment methods to perturb genes?
And 3 or more observations (phenotypes) after perturbation?

If it could be explained in the context of Microarray, it will be well appreciated.

The question is not that organised, if you can tell a whole story before the computational work started, I will thank you so much.

Here are 3:

1) gene knockout.  Just delete the gene from the genome.  The function is gone - useful for demonstrating a direct involvement of the gene in the phenotype.  As a phenotype, the microarray will register all sorts of reactions to the loss of the gene in addition to the RNA in question being gone.

2) use selection to find mutants for the gene.  Expose the organism to a mutagen or high amounts of UV radiation.  Useful mutants vary by what the function of the genes are.  Temperature sensitivity - the gene doesn't function above 30 deg C is an example of a phenotype for a mutant that has been used classically.  In this case the functioning of the gene itself is a phenotype.  This is an example of a weaker perturbation.  Can be used when knockouts are fatal or when the system is too sensitive for a knockout.

3) change the environmental conditions. increase the concentration of a substrate or lower the availability of nutrients.  Phenotypes can be rate of growth/division, production of a given metabolite from the cells, but it goes on and on.

The affect on whole genome microarray data can be quite complex in such perturbation experiments because the coupling of many genes, even in bacteria can be broad and significant.


How is the subunit molecular weight different from the native molecular weight? I noticed that the native molecular weight for an enzyme is different from its subunit molecular weight. Why are they different? Aren't the genes needed to express the enzyme the same in the native organism and in the heterologous expression system?

Does the heterologous expression system happen to affect the molecular weight of the final enzyme product? If so, how?

Your question is answered in the paper, the protein likely exists as a homodimer in vivo and denaturation (such as performed with SDS PAGE -> Western Blot) separates the dimers into monomers:

"To determine the quaternary structure, size exclusion high-performance liquid chromatography was performed using an Agilent 1100 series high-performance liquid chromatography system with a Bio-Sil SEC-250 column (300 by 7.8 mm) and a mobile phase of 0.1 M Na2PO4, 0.15 M NaCl, and 0.01 M NaN3, pH 6.8. A Bio-Rad standard was used to standardize the column's retention time with respect to molecular mass (supplemental data). All experiments were repeated twice with <0.05 min of deviation in the retention times. The molecular mass of XR was calculated from its retention time to be ∼53 kDa. Monomerization could be induced in the presence of 15% SDS, causing XR to elute as a single peak, with a retention time corresponding to a molecular mass of ∼34 kDa. The data suggest that the native XR is a noncovalently linked dimer. The significant difference between the calculated molecular weight of the dimer and its apparent molecular weight is not uncommon for XRs from other species (7, 21, 33), which also typically exist as dimers. However, to be certain of the protein size, N. crassa XR was subjected to mass analysis by electrospray ionization-quadrupole time of flight mass spectrometry. The highest abundance peak had a value of 38,381 m/z, corresponding exactly with the predicted molecular mass for the His6-tagged XR with the N-terminal fMet removed (supplemental data). Additionally, a 2M+ peak of about 20% abundance at 76,759 m/z corresponds well with the predicted mass of the dimeric form of the enzyme (76,762 Da)."


Does the Michaelis-Menten equation take in account the non-enzyme formation of products? I only recently learned about the Michaelis-Menten equation, since I am not studying biology or anything related. Let's write the equation as
$$\frac{d[P]}{dt} = V_{max} \cdot \frac{[S]}{K + [S]}$$
If I'm not mistaken, this equation describes the rate at which products are formed ($\frac{d[P]}{dt}$) as a function of substrate concentration $[S]$ in steady-state. In a translation of Michaelis' paper I read that $V_{max}$ can be written as $k [E]$, where $k$ is a constant and $[E]$ is the total enzyme concentration.

Mathematically one would say that when the total enzyme concentration is zero ($[E] = 0$), the rate at which the product is formed should equal zero. If I recall correctly, in several reactions products are formed without enzymes (Enzymes only enhance the reaction rate?). Is the Michaelis-Menten equation specifically used for situations where $[E]>0$? If so, how does it account for very low enzyme concentrations where product formation from non-enzyme reactions cannot be neglected?

In any study of enzyme kinetics it is essential to subtract all 'blank' rates and to ensure that the measured rate is due only to enzyme catalysis.

That is, in kinetic 'parlance', the velocity vs [enzyme concentration] should be linear and go through the origin.  Doubling the enzyme concentration should double the (enzymic) rate, and halving the enzyme concentration should halve the (enzymic) rate.

Failure to subtract blank rates may give rise to a variety of spurious kinetic effects such as downwardly-curving double-reciprocal plots (Lineweaver-Burk plots).

Downwardly-curving Lineweaver-Burk plots are diagnostic of negative co-operativity, but such a conclusion may be artefactual if blank rates are not subtracted.

A very good reference to this sort of this is Enzymes, (1979) by Dixon, M, Webb, E.C.,  Thorne, C.  & Tipton, K.F. (3rd Edn), Longmans,  in particular pp 461 - 462.


Can plants live forever? I know that some plants die for old age like a
lettuce. But there are trees like Baobabs or larger Ficus in the tropics of whom we don't know their age. And trees like spruce reaching 9950 years old, which die for environmental factors and not by age.

However, E.g. when we multiply vegetatively an olive or cacao tree, we use a fragment or clone from a unique individual passing the same genetic information, again and again.

Then, can these plants live forever?

The answers to these questions often boil down to "what do you mean by live forever?".

You've included vegetative cloning, so I infer that counts as one living organism for your purposes. In that case, the answer is absolutely.

Pando is at least 10 thousand years old and only getting larger. The Cavendish banana is about 150 years old, but produces at least 70 million tons of bananas yearly.

See here for other giant clones. Of particular interest is King's Lomatia, represented as a species by a single, sterile, individual. Fossilized triploid leaves are too old for carbon dating(at least 45 thousand years old), so it's essentially unknown how old it is.

I would be comfortable declaring Pando immortal, since it's way too big to be eaten, too resilient to burn down, and has already survived the middle and end(at least!) of an ice age. That just leaves (ha) disease and basically nothing else as possible threats.


In the endomembrane system, after a protein leaves the rough ER, where does it go? It can either go to the smooth ER then to the Golgi or it can go directly to the Golgi, right? Also, the smooth ER gets all of its material to synthesize things from the rough ER, right? Sorry, I looked around but couldn't really find a direct answer to my question. Thanks!

I'm no expert at this but will do my best to answer your question based on the title. It depends on the protein! proteins can either be cytoplasmic, nuclear, transmembrane or secretory. Cytoplasmic proteins (as far as I know) get released to the cytoplasm after they have been folded correctly (through chaperones) and gone through the quality control mechanism. Nuclear proteins get transported through the nuclear pores, across the nuclear envelope through chaperones. Now for the transmembrane or secretory proteins, the fate of these proteins and where they go is decided by the ER (but obviously the information is there in the protein sequence). Transmembrane proteins have a signalling peptide and a transmembrane domain signal anchor sequence which ER recognises and through fancy looping and elongation across the ER membrane, the proteins is further translated by the ribosomes and eventually gets translocated to the cell membrane. There is very very nice nature review paper (Rapoport, 2007) about this and if you look at Figure 5, you will get a good ideas as to what goes on. For the secretory protein again its the interaction of the protein sequence with the ER membrane, helped with the ribosomes (in fact the groves in the ribosomes are key for making these fancy looping happen as the protein residues in ribosomes interact with peptide residues (amino acids) that are being produced on the fly), that processes it and sends it for secretion (Rapoport, 2007) and trans-golgi network is also important in the secretion process (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1424219/).

Hopefully these information would provide you with some hints.


Statistical Analysis for Blood Sugar Measurements I've conducted a lab aimed towards finding the impact of soluble fiber intake on the change in blood sugar levels. Following an 8 hour fast, I had test subjects consume a fixed amount of carbohydrates, with a varying amount of soluble fiber, and measured their blood sugar in 20 minute intervals. This was done for two hours each test, generally until blood sugar levels dropped to normal.

5 test subjects were used for the test, each with individual blood sugar responses - for instance, each had consistently different fasting blood sugar levels before food consumption, each had consistently different blood sugar peaks, and so on. Each test subject was tested 4 times, once with no soluble fiber, and 3 more with varying amounts of soluble fiber. The raw data I am now left with is simply a collection of scatter plot graphs displaying rises in blood sugar from normal condition, a peak, and a subsequent drop to normal condition.

I can visibly see from my graphs that more soluble fiber made blood sugar peaks smaller and longer to reach. Data did not always follow this trend, due to some source of error, but a relationship is nevertheless evident. I hope to make a conclusion from this data. What method of statistical analysis could I use to conclude a relationship from these scatter plots? I would like the method to take into account different individual responses, as well as the few data sets that did not confirm a relationship.

I appreciate your help!

It would help to see your plots. The way I would imagine to present this data is not scatter plots but line plots:

(Each line would have a confidence interval/standard deviation from your different test subjects. This is just a schematic representation. Color represents different experimental conditions. Let me know if I misunderstood your experiment.)

Now, what is your actual question? Your hypothesis? You want to know if the time or height of the peak of blood sugar levels is different between the different fiber levels, right?

So, why not measure this? At what time do you find the peak for each subject and experimental condition and what's the blood sugar level at that time point? Your null hypothesis would be that there is no difference between the test conditions.

Here some mock data show the data spread from your 5 test subjects of the peak height measurements in the 4 different test conditions. Now you reduced your data to a question, where you could use a statistical test to see if you can reject the null hypothesis.

One thing you could do is to perform an ANOVA with e.g. Dunnett's post hoc test to compare your fiber conditions to the control condition

A problem with that is that your conditions are not really independent. And your actual question is not if any of these conditions is different. Your hypothesis would rather be if there is a relationship between fiber content and peak height/delay (null hypothesis would be: there is no relationship).

Here is the same mock data in a scatter plot (color represents test subjects, they overlap, but let's assume there are 5 data points for each condition) with a trendline showing, that with increasing fiber content there is a reduction in peak height:

You could therefore try a correlation analysis and test the statistical significance of your correlation coefficient.

As you see, the statistical analysis very much depends on your hypothesis and how you analyse your raw measurements. I hope, I have correctly identified the issue and this helps you with your analysis.


Large nocturnal butterfly with red and black hindwings Location:

Central Poland, urban environment.

Size:

Around 4 centimeters long.

Time:

Early July.

Images:

That is a moth, in the family Erebidae. It is in the genus Catocala. Wikipedia has a nice page on Lepidoptera of Poland. https://en.wikipedia.org/wiki/List_of_Lepidoptera_of_Poland
including all the Catocala there.


Human Blood vessels, Why is blood drawn from veins? Is it because veins have a large lumen? Or is it because the blood is flowing at a lower pressure and makes discharge easier? Is it safer to draw blood from veins?

If you draw blood from arteries,it will spout out because the arterial blood flows at some pressure. Moreover, it is too hard to stick a needle because arteries consist of thick blood walls.


Does the formation of water inside the mitochondrial matrix help contribute to the proton gradient during the electron transport chain? Does the synthesis of water in the final step of the electron transport chain significantly increase the electrochemical gradient across the matrix? I understand that pumping protons out of the matrix clearly increases the positive charge in the intermembrane space, but the chemical reaction in Complex IV O2 + 4H+ + 4e− → 2H2O also reduces the protons in the matrix by binding them in water.

Since ATP synthase relies entirely on the electrochemical proton gradient, it seems like this might be worth mentioning, yet I haven't seen this explicitly explored in any textbooks. If there is any literature about this topic, I would love to see it.

Your description of it is largely correct, but the electron transport chain does not simply "dump" charged oxygen ions in the mitochondrial matrix. Instead, cytochrome C oxidase (complex IV) binds the O$_2$ molecule to one of its heme groups, and the reduction O$_2$ + 4 H$^+$ + 4 e$^-$ $\rightarrow$ 2 H$_2$O occurs at the heme group before water is released. Some more details on the enzyme is found here and here (or in any biochemistry book).

In theory you're right that producing water in the mitochondrial matrix would dilute the H$^+$ concentration there a little (along with the concentration of everything else). But this dilution is negligible: the mitochondrial matrix has pH $\approx$ 7.8, which is the same as a H$^+$ concentration of about 15 x 10$^{-9}$M, while the concentration of water (yes, there is such a thing ;) is 55 M. So adding a water molecule has virtually no effect compared to removing a proton.


What is this red orange insect with black dots found in Japan? I searched with picture to Google, and they suggest it might be

Fire-coloured beetle

I also went through the list of insects from this page, http://www7a.biglobe.ne.jp/~yabuyama/koucyuumoku.html, it is in Japanese. The bug that looked like the one in picture the most was a ベニカミキリ (latin name: Purpuricenus temminckii), but it did not have the black dots, and it seems too small.

The insect was found near a pond in a Japanese garden in Fukuoka, Kyushu in June. I do not recall the size of it, but I think it was somewhere between 1cm and 3cm long.

I was able to find it in an insect lexicon. It is all in Japanese, but the description fits the image. The insect is in fact a カミキリ、a ホシべ二カミキリto be exact. And the binomial name is Eupromus ruber

Here is also some more information https://www.insects.jp/kon-kamihosibeni.htm
And a Wiki page in english https://en.m.wikipedia.org/wiki/Eupromus_ruber


What is the neural coding of rod and cone cells? In Rushton's paper on the Principle of Univariance, he states:

  Thus, though the rod input has two variables, wave-length and energy, the output differs only in one respect, namely 'brightness'.

However, as far as I understand, a photon can only vary according to one dimension, namely wavelength (vibrational energy), because the wavelength and energy of a photon are interdependent.

This suggests then that the input to a cone cell, for brightness to be perceived (i.e. the intensity of light), must be a beam of photons, so that the input can vary in wavelength and amplitude (does this equate to the number of quanta being absorbed by the photopigment per unit of time?).

My question, then, is how can a discrete event (the changing of shape of a photopigment) encode a continuous value (i.e. intensity)?

Indeed, brightness is a matter of photon count.

In any given rod, there are numerous photopigment molecules. There are about 1 billion rhodopsin molecules in any given rod, so although a change in conformation of any single rhodopsin molecule is a discrete event, you can consider the fraction of 11-cis- versus all-trans retinal (a photoreceptor's initial readout of brightness) to be effectively continuous, even more so because there is a <1 probability of a photon of light being absorbed by any rhodopsin molecule, so the discrete measure itself is an approximation of the 'actual' brightness/photon count.

Although it isn't perfectly analogous, because here we are talking about proportions rather than actual bitwise encoding, consider that computers are also able to represent fairly continuous values, but they are still always discrete approximations to those continuous values. A 24-bit computer monitor, for example, can actually only display 256 different intensities for each R, G, and B color stream (8 bits each).

The principle being discussed in the paper you describe is that once a rod (or cone) absorbs a photon, it loses any information about what the wavelength was, only that it was sufficient energy to activate the rhodopsin in that photoreceptor. There are several other questions and answers here on Biology.SE that discuss how wavelength (i.e. color) information can be extracted by differential activation of different cone types, for example:

Why can cones detect color but rods can't?

How do our eyes detect light at different frequencies?


Ways to identify that proteins are regulating different genes experimentally As part of my study I have been given this hypothesis:

  HIF 1a and HIF 2a regulate different genes in multiple myeloma

What ways do we have to identify that these proteins are regulating different genes in multiple myeloma? I recall in lectures something being mentioned about using antibodies to isolate the regulatory elements, but can't find any specifics.

Any help is seriously appreciated!

Chromatin immunoprecipitation (ChIP) or ChIP-Seq are the first methods that pop into my mind. Essentially, DNA is cross-linked to bound proteins (transcription factors, histones, etc.) by various methods, then broken into pieces by either sonication or digestion with micrococcal nuclease. An immunoprecipitation is then performed by adding antibodies targeting your protein of interest (HIF-1α and HIF-2α in this case), allowing them to bind to their targets, enriching them using bead-conjugated Protein G (or Protein A), then reversing the cross-linking. The enriched DNA can then either be subjected to PCR for known genes (ChIP), or it can be sequenced and aligned with a reference genome to determine all bound sequences (ChIP-Seq).


Why is most tissue cellular? Most tissue is comprised of cells.  Why? It would seem inefficient to have so many individual nucleus, membranes, etc.?

Specifically: Not all tissue is cellular.  Much tissue is extracellular matrix.  Since the body can use noncellular tissue, what is the role of cells in cellular tissue?

Another way to ask my question: Do the cellular organelles directly contribute to the tissue and organ's function? Or are they just there to maintain the cell itself?

My hypothesis is:

In some cases, the cellular organelles directly provide the tissue's function.  Eg endocrine system - synthesized at the cellular level.
In other cases, individual cells function discretely in the tissue.  Eg, nervous or muscular tissue.
In other cases, the cell doesn't directly support the tissue's function.  But it's needed to grow and preserve the tissue.  Eg connective tissue.
And finally, in cases where preserving and growing the tissue is a small enough task, a small number of cells simply extracellular tissue.  Eg bone tissue.

The above is my hypothesis.  Is it correct? Fix, revise, or replace it with something better!

Since cells are the origin of every life, any tissue must at least be based on cells. Some tissue matter is outside the cells (plant cell walls), some apparently non-cellular tissue is really a bloated organelle. Both happens. As to your theses,

yes, an example are oil reservoirs in plants
no, these are just big cells. A striking example is spinal cord nerves that can be very long; irreparable if injured, because you can't repair single cells
connective tissue is cartilage, bone, adipose tissue, blood, hematopoietic tissue and lymphatic tissue. These together fit in both the organelle and extracellular substance slots, so you would have to differentiate
bone belongs to connective tissue

So, yes, you can differentiate between functions belonging to whole cells, cell organelles, or extracellular material. And there is no reason to narrow this question to humans.


T7 Tagging Next to Met Will a T7 tag still work if it is placed next to a start codon? Meaning, will it still work with a Met attached to it in the amino acid sequence?

Thank you!

By "still work" I assume you are asking if it will still be recognized by an antibody? It might. Internal T7 tag fusions are done, though they may require different antibodies than terminally tagged fusions.

That said, do you have a reason for inserting the the tag after methionine? The T7 tag already starts with methionine and naturally functions to initiate translation of T7 gene10. pET based vectors also contain it for this purpose.

[source]

In this vector, your gene of interest is typically inserted after the tag to create a fusion protein (using BamHI) or immediately after the start codon (using NheI). In either case, the T7 tag start codon is used.


DNA methylation on the forward vs reverse strand? I'm wondering if there are meant to be differences in DNA methylation between the forward and the reverse strand of the gene? I'm wondering because in primer design for bisulfite pyrosequencing one might only design primers for the forward strand. Should this matter for human/mouse DNA?

cheers and thanks in advance for any advice.

In most tissues, close to 100% of DNA methylation occurs at CpG sites. This provides a straightforward mechanism for epigenetic inheritance. Since C and G are complementary, both strands have the CpG site at the same locus and methylation is either present on both strands or on neither. During replication, each daughter DNA molecule inherits a parent strand with the (un)methylated CpG sites. Enzymes can recognise when there is asymmetrical CpG methylation and subsequently methylate the new strand where required. So, for CpG sites, both strands are methylated or not.

In embryonic and induced stem cells, however, ~25% of the total methylation occurs at non-CpG sites (especially CpA). Thus, methylation at a specific locus would only occur on one strand. As far as I know, how/if this methylation pattern is inherited has not yet been elucidated. Furthermore, this type of methylation occurs throughout the chromosome and is particularly high in exons whereas CpG methylation generally occurs upstream of a transcription start site.


Michaelis-Menten equation type - how it is derived? Can somebody explain how is the following differential equation found? It is about the blood alcohol content.

See this article (pages 3 and 4).

They say the concentration of blood alcohol satisfies (in the drinking phase): $$\dfrac{dC}{dt}=u-\dfrac{\alpha C}{C+\beta}\quad; \quad C(0)=0,$$ where $\alpha, \beta$ are the liver and the kidney parameters. For the Recovery Phase we have: $$\dfrac{dC}{dt}=-\dfrac{\alpha C}{C+\beta}\quad; \quad C=C_{max}.$$

I can't see how they came to these equations. The only thing they say about the origin of this model is that it comes from a continuity argument: the amount of alcohol that is introduced in the body, equals the amount of the alcohol that leave the body.

I wonder if there is a model which takes into account all parameters in the above article plus the amount of food in the stomach.

These kind of equations (the Michaelis-Menten [MM] like term) denote  saturation kinetics. The basic mechanistic assumption behind saturation kinetics is this:

A rate (of lets say product formation) is dependent on the concentration of a molecule such that the rate increases linearly with increase in the concentration of the molecule.

Example 1: Substrate in an enzyme catalysed reaction
Example 2: Transcription factor in a transcriptional activation

However at a certain point increasing the concentration of the molecule will have no effect on the rate of reaction. For the above examples this point will arrive when (respectively):

Active sites in all the enzyme molecules are bound and there is no more space to accommodate a new substrate molecule.
All the binding sites in the DNA are occupied by the existing TF molecules and no more can bind.

In other words, the reaction kinetics changes from first order to zeroth order.

We can provide mechanistic explanations for some cases but in many we do not know how exactly the saturation happens. In modelling we just use a function that will mimic this kind of behaviour.

  Why functions of the form $\dfrac{X}{K+X}$ ?

In deterministic modelling using differential equations, it would be preferred to use a continuous function (instead of using a piecewise linear function) because:

Numerical integration is better in case of continuous functions
In biochemical systems, operations are always continuous. There is no digital logic.

The MM function can actually be derived using an equilibrium or a quasi-steady state approximation (See the wikipedia page for the explanation).

In the MM function, when $X \gg K$ then the function is almost 1. This multiplied by the maximum rate constant will give you the max catalytic rate. At $X=0$ the rate will also be equal to zero. Note that in this model the catalytic rate will not indefinitely increase with $X$.

There are several functions that have values between 0 and 1 for increasing concentration of the substrate. Hill function and logistic function are common examples. However MM is a simpler model. You can always revise your modelling approach when you have better information of the biological system.

Now back to your question:

In this model $C$ denotes alcohol concentration $\alpha$ denotes maximum clearance rate and $\beta$ denotes half saturation concentration (concentration of alcohol at which the rate of clearance is half the maximum rate). Intuitively you can think about the mechanism like this: rate of clearance of alcohol depends on the level of alcohol i.e. if you have a lot of alcohol the amount of it removed per unit time will be higher. Think of it as water that is pumped through a pipe; more water in the tank will result in higher flow rate. However when the kidney (or pipe) is overloaded or "clogged" with an already excess of alcohol then clearance rate would remain the same (the maximum that the kidneys can excrete).

  the amount of alcohol that is introduced in the body, equals the amount of the alcohol that leave the body

That is called mass balance which can be summarized as follows:

Accumulation = Input + Production - (Output + Degradation)


How it is determined that a particular gene or set of genes is responsible for a trait? How it is determined that a particular gene or set of genes is responsible for a trait? Is it just a statistical analysis of people showing and not showing the trait and the genes they have (or don't have) and their variants (alleles)? Or, there is something more.

In the below list of technics, I am assuming we are talking about haploid individuals (to avoid discussion about dominance relationship) and assuming no epistasis but the technics can 'easily' be extended to include these cases. I also assume we are talking about coding regions.

Note that I am more of a biostatistician / population geneticist than a molecular geneticist, so I am pretty sure I will unwillingly bias my list toward what I know most. There is a lot to say about every single technic but of course, this cannot be covered in a single StackExchange post.

Technics

Statistical association (observational study) with existing variance in natural population. Do carrier of a given allele have another trait value than the carrier of the other allele. Possible confounding variables include population structure and linkage disequilibrium.

Population structure: To deal with this confounding variable, we can make a genetic PCA and include the first two axes as covariate in a type I sum of squares regression. We can also use tools such as STRUCTURE to infer the population structure and then use the inferred groups as a nominal covariate.
Linkage disequilibrium: We typically consider a number of marker that we try to associate to a specific phenotypic trait. It is impossible to tell whether the observed association is directly caused by the marker we observe or by a tightly linked marker. For further investigations below technics must be considered.

Statistical association (experimental study). It is possible to create the treatment groups by knocking out (or other technics such as the now popular CRISPR technic) specific gene in out in some individuals and look for a statistical association. The advantage of such manipulation is that we can create the optimal level of genetic variance we need to increase our statistical power.
Transcriptome analysis. Making sure the coding region is being expressed in the tissue of interest. E.g. if you expect a given gene to affect myosin tertiary structure, you might want to make sure the coding region is indeed expressed in the muscles and not only in the brain!
Protein action. It is also possible to study the specific action of the protein coded by the coding region of interest. Such studies typically require the study of an entire biological pathway and is often demanding and quite expensive. Here the methodology are diverse but they're discussion is both outside the scope of the question and outside the scope of my knowledge.

Example - Genetic Basis of Color Adaptation in mice

In a comment, you asked

  Is there any research paper, review paper or blog which covers entire details how the association and mechanism was established for any of those discoveries?

In most study cases, not all of the above steps are being considered. Also, even if it is the case, such study will be covered by several peer-reviewed papers and not a single one. I don't know of any peer-review paper that explains the whole process for a particular case but those probably exist.

There are documents that explain such process for layman. For example From Darwin to DNA: The Genetic Basis of Color Adaptations by Hoekstra is a standard reading for undergraduate that will interest you. It is easy and pleasant to read. Quoting from this article

  In this essay, we will take a journey — into the laboratory and the field — to understand the genetic basis of adaptation in natural populations of mice, and the phenotype we will focus on is the color of their fur.

The gene of interest in this paper is melanocortin-1 receptor (Mc1r). Depending on what level of understanding you want to reach, the article might be a bit too introductory but it refers to some good peer review papers that will allow you to further your knowledge.


Where in the world does blue eyed whites originate from? I know that there were no blue eyed people until ~6000 years ago due to a mutation and all blue eyed people have a single common anchestor.

But where in the world does it originate? I assume it originates from somewhere in Europe but is it known more specifically where like Scandinavia, Eastern Europe, and so on or is it impossible to know?

According to this discussion, blues first appeared exactly where one would expect - in northern Europe.

The interesting thing is the survival value (if any) that blue eyes offer. One theory is that blue eyes are merely a side effect of light skin. The other theory is that blue eyes are simply sexy and irresistible.


How would our circadian rhythm change over time if we had no sunlight whatsoever? Of course, over the span of a couple days, our circadian rhythms would lengthen a few hours. But what would happen to the circadian rhythms of humans overall if we had no daylight ever? Say we can live for 10,000 years, how would our circadian rhythm be different 10,000 years from now after zero exposure to sunlight? Would it still be slightly more than 24 hours?

Say we can live for 10,000 years, how would our circadian rhythm be different 10,000 years from now after zero exposure to sunlight?

Probably almost the same.

A circadian rhythm has - by definition - a free running period of more or less 24h. Of course this might change over time, but 10,000 years are not very much on an evolutionary time scale.

As an example there are some studies about the circadian clocks of fish that have lived in underground caves for over 1 million years: They still have a circadian rhythm (even though its doesn't react to light anymore), but even after 1million years the free running rhythm only changed from 24h to 47h. Interestingly it can also still be 'entrained' (synchronised) to other regular cues like feeding time (this is also the case for normal circadian rhythms).


How to model missing residues on a protein from multiple PDB files? I have multiple X-ray structures (PDB files) of the same protein. All of them have missing stretches of residues. I want to use all of them to build a single model, with as little missing residues as possible. Is there a tool (web-server, software) available to do this?

In a particular application, I have one additional requirement. One of the PDB files is special (call it the template), in the sense that I only want to add missing residues to it. That is, the resulting model should contain the special pdb file, and align perfectly to it, the only difference being that the resulting model has some additional residues that were completed from the information in the other pdb files. Okay, the resulting model should not align "perfectly" to the template. I'll allow some relaxation in the connecting points. But still, the idea is that the template PDB should carry a "larger weight".

So, those are the two problems: 1) How to reconstruct a more complete model from a bunch of PDB files of the same protein? 2) How to complete missing residues in one PDB file using information from other PDB files of the same protein?

I suggest you to use modeller - advance modelling (https://salilab.org/modeller/tutorial/advanced.html), Where you can use multiple template PDB to get final model structure.

All the best..:)


Can I change the genetics of a group of plants naturally? I have been thinking about introducing all sorts of types to certain environments where the plants will have to adjust to survive.

For example having a dark area with one light source right next to the plants so they all want to grow towards the light.. however this could be made more difficult by either introducing slight angle adjustments or artificial wind (custom controlled fans).

Would it be possible to start slowly introducing such challenges to change the plants? for example strengthen their stems to be able to fight the gravity or wind?

Of course, you can place a population of anything (incl. a population of plants) into a specific environment and you could expect this population to slowly adapt to it.

Most plants don't have a particularly fast generation time and therefore, the evolutionary experiment might take longer than your lifetime. The experiment would be much faster if you choose some unicellular algae such as Chlamydomonas reinhardtii for example.


how body doesn't make antibodies against adjuvants of vaccine? we know that all antigenic molecules don't have PRR on phagocytes and so they use an adjuvant that has a receptor for pattern recognation and fuse it with in order to phagocyte the antigen-adjuvant complex and present it on MHC II molecules for antibody syntheses now the question arises the phagocytes don't know which molecule is antigen and which is adjuvant then why MHC II molecules don't present the adjuvants for antibody syntheses and make the body sensitive against adjuvant and future vaccination should not be successful because the antibody recognises the adjuvant binds with it and not letting the vaccine to be processed?

Basically, this is what is happening when you receive a vaccine.

Immunoglobulins are being made agains protein adjuvants such as flagellin
Some of the adjuvants based on endotoxins such a lipopolysaccharides are not proteins. While there are some immunoglobulins produced that detect these molecules, the majority detect proteins
Most antibodies are produced against the functional conformation of the protein, so its tertiary or quaternary structure. When polypeptides are loaded into MHC II, it is a small piece of the primary sequence of amino acids. This is used to activate CD4+ helper T-Cells.
Vaccine is given in one of three ways; subcutaneously, intramuscularly, or orally (including nasally). Most antibodies circulate in the blood until they leak out of the blood vessels at the site of an infection. Also free antibody have half-lives of between 7 to 21 days, so even if there had been IgG in the tissue from a prior inoculation, it is unlikely that any will be at the site of the new inoculation without an inflammatory response taking place.

Oral vaccines will encounter IgA molecules in the mucus, so if they were made from a prior immunization, they could opsonize the vaccine, however, it is likely given in a high enough dose that some of the vaccine will reach the antigen presenting cells.

When delivered subcutaneously or intramuscularly, the vaccine will first be encountered by the innate immune system, even if adaptive immune cells were activated in previous rounds of vaccination. It is very unlikely that IgG will be encountered at the site of the inoculation, as IgG circulates in the blood and only ever really gets into the site of inoculation or infection after the innate immune cells have initiated an inflammatory response leading to the permeabilization of the blood vessels, allowing other immune cells and immunoproteins access to the site of the infection. Either way, APCs will be taking up the vaccine before the antibodies against them can neutralize them.

It is also likely a good thing that there are CD4+ cells in circulation that recognize a sequence of the adjuvant. If the B cell phagocytoses the vaccine and adjuvant, such as with a flagellin fusion vaccine, because there was specificity for an epitope on the target protein (vaccine), then even though the B cell is not making an antibody to the adjuvant, putting the adjuvant sequence on the MHC II means that it can be activated by a helper T-cell that recognized the adjuvant polypeptide, even if there is no T-cells that recognize the vaccine.


Why was it initially thought that Mendel's findings were contradictory to Darwin's natural selection? When I read about the modern evolutionary synthesis, the text said that it showed both ideas to be compatible, once thought to be contradictory. Would it be because Mendel described an element of "randomness" in character transmission, as opposed to the mechanism of natural selection originally described by Darwin, or is it something else? I do not yet have a big knowledge on evolution, so pardon any mistakes.

It's thought that Mendel's communications were anti-Darwinist, and some argue that his original paper was written specifically as a refutation of Darwin's descent with modification. Mendel believed species were created by God and not Darwinian evolution. Because of this, when he found a law defining constant probabilities of heredity, he saw it as more of an argument for the consitency of genetic information and thus species. To him this was in contrast to the ability of heritable traits to vary slightly in progeny, leading to selective advantages. Source I paraphrased: http://jhered.oxfordjournals.org/content/87/3/205.full.pdf


what does sequences overlap indicate what does it mean if different protein sequences overlap upon multiple alignment, are they the same, do they have a common ancestor, are they recombinants of each other
and how does one go on to prove this
many thanks

Expanding on the comment by @Chris:

Short Answer

Overlapping sequences imply evolutionarily conserved regions, i.e. preserved by evolution through time due to theirs having some important function.

Long Answer

Assuming the sequences are homologous, overlapping regions of similarity reveal "evolutionarily conserved regions".

These are regions in the protein sequence that are shared by the ancestors through ancestral history due to that shared sequence bearing some important function at the phenotypic level. Evolution acts to "preserve" the sequence through natural selection if that function was important for fitness (see Negative selection).

E.g. Perhaps the shared sequence codes for an active site for an enzyme that is shared by all the ancestors you are using in the multiple sequence alignment - natural selection will then prevent changes to that sequence from occurring.

Look at this online lecture for finer detail.


Any studies on the effects and/or benefits of oil pulling? A friend recently recommended me a process called 'oil pulling' for my teeth as I am struggling with my dental health at the moment. The process involves using a tablespoon of some kind of vegetable oil (like coconut oil) and swilling it around in your mouth for 20 minutes without swallowing. This supposedly acts as an anti bacterial and pulls toxins out of the body and helps with dental hygiene.

Are there any studies demonstrating or refuting its validity? Any help would be much appreciated.

This is a classical pseudoscientific claim: It is supposed to help against everything, including AIDS, Diabetes, Bronchitis, Cancer and so on. See for example this table I found online:

First, there is no real mechanism, and it is rather implausible to have an universal cure-all drug for all these completely unrelated diseases. There seems to be some weak evidence for the dental hygiene claims, but as the first reference writes, study groups where too small, not effectively blinded, so there is no final clue if this is true:

  Oil pulling’s positive effects are based entirely on anecdote and not
  at all on clinical research – because there’s been very little. Pubmed
  lists six clinical studies related to oil pulling, all performed in
  India, and their quality and results seem all over the map. Some do
  indicate mild improvement in gum health, comparable to mouthwash use.
  But they’re not well blinded, use very small sample sizes and involve
  oil pulling only as part of a proper oral hygiene regimen. So it’s
  impossible to tell what’s causing said improvement.

What clearly does not happen is the detoxification, as this is a pseudoscientific myth itself. Our detoxification is done pretty efficiently by liver and kidney, so there is no need to remove whatever toxin by a treatment.

See references 1-3 (especially 1) for background on the "oil pulling" and reference 4 for the detoxification.

References:

Oil Pulling: Miracle Treatment or Woo Mouthwash?
Oil Pulling Your Leg
Is Oil Pulling Effective for Curing Medical Ailments?
Fashionably toxic


Do blind people learn Braille equally fast as the sighted? The visually deprived brain undergoes extensive remodeling due to cross-modal plasticity. This leads to increased areas of the cortex being available for other purposes such as tactile processing. Now I am wondering if there is anything known about how long it takes for the blind to learn Braille as compared to normally sighted people?

I have had a very difficult time finding information that was well-written and what you were looking for. So, I did my best!

From what I have read it takes about four months - everyone is a little bit different and some take longer! Those of us with no visual impairment that try to learn it have no advantage and maybe a slight disadvantage with learning it... I know because I am trying to learn it. It does take a lot a patience and perseverance!

This is the article I referred to:
Learning braille; how long does it take and does it get harder with age?

Hope this was helpful!


Book recommended for neurobiology I am looking for a good explanatory book concerning Neurobiology. I am interested on how the brain works but prior to this I believe that I have to start learning things about the biology of neurons. So I searched on the net and found a book called "From Neuron to Brain" from John G. Nicholls et. al.

Actually there are so many books out there and because I have never worked on that subject, all these results are confusing me.

So i would like someone's opinion who has dealt with this subject to help me choose a book for beginners.

Thank you.

I can highly recommend Kandel's "Principles of neural science". I have not had any biology courses since highschool, but I was able to understand it well. It is really a book meant to teach. The style is beginner friendly, and not tedious/boring at all.

It is an expensive buy and a very long read (I think the paper version is close to 2000 pages), but given the complexity of the subject matter, I find it reasonable.

If you decide to go for it (or for any other neurobiology work, actually) get the newest edition. Getting an older one is a false economy here - our understanding of how this stuff works gets better by the year, and there is lots of missing (or sometimes even not-valid-any-longer) information in the older editions.

A few examples of what might make the book hard to understand for beginners

"Principals of neural science" does not require much preexisting biology knowledge. It is sufficient to roughly know that a cell has a nucleus, plasma with organelles swimming inside, and a membrane. But you have to be comfortable with a bit of biochemistry. This is an example passage concerning the behavior of ions in solution. I found this perfectly understandable with my prior knowledge, I don't know if you need brushing up on chemistry or not.

  The cell membrane is selectively permeable to K+ because the otherwise impermeable membrane contains proteins that form pores called ion channels. The channels that are active when the cell is at rest are highly permeable to K+ but considerably less permeable to Na+. The K+ ions tend to leak out of these open channels, down the ion's concentration gradient. As K+ ions exit the cell, they leave behind a cloud of unneutralized negative charge on the inner surface of the membrane, so that the net charge inside the membrane is more negative than that outside.

And then there are examples like this one:

  Isoprenylation is another post-translational modification important for anchoring proteins to the cytosolic side of membranes. It occurs shortly after the synthesis of the protein is completed and involves a series of enzymatic steps that result in thioacylation by one of the two long-chain hydrophobic polyisoprenyl moieties (farnesyl, with 15 carbons, or geranyl-geranyl, with 20) of the dulfhydril group of a cysteine at the C-terminus of proteins.

Here, my own chemistry is bad enough that I could only understand that a protein is modified by attaching some molecular structure to it, and this makes it possible to attach the protein to the cell membrane. The lack of understanding of the details (what is a geranyl-geranyl?) did not stop me from understanding the rest of the section, so I don't mind, but I know that there are readers who'd have a problem with that. Sadly, I don't know of a source which does not require such knowledge, and if you feel the need to know every single word, you might need to use a reference while reading, or start with a course in biochemistry first before switching to the neurobiology.

Finally, if you don't have a life science background, there might be words outside of the chemistry you might have to look up, or understand from context, but they will be unfamiliar at first. For example, I was surprised to see the word "process" used in the meaning of a physical protrusion from the cell body. But this is not such a high hurdle, you have to either read ahead and puzzle such words out, or use a dictionary. They are not so frequent to prevent comfortable reading.


How is the rate of transcription influenced by temperature? How is the rate of transcription influenced by temperature? More precisely, I am looking for an article who quantitatively measured the rate of transcription of an "average gene" and show how this rate is influenced by temperature.

On this question @Chris found this article where such measurement were performed but they were using some arbitrary unit (as it as been pointed out by @shigeta here) that cannot be related to any comprehensive unit such as "mole of amino acid per hours" or something like that.

If your looking at transcription then your talking about RNA POLYMERASE.

And there are many variants. Here's a good Nature paper that discusses temperature and RNA Pol

http://www.nature.com/ncomms/journal/v1/n6/full/ncomms1076.html

And another:

http://www.ncbi.nlm.nih.gov/m/pubmed/12729734/

I couldn't get full access to this JBC paper but I think the answer would be clearly in here, prob worth a look

M. Chamberlin and J. Ring. Characterization of T7-specific ribonucleic acid polymerase. 1. General properties of the enzymatic reaction and the template specificity of the enzyme. J Biol Chem. 248: 2235-44 (1973)


What conditions should I use for Gel Red staining? What are the optimal staining conditions when using Gel Red? So far, since we have started using it, the gels ran in our lab have been of very poor quality. The bands are very blurred and often indistinguishable. We have tried both pre- and post-staining, together with varying concentrations of Gel Red.

Any advice about how to fix this problem?

I have had success with 1.5% agarose gels in TBE pre-stained with gelred.  I use a 10,000x stock solution of gelred sold by http://biotium.com.  I visualize the gel on an old fotodyne UV transilluminator.

After melting agarose in the appropriate volume of TBE in a microwave, I let it cool to about 50 C (I can touch the flask with the back of my hand without snatching it away) and then add the appropriate volume of stock gelred.

For a 30 mL 1.5% agarose gel:

mix 0.45g agarose + 30 mL 1x TBE
microwave until agarose solution boils and clarifies
let cool to around 50 C
add 3 uL gelred
swirl the mixture
cast the gel (don't forget comb)

This typically works for me.  I run the gel in a 1x TBE buffer at around 120 volts.


Are there any side-effects from a mosquitoes extinction? Suppose that we have the ability to make mosquitoes extinct, what would be the likely effects (on disease and ecosystems for example) of such extinction? Essentially, what roles in nature do mosquitoes perform?

There was actually just such an article in Nature recently.

"They don't occupy an unassailable niche in the environment," says entomologist Joe Conlon, of the American Mosquito Control Association in Jacksonville, Florida. "If we eradicated them tomorrow, the ecosystems where they are active will hiccup and then get on with life. Something better or worse would take over."


Is cancer a defect of the immune system? Is cancer due to a defect in the immune system?

Cancer is uncontrolled division of abnormal cells. This is caused by mutations in a cell which causes a cell to divide more frequently and the lack of control by intracellular AND extracellular mechanisms. The extracellular mechanisms include growth inhibition by hormones, local factors, contact and also the immune system.

These cancerous cells could be immune system cells and then, in that respect, the cancer could be considered an immune system disorder. Or the cells could be of different origin, but due to the lack of a functioning immune system (particularly NK cells), the cells may divide uncontrollably whereas otherwise they would've been tagged for immune or self destruction. Or a cancer may be caused by a virus; in this situation an immunocompromised patient is more susceptible to a cancer caused by this oncogenic virus. In these cases the risk of cancer is increased due to a compromised immune system. So cancer risk may be increased in these circumstances but cancer still is not an immune disorder.


Could someone please identify this species? I have come across these insects a lot more lately, as far as I can tell, they can sustain a hover state in flight. I'm actually quite interested to know what these are, seeing they look like a cross between a bumblebee and a common housefly...

Looks very similar to Eupeodes corollae (Syrphidae). But only a specialist in the group will tell you if its the same species, genus or family. And not with that low-resolution photograph (sometimes they need to take the genitals off for proper identification).


Species that murder their own counterparts when put in captivity Mary Midgley writes in her book, Beast and Man (p. 54 in this eBook: https://goo.gl/3NnhtP):

  Lorenz gives chilling examples from roe deer and doves, in both of which species stronger members will slowly murder weaker ones if kept in captivity with them[...]

I find this fascinating but I was not successful in finding any more info on this phenomena on the internet.

Can any biologists point me into a good direction? I do not have the work of Konrad Lorenz at hand, and would not know where to exactly look for in them.

Thanks a lot!

Some individuals kill their own offspring (https://en.wikipedia.org/wiki/Infanticide) or eat their offspring (https://en.wikipedia.org/wiki/Filial_cannibalism) or their own siblings (https://en.wikipedia.org/wiki/Siblicide).  See this article about siblicide and fratricide in bacteria:  https://www.webmedcentral.com/article_view/4804.

Other conflict and killing between members of a population occurs in many species, including humans (https://en.wikipedia.org/wiki/Homicide), mice (https://sci-hub.tw/10.1111/j.1469-185X.1991.tb01147.x), and other primates (https://www.sciencedirect.com/science/article/pii/S0140175082920632).

Search "intraspecific killing" on Google or Google Scholar.

See also a similar question here:  Why social animals attack odd members of their own group?


Under what circumstances and why is terrific broth preferred to LB broth for E.coli growth? Terrific Broth will result in a greater density of cells compared to LB but I have certainly seen it isn't as effective for the protein production of certain proteins compared to LB or defined media. I was curious what other limits and constraints exist with TB.

Migrated and derived from Quora http://www.quora.com/Under-what-circumstances-and-why-is-terrific-broth-preferred-to-LB-broth-for-E-coli-growth

I have used terrific broth to grow up transformed E. coli so they grow faster.  Often people will conduct a transformation, screen the cells, and grow them up in broth for plasmid extraction.  This growth would be for 12-16 hours.  Instead a person could use terrific broth to grow up the cells and it would take may 6-8 hours for adequate cell density for plasmid extraction.  If you are trying to express a protein then I would go with LB.

Also, I learned recently that terrific broth is also preferred over LB when needing to express proteins after transformation.


What should be evaluated in food decomposition experiment? Briefing
Some days ago I noted that 3 cookies left on my desk since 3 months ago are still "fresh", and by that I mean... not spongy like some cookies that get soft after some time outside.
However this particular brand of cookies do get spongy, I'm not sure why don't these do!
I also noted that there is a cockroaches/flies infestation in a home nearby, so these are getting in my house, but none of those insects dare to eat the cookies.
So, I decided to make an experiment inspired in the well known experiment of Watermelon vs McDonalds Burger where a watermelon decomposes extremely quick, and the burger does not. This article even mentions one that hasn't decomposed after two decades!
I understand that watermelon decomposes so fast mainly because of the sugar/water that it contains, but that is another story, let me tell you what I want to do.
Problem
In this experiment the only notable variables taken into account were: Visual appearance (picture), and time.
For my cookies I want to do a similar experiment, but I want to know which variables should I consider, so far I only have these in mind, but I want to know what else can be considered for food products:

Date of packaging
"Best before" date label
Visual appearance (daily pics)
Time gone by before going spongy
Humidity of room (3 daily measures across the day)
Temperature of room (3 daily measures across the day)

And the samples will be:

Being in a closed room (eg. my room)
Being in an open room (eg. dinning room)
Exposing to insects directly (eg. roaches, ants, flies)
Adding a drop of "morning saliva" (mainly for the bacteria)

Question is
In general, what do I need for food experiments? I think these are OK, but maybe I'm overdoing it on some, and maybe I need to consider some other parameters.
My experiment's objective is to see if it decomposes, why does it take X time to do so, or why doesn't it decompose at all, if it is safe to eat, or if it shenanigans like McBurgers.

You could weigh the cookies in a time course to see how quickly the cookies are degraded. Also, you could take some samples and make cultures in Petri dishes to see if there are differences in the microbiota associated with each one. In this line, maybe you'd want to sterilize the samples by some means, just to ensure they have the same microbial conditions. You could also measure the porosity of the samples by pacing them in water and measure how much water it can absorb, or something like that. I assume you do not have an HPLC engine, but you could also make extracts and see how the spectra varies over time.


Is apparent competition a suitable term in situations where one species is not negatively affected? When two prey (or resource) species share a common predator (consumer), they can be in apparent competition. An increase in one prey species can increase the common predator density, which negatively influences the other prey species.

A textbook (Molles, Seventh edition, ISBN-10: 0077837282) gives an example of apparent competition that confuses me. It gives another definition "one species facilitating populations of a predator or herbivore of the second species." Thus, one of the species does not have to be consumed by the predator/herbivore.

The specific example is that there are two plant species. Species A becomes the habitat for the herbivore (but is not consumed by the herbivore). Species B is consumed by the herbivore. Therefore, an increase in species A will increase the herbivore density and has negative effects on species B. I thought that to form an apparent competition relationship, it has to be mutually negative relationship (-,-).  In this example, there is no mutually negative relationship. Furthermore, the plants do not share the common herbivore.

This is simply a definition question. Different sources have variable definitions, but is the example really considered an apparent competition?

Competition-like interactions where only one species suffers ([0,-]) are usually labelled amensalism, so a suitable term for the situation you describe should be "apparent amensalism". I hadn't actually seen this term in use from before, but a quick Google search reveals that is in fact used. One example is in Jaworski et al. (2015):

  Indirect interactions mediated by shared natural enemies are known as apparent competition, if negative interactions are reciprocal, or apparent amensalism, if one prey suffers from the presence of the other prey (Holt 1977; Holt and Lawton 1994).