Why does maintaining contraction of muscles require ATP? So from my understanding, if I maintain the contraction of my muscle, the myosin head will be bonded to the actin. Why is ATP needed to maintain this bond?

Actually, it is not. ATP releases the myosin bonded to the actin, so when it is absent, the muscle remains contracted. This is, actually, precisely what happens during rigor mortis after death.

However, as long as you are alive, on a molecular level this is a dynamic process - actin release and bonding - and maintaining it requires energy. Moreover, muscle relaxation is not achieved by stopping the ATP flow, but incurrs additional ATP cost - it happens by actively removing calcium ions required to enable the actin to bind the myosin.


What is this long cylindrical white fruit called? Location: West Bengal, India
Temperature: 27 °C
Weather: Survive all seasons, although it was raining today
Length: 35 cm (although it can be small or big typically 10 to 40 cm length), girth:10 cm
Weight: 1 kg (estimate)
Appearance: Cylindrical in shape, the outer shell is very hard, color  of shell is typically white to pale yellow(the dark patches is due to mud and dirt). It is really tough to crack the shell but the inside (I believe) is pulpy and fibrous but dry.
Extra information: Not edible (never tried to eat), no smell emitted, colloquially called "monkey's club"(in native language), typically hangs on branches of trees in groups (typically 4 to 6 together)

It appears this is a Kigela (and commonly referred to as a "Sausage tree" in English).

It is - as you suspected - considered inedible and even poisonous in its fresh form (but apparently it can be dried or fermented). It has, as you said, a hard shell which can make this fruit usable as a container after it is hollowed-out.
The wikipedia article on this tree says it grows throughout tropical Africa, but looking at iNaturalist, it has been observed growing all over the world:


What is a tardigrade "in tun form"? While reading this article about tardigrades that had been previously frozen, I came across some verbiage I wasn't sure of and couldn't find any real explanation given the context. The article kept making mention of the tardigrades "in tun form", yet the only references I could find to the meaning of tun dealt with weight or casks (like for holding liquid).

So does tun mean cask (like a casing) in this context?

From Illinois Wesleyan University:

  One way in which tardigrades have adapted to various types of
  environments, has been to reversibly suspend their metabolism. This
  state is known as cryptobiosis [ 'hidden life' (Clegg, 2001) ] and is a truly deathlike state.
  Metabolism lowers to 0.01% of normal or is entirely undetectable and
  the water content of the body decreases to less than 1%. [...]

  The most intensely studied type of cryptobiosis is anhydrobiosis, a
  form of cryptobiosis initiated by desiccation. [...] Anhydrobiosis is an almost complete
  loss of body water and the animal can stay in this state for an
  extended period of time. Tun formation, a vital part of the process [Fig. 1.],
  results in a body that is constricted and folded. The first step is
  invagination of the limbs, longitudinal contraction of the body, and
  infolding of the intersegmental cuticle. Wax extrusion covers the
  surface and may help to reduce transpiration (water loss by
  evaporation). The tun formation process requires active metabolism. [...]

Fig. 1. Tardigrade before and after entering the tun state. Note the decreased body length and infoldings. Source: Media & Society Journal.

Reference
- Clegg, Comp Biochem Physiol B Biochem Mol Biol (2001); 128(4): 613-24


Functions of the CFTR gene? I am a senior in high school and I am studying cystic fibrosis.

I don't quite get the function of the CFTR gene as this is my first time dealing with this type of heavy scientific  info.

I had searched up its function on a website like this:
http://omim.org/entry/602421?search=cystic%20fibrosis&highlight=fibrosi%20cystic

By reading the gene functions section, I learned that CFTR regulate the formation of a chloride channel, changes the regulation of other transport pathways (i.e increase sodium ion absorption in sodium ion absortion). At the same time it also regulate the chloride-coupled bicarbonate receptor. And that is about all I got from that section.

I would greatly appreciate if someone can summarize all the functions of the CFTR gene listed in layman terms (i.e grandma language)  and also explain to me why decreased  chloride channel leads to thicken mucus or increase sodium ion absorption leads to CF Symptoms. In addition I would also appreciate it if someone can tell me does decreased CFTR gene function also lead to other diseases on top of Cystic fibrosis.

Thanks

CFTR is the gene which encodes the "Cystic fibrosis transmembrane conductance regulator", which is a membrane protein. Its function is to transport chloride and other negatively charged ion like thiocyanate ions from the inside of the cell to the outside (into the extra cellular space). This happens along a gradient, meaning the ions flow from the place of high concentration (inside the cell) to the place of low concentration (outside the cell). Since this would mean that a negative charge would build up on the outside of the cell, positively charged sodium ions follow the chloride ions by passive diffusion. This ions are secreted into the mucus in the extra cellular space.

This leads to a higher concentrations of electrolytes (salts) outside of the cell, which causes water to leave the cell (following the higher concentration of electrolytes), which makes the mucus thinner.

When the CFTR gene is mutated, this function is impaired and ions cannot be transported across the membrane. This causes a higher electrolyte concentration inside the cell and water stays there. This causes the mucus to get thicker (due to less influx of water), which then can block fine channels of the lung. Additionally bacteria can grow in the thicker mucus, which can cause severe problems as pneumonia. The process functions as shown in the figure below (from here), the sodium ions are not shown here:

If you want to read further about cystic fibrosis, I recommend this website.

Regarding the immune system there are different functions affected. First, the reduced (or prevented) secretion if thiocyanate ions lead to a reduction in the production of Hypothiocyanite ions which kill bacteria. Then different cells which are of importance to a proper immune reaction are impaired in their function, as shown in the figure below (from the first reference):

The function of CFTR is impaired in all cell types, not only in epithelial cells in the lung (although these are the most obvious consequences). In the cells of the immune system (T-cells for example) the intracellular ion concentration is disturbed including Ca2+ which plays an important role in the regulation of other genes. Other observations show that the activation of the immune system itself is also affected.

Further informations can be found in the articles I linked below. They require some knowledge of immunology, but when there are question, ask.

References:

Immune Responses in Cystic Fibrosis
The innate immune system in cystic fibrosis lung disease


If dinosaurs could have feathers, would they still be reptiles? I just finished watching a video where it was mentioned that nowadays birds are dinosaurs and non-avians dinosaurs could have feathers.

I confirmed this from wikipedia:

  Birds are highly advanced theropod dinosaurs, characterised
  by feathers, a beak with no teeth, the laying of hard-shelled eggs, a
  high metabolic rate, a four-chambered heart, and a lightweight but
  strong skeleton.

And:

  Direct fossil evidence of feathers or feather-like structures has
  been discovered in a diverse array of species in many non-avian
  dinosaur groups, both among saurischians and ornithischians.

And this family tree of reptiles mentions:

  Archosauriformes (crocodiles, birds, dinosaurs and extinct relatives)

And later in the Mesozoic era:

  The dinosaurs also developed smaller forms, including the feather-bearing smaller theropods.

So, were these non-avian dinosaurs with feathers actually reptiles?

Source of information on Biology.SE

This answer offers an introduction to phylogeny on the case study of dinosaurs and birds. If you are not at ease with the concept of monophyletic group, you should definitely have started with this introduction.

This post is somewhat related.

Origin of your misunderstanding

The question is all about nomenclature (and a little bit of semantics). One can call reptiles whatever (s)he wants. The question is what do we define as being a reptile? And the answer is that there are two possible definitions, a common "bad" definition (Definition 1) and a phylogenetic-based "good" definition (definition 2). I think your confusion comes from the use of the same term to mean two different (but related) things.

Definition 1: reptiles

In general, when people talk about reptiles, they talk about turtles, Rhynchocephalia, Squamata and Crocodilia. In this sense, the term reptile is NOT a monophyletic group. In other words, all species being called reptiles (according to this definition) do not share a common ancestor who has no other descendants that the species being called reptiles.

Definition 2: Reptilia

However, there is a defined monophyletic group called Reptilia. Reptilia is a group that contains all Amniota except the Synapsida (mammals and their extinct close relatives). In other words, Reptilia contains all generally called reptiles (as defined above) and all birds as well as all extinct species that are descendent from this same common ancestor.

Exploring the tree of life by yourself

You will find the tree of life on tolweb.org or on onezoom.org (see The best free and most up to date phylogenetic tree on the internet? for more info).

Using tolweb.org: here are the roots of the tree of the Amniota. And you will probably want to search for the Dinosauria (there) and see how closely related they are to the birds but not so much to the turtles.

Addressing your question directly

  If dinosaurs could have feathers, would they still be reptiles?

If by reptiles you mean Reptilia, then whether a given dinosaur has feathers, endothermy, or an exoskeleton (!) doesn't change anything to the fact that this dinosaur is a reptile.

If by reptiles you mean turtles, Rhynchocephalia, Squamata and Crocodilia, then whether a given dinosaur has feathers or not doesn't change anything to the fact that this dinosaur is NOT a reptile!

Known Dinosaurs with feathers?

Given that birds are the only animals that have feathers and that birds are dinosaurs, we don't know of any species that has a feather that is not a dinosaur! However, when we think of dinosaurs, we usually don't think about a pigeon.

Of course, the Archaeopteryx had feathers too. Archaeopteryx is an avian (bird-like) dinosaur.

But even non-avian dinosaurs such as Velociraptor probably had feathers as well. More info about how closely related is Velociraptor to the birds (Aves) there on tolweb.org. You probably remember the so-called Velociraptor from Jurassic Park movie (on the left) but here is what a Velociraptor probably really looked like (on the right).

The "velociraptors" from Jurassic park actually look more like a large Deinonychus without feathers than a Velociraptor (Thank you @Gaurav in the comments). However as Deinonychus is much harder to pronounce and way less sexy than Velociraptor, they chose to use Velociraptor in the movie Jurassic Park and deceived an entire generation about what a Velociraptor is! More information about what the species of Dinosaurs the Jurassic Park movie features in the youtube video (in French): Le Vélociraptor from Max Bird.

You might want to have a look at the post Were there any flying dinosaurs? that is very related.

At least, all these big and extinct things with scales are dinosaurs, right?

Well.... not exactly. There are species that you would probably call dinosaurs that we typically don't consider as dinosaurs. Have a look at the MinuteEarth video called "What makes a dinosaur?" for more information in this regard.

Fun and instructive videos

Les dinosaures ont disparu ? from Max Bird and Jamy (in french)
Le Vélociraptor from Max Bird (in French)
What makes a dinosaur? from MinuteEarth


Simplified molecular-input line-entry system This may be a bit abrupt/vague question, but I didn't know how to proceed the search to get the answer.
What are the properties of a 3D biomolecule which gets ignored when a 3D biomolecule is converted to 1D representation in SMILES(Simplified molecular-input line-entry system)? two properties I found that gets neglected are linkages,interaction properties. By properties I meant isomeric count,isomeric threshold etc. Are there anymore properties that gets neglected?

A 3D model of a (bio)moelcule represents a physical 3-dimensions. For an experimental structure, each atom has a 3D coordinate (x, y, z) and, if determined by crystallography, an additional isotropic or aniosotropic B-factor (that models atom fluctuations).

A '1D' SMILES is not a physical 1-dimensional representation, and can be converted to a graph (mathematics) representing the chemical structure. The specification of SMILES CAN retain information about structural isomers, stereoisomers (cis/trans; D/L), but not conformers/rotomers, which, unlike smaller chemical structures, IS restricted to certain favorable regions for larger biomolecules.

By "linkage" if you mean chemical linkage such as a disulfide bond, then SMILES can retain such information. By "interactions", if you mean hydrogen-bonding, salt-bridges and even hydrophobic interactions etc., then SMILES does not code in such information, but neither does a 3D model explicitly -- they are implied from the 3D coordinates for each atom.

Thus, converting from a 3D model to SMILES, you would lose

Unusual bond length and bond angle: they are necessarily specified from the 3D coordinates, but in SMILES (or the subsequent graph), they are taken as 'ideal'.
B-factor or temperature factor
Rotomers: e.g. Proteins have favored dihedral angles in both backbone and side chains, which is not specified in SMILES.
"Interactions": certain intramolecular interaction that is inevitable (e.g. salicylaldehyde) is implied in both SMILES and a 3D model. Most others can only be inferred in the 3D model.


Examples of plant families that contain species that are safe for human consumption and species that are poisonous to humans? I am trying to make a point to someone that just because two plants share a family and one plant is safe for human consumption, it does not follow that the other plant also is safe for human consumption. Can anyone provide an example I can use as proof?

The most classic example if you want to win this argument would be the family Solanaceae.

Also referred to as the Nightshade family, it includes the deadly nightshade or Atropa belladonna and many other plants not safe to eat.

Other members of the family are tomatoes, peppers, potatoes, and more.

Plant families can be massively diverse, and toxicity doesn't really have much relationship to family. Most of the compounds that are found in plants that are toxic are found in other non-toxic plants as well: dose is crucial.


Absorption ratios 260/280 and 260/230 for RNA I extracted RNA from different cell lines, an I want to perform reverse transcription and then PCR. To get good results, in which range should the absorption ratios 260/280 nm and 260/230 nm be? And what is the idea behind measuring those ratios?

I got values for the 260/280 ratio from 2.1 to 2.13 and values for the 260/230 ratio from 0.98 to 2.01. Are these values acceptable, and what information can I gain from them?

DNA and RNA absorb at 260nm. Proteins absorb at 280nm. The 260/280 ratio is a good estimate of how pure your sample is. For RNA, the 260/280 should be around 2. If it is lower, this might be an indication from contamination or proteins, phenol, or other contaminants in your sample. The 260/230 ratio is a second measure for purity of the sample, as the contaminants absorb at 230nm (like EDTA). The 260/230 ratio should be higher than the 260/280 ratio, as it is usually between 2 and 2.2. Lower ratio might be an indication of contamination.

In your case, I would be worried about the purity of the sample which gave you 260/230 ratio of 0.98. If you are using nanodrop, looking at the plot can also be a good indication of the quality of your sample. For a pure sample, a well defined peak (no shoulders or wiggles) at 260nm is expected.

Take a look at the NanoDrop manual for more information.


How is e-value calculated in BLAST 2 sequences (BLAST+)? In the BLAST+ packages, you can align two sequences instead of searching a database:

tblastn -query seq1.fa -subject seq1.fa

The web BLAST documentation states that e-values are calculated from the nr database:

  Because BLAST 2 Sequences uses the size of the current nucleotide or protein nr database to calculate Expect values, you may need to significantly increase the Expect threshold in order to see shorter alignments.

However, the command-line documentation explicitly states that you cannot provide both a database and a subject sequence:

-db <String>
BLAST database name
 * Incompatible with:  subject, subject_loc
-subject <File_In>
Subject sequence(s) to search
 * Incompatible with:  db, gilist, seqidlist, negative_gilist,
   db_soft_mask, db_hard_mask

How is the e-value calculated when using BLAST-2-Sequences on the command line? (I am fairly certain I do not have the nr database downloaded.)

Thanks!

You do not need the nr database for BLAST to calculate an E-value.
It will be calculated based on the alignment of n sequences.
The exact procedure is mathematically complex but if you want to read the original paper it is here:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC53667/pdf/pnas01031-0226.pdf

a simplified version you will find here:

http://homepages.ulb.ac.be/~dgonze/TEACHING/stat_scores.pdf


Why arent mosquitoes found near neem trees? I read an article yesterday that wherever neem trees or spices are cultivated mosquitoes are not seen there. So why arent  mosquitoes seen near these places (neem trees , spices, etc).
What is it that prevents mosquitoes from living near these places?

The growing accumulation of experience demonstrates that neem products work by intervening at several stages of an insect's life. The ingredients from this tree approximate the shape and structure of hormones vital to the lives of insects (not to mention some other invertebrates and even some microbes). The bodies of these insects absorb the neem compounds as if they were the real hormones, but this only blocks their endocrine systems. The resulting deep-seated behavioral and physiological aberrations leave the insects so confused in brain and body that they cannot reproduce and their populations plummet.

In case of a regular (house) mosquito, the effects of neem are as follows:
1. Retardation of growth
2. Inhibition of feeding
3. Eggs are unable to hatch

Apart from this, larvae of a number of mosquito species are sensitive to neem. They stop feeding (as mentioned above) and die within 24 hours after treatment.

Studies regarding your question are still in process so it's hard to narrow down to one exact reason.

Sources referred: The National Academies Press


How to recognize a conserved motifs of the protein I would like ensure that my reasoning is correct. Assuming that I know the aminoacids sequence of the protein of interest. I can't say anything about the structure looking only at the aminoacids sequence of this protein. But if I know this protein from another organism and the structure of this protein is known, then I can compare both of the sequences and conclude something, right? what I mean, is that there is no specific sequence corresponding to, for example, helix-two- turn-helix motif, and that I can take this sequence, check if my protein has it and say that there is helix-two- turn-helix motif or not. I can do this only by comparison to the protein which structure is already known, right?

It seems to me that you're asking about homology modelling. In that case, yes you need to compare your protein of interest to a protein (or proteins) of known structure. Homology modelling in a nutshell includes three (four?) steps: template identification/template alignment, modelling, quality assessment.

You start with finding a template for your modelling. This is usually done by sequence alignment, for instance BLASTing. Preferably you use multiple sequence alignment which more sensitively aligns conserved regions. You then want a template with as high sequence identity as possible (above 50 % usually produces models with about 1 Å RMSE [1] in main chain atoms. Avoid less than 30 % where modelling errors rapidly increase.)

There are then a number of different modelling strategies (wikipedia). But basically, they all aim to predict the structure of the conserved protein core as well as possible (which usually is what you're really interested in). Peripheral amino acids are more dynamic and more prone to evolution and are therefore more difficult to predict. Then, most importantly, you assess the quality of your model. This can be done by calculating violations of statistical potentials or physics based conformational energies (or using more advanced methods like multivariate regression methods). As in all modelling, this really is a most crucial step because prediction with a poor model is misleading and utterly useless.

If you don't find any template you could resort to the exciting field of De novo protein structure prediction, where the aim is to predict the structure from the amino acid sequence alone. I am not very familiar with their methods, but de novo prediction is hard (!). I don't remember any exact numbers but the number of conformations in a normal sized protein is astronomically large, which leads to great algorithmic and computational challenges. Additionally, without any reference sequence the model assumptions are greater than those of homology modelling. Although, I have heard that the field has been making great progress the last few years.

Edit:
It struck me that you might be asking about protein fold recognition as well. There exists a large number of different tools and methods for recognizing and locating protein domains using the amino acid sequence as input. Many of them are available as web servers. For instance phyre which uses the amino acid profile and predicted secondary structures to search structure libraries. Threading based methods like MUSTER. A number based on Hidden Markov Models (HMMs) also exist. For instance FISH which uses structure anchored HMMs.


What fish (and/or shellfish) species with a multi-year life-cycle, besides salmon, die after spawning? Most species of salmon die after spawning. Are there any other types of fish that spawn once and then die after a multi-year life-cylce? Is this a rare life history strategy among our human exploited marine species? Googling this question only yields articles about Salmon.

Many species of Eel (order Anguilliformes) have a semelparous life history (most species? all?), i.e. they only reproduce once and then die (as opposed to an iteroparous life history). Many species are now threatened by extinction (e.g. American eel and European eel), since they have been heavily exploited by fisheries and they are also vulnerable to habitat modifications (e.g. hydroelectric dams) and pollution. The nature of their life history was also unknown for a long time, since they migrate and spawn in the Sargasso Sea after living many years in fresh water (so the opposite migration path compared to Salmon), which is called a catadromous life history. However, there are also many species of eel that are strictly marine, for instance the very large Conger conger, but many of these species still migrate long distances before mating.

(American eel, Anguilla rostrata, picture from Wikipedia in public domain)

As a fun sidenote, captive eel can become very old, and earlier this year a more than 155-year-old European eel that was kept in a well died (see newsstory) - the oldest known eel from what I know. Eels were often put in wells because they were believed to keep the well water clean.

Semelpary is also found in other fish species, for instance in the Smelt (Osmeridae) family, where many species are fished commercially. Some (most?) species in the family have multiyear life histories, but some, e.g. the Delta smelt (Hypomesus transpacificus) only live for a single year. Similarly to Salmon, Smelt also migrate from sea to freshwater to spawn, i.e. an anadromous life history.

Overall, less than 1% of teleost fish are semelparous according to Finch (1994) - see link for more examples of semelparous fish species and background. However, this figure is most likely uncertain, given that we know very little about the life history of many marine species. In some cases, you can also find a range of life-history strategies from semelparous to partially or totally iteroparous within the same species, depending on ecological context. Nevertheless, the low overall proportion of semelparous fish means that semelpary is generally a rare life history strategy in human exploited fish species.

(Delta smelt, Hypomesus transpacificus, picture from Wikipedia in public domain)


Mass production of bacteria Is there a way to mass produce a certain species of bacteria?

Answers I am looking for should not involve a Petri dish: I am only interested in protocols involving, perhaps, more efficient mediums to grow the bacterium-in-question.

Is it done with any yet? In a factory or where etc?

How is it done?

The fed batch culture is a means of bacterial production that is used in industrial setups. Nutrients are fed into the chamber with controlled ideal conditions for growth of a particular species of microorganisms.

Upon reaching the desired yield temperatures can be increased (depending on the species of bacteria) to facilitate spore formation for eventual harvesting.


Alternatives to ethidium bromide for staining small nucleic acids? While ethidium bromide works well for staining larger single-stranded RNA or double-stranded DNA molecules, it doesn't stain smaller nucleic acids very well. I observed that at around 20 bases and below single-stranded nucleic acids are difficult to see with EtBr-staining unless the nucleic acids are highly concentrated.

What are good alternatives for observing small nucleic acids in polyacrylamide gels? The main consideration would be ease-of-use, and it should be possible without any unusual equipment.

A list of dyes is available here and a list of dyes specific to nucleic acids is available here. I think you have two choices the SYBR Gold nucleic acid gel stain (S11494) which can be detected under UV light (not sure if it can be used with polyacrylamide gels). Your other option which can be used with polyacrylamide gels is the SYBR Green II RNA gel stain (S7564, S7568, S7586), this stain can be detected with UV light post-electrophoresis. It states RNA in the name but it can also be used for ssDNA.

Hope this helps


DNA polymerase in PCR (polymerase chain reaction) Can the DNA polymerase in PCR (polymerase chain reaction) recognize both DNA and RNA for use as a template?

I want to know is it possible if my primers bind to contaminant RNA and then any DNA polymerase like Taq DNA polymerase use this strand as the template for elongation?

No, this does not happen, as the DNA polymerases used for PCR are DNA dependent. This means that they only synthesize DNA when it is bound to DNA. Even if your primers bind to the RNA, the polymerase will not starting new strands here. To use RNA as a template for PCR you first need to reverse transcribe it.


What can saliva tell about ones health? I was wondering if I d want to analyze something related to my current health based on my saliva. What could it be?

I mean e.g. by putting a thermometer in your mouth you can know your body temperature and know whether your immune system is eventually fighting some disease. But as you already have that apparatus in your mouth I think it would be usefull to prelevate some saliva (hit two birds withone stone) or other stuff in order to eventually easily investigate ones health.

Well, saliva (or the rate of production of saliva in your mouth) can tell you a lot about health, but the information you acquire is extremely general, so it won't really give you an entire health analysis in terms of diseases, sugar levels, body temperature, likewise.

As for what saliva does tell about your health, here is an extract from a source:

  "Dr. Stuart Froum, president of the American Academy of Periodontists, says: “If the eye is the window to the soul, the mouth is the window to the body.” Saliva in the mouth is one of the best indicators of health. If something is off, there is a good chance your saliva will change as a direct reflection.

  Saliva is produced around the clock and is affected not only by every bite of food you take, but also every other thing you put in your mouth. If you notice your saliva is too stringy or thick, your body might be having a hard time producing saliva. This could be because of the prescription and over-the-counter medication you are taking.

  Studies indicate that an imbalance of the ‘stress hormone’ cortisol in saliva points to emotional sensitivity to stressful situations...the measurement of cortisol in saliva is becoming increasingly acceptable as a screening test for hypercortisolism, such as depression, hypertension and diabetes.

Source: http://healthtoday.com/5-things-your-saliva-can-tell-you-about-your-health/
http://www.medicaldaily.com


What cell types produce immunoglobins and where are those cells found? I know B cells found in bone marrow produce immunoglobin G.  But IgM is produced in mucosal cells at least in the gut.  Can you find immunoglobin expressing cells in other tissues in the human body?  Are B cells or IgG mRNA ever found in blood or tissues?

First: B cells do not produce antibodies, but rather they synthesise the B cell receptor. This may sound a bit picky, but is not, since the B cell receptor is anchored in the membrane of B cells and not secreted. Its this receptor which recognizes antigens and causes the production of highly specific antibodies (including somatic hypermutation and all related processes).

Antibodies are produced by plasma cells (and that basically the only thing they do), which are differentiated from activated B cells which have undergone the selection process on the given antigen.
IgM is the first set of antibodies produced by the mature B cell, later on this often changes to IgG (different heavy chain, same antigen recognition site) by class switching.

The secreted antibody is IgA, which is found basically in all body fluids and is also secreted into the different mucosas of the body. It has two subtypes: IgA1 and IgA2 with A1 mostly present in the serum and A2 mostly secreted (see: "IgA subclasses in various secretions and in serum." for details).
IgA is made by plasma cells which are located in the lamina propria adjacent to mucosal surfaces. For details see thesetwo papers:

Intestinal IgA synthesis: regulation of front-line body defences.
The polymeric immunoglobulin receptor (secretory component) mediates
transport of immune complexes across epithelial cells: a local
defense function for IgA.

B cells (and also plasma cells) are found in the blood, they are then called peripheral cells. B cells have to be present outside the lymphatic tissues (not only bone marrow but also lymph nodes and the spleen) to be able to get in contact with antigens. Upon contact with an antigen they move into the adjacent lymphatic tissue.
You will not find IgG mRNA in the blood, as this will trigger immune responses. And it has no function outside of the cell.


How does a microelectrode work? On Wikipedia, the entire microelectrode page states only the following:

  A microelectrode is an electrode of very small size, used in electrophysiology for either recording of neural signals or electrical stimulation of nervous tissue. Initially, pulled glass pipette microelectrode was used with later introduction of insulated metal wires. These microelectrodes are made from inert metals with high Young modulus such as tungsten, stainless steel, platinum and iridium oxide and coated with glass or polymer insulator with exposed conductive tips. More recent advances in lithography yielded to silicon based microelectrodes.

Can someone provide a more elaborate explanation of how it works?

Like ideally, I would like something as specific as the usual descriptions you see in introductory chemistry books for how emf works in a battery. In other words, I know how electric potential works, but I am not understanding the exact mechanism of the microelectrode works.

If there are many types of microelectrodes, just give me the properties of one involving small shafts of hollow glass filled with a conductive salt solution.

Pictures would be great.

A microelectrode is quite literally a small electrode and they come in a variety of shapes.

The glass pipette electrode you are specifically referring to is mostly used for patch clamp experiments. Patch clamp experiments are performed using various configurations:

Source: Leica

So basically there is the cell-attached configuration, where a patch of cell membrane is sucked slightly into the pipette. Upon stronger suction the membrane is ruptured and the whole-cell patch clamp configuration is obtained. Here, access is gained to the cell, but a high-impedance seal is maintained between pipette and cell membrane. Lastly, there is a configuration where the patch is broken off the cell to exclude effects of the entire cell. This patch configuration is often used to obtain single-channel recordings. Dependent on the exact technique an inside-out or outside-out patch configuration is reached (see the picture above).

Hence, the glass pipette is basically only there to obtain a proper seal (cell-attached), to gain access to the cell (whole-cell), or to break off a piece of membrane. Notably, in whole-cell mode the pipette provides a means to administer compounds into the cell (think ions or drugs).

The recording electrode is situated inside the pipette and is a simple metal wire (platinum or platinum/iridium) and nothing different from any microelectrode as you rightfully state in your question. The electrode wire simply picks up a voltage difference (or current flow) between the interior of the cell (in whole-cell mode) and the exterior. The exterior is measured using a reference electrode outside the cell.

Furthermore, current can be injected to stimulate the cell, or to current-clamp the cell at a specific current. Likewise, voltage can be applied to voltage-clamp the cell. Therefore, an inert material is often chosen such as platinum or platinum/iridium to maintain integrity and prevent electrolytic breakdown. Electrodes are made out of metal to provide a low-resistance means to pick up currents or voltage-differences.

Voltage differences or currents can be amplified with an amplifier, registered and analyzed. See the following picture for the basic recording setup:

Source: Robinson et al. (2013)

Reference
 - Robinson et al. Front Neur Circuits 2013; 7: 1-7


Is the "Great Pacific Garbage Patch" beneficial for marine wildlife? A study was just released by researchers at Scripps Institute of Oceanography revealing a drastic increase in the amount of plastic adrift in the Pacific Ocean. According to the paper, the amount of plastic in the North Pacific Subtropical Convergence Zone has increased 100-fold over the last 40 years.

But most of the news stories coming out about this discovery are thin on facts about the dangers of plastic. And the research even suggests marine wildlife may be benefiting from the artificial flotsam.

Clearly this increase in trash can't be good. Can it?

There are very few things in the world that aren't beneficial to some lifeform.  Even if you were to, say, spill a mixture of persistent broad-spectrum poisons on an area that killed off 99.9% of all species there, the remaining 0.1% that did survive would benefit from the lack of competition.

The "great garbage patch" is hardly so extreme a phenomenon, but similar effects can be seen there: some species suffer, others benefit.  In that sense, it's no different from any other changing habitat.

From a conservation viewpoint, there are two issues here that one might find worrying:

First, novel, extreme or rapidly changing habitats tend to have lower than average biodiversity, at least initially: the few species that thrive in the new environment tend to proliferate at the expense of others, forming a relatively simple (and often not very stable) food web.  Of course, over evolutionary timescales we'd expect the surviving species to adapt and diversify and the ecosystem to settle into a more stable state, but that tends to take a long time compared to the human timescale on which such novel habitats are created.
Also, the effects of the "garbage patch", or ecological changes in general, are not limited to the directly changed area.  Creating a new habitat in one part of the ocean is one thing; disrupting the ecosystem of the entire ocean is something else, as doing so leaves no unaffected refuge for the species that are harmed.

For example, fish, birds and marine mammals passing even just occasionally through the patch might end up swallowing plastic and accumulating it in their gut; meanwhile, even for less motile organisms, the patch might act as a population sink, depleting their population density in nearby areas.  And if some organisms, such as the sea skaters mentioned in the article you cite, thrive in the patch, the increased population will likely spill into other areas, potentially harming their competitors or prey species.

As for why the news are focusing on the beneficial effects of the garbage to the sea skaters, well, that's what the study that prompted this current batch of news stories was about.  It's also seen as newsworthy precisely because it seems so unexpected: we've all heard stories of plastic flotsam harming wildlife, so finding out that some species are actually benefiting from it has some "man bites dog" style news value.

Also, it's a lot easier and more convincing to observe something that is there than something that isn't: we can directly see these insects laying their eggs on the bits of plastic, giving direct and incontrovertible proof of a causal connection.  Meanwhile, simply observing that some species used to be more common in the area of the patch than it is now is a lot less direct and informative: we might never be sure just how the patch is harming that species, and it always leaves skeptics an opening to claim that the decline might be caused by other factors.  With the sea skates, on the other hand, we're not just observing the effect, but the direct mechanism as well.


Why doesn't the ambient lighting condition change the perception of colors we see on a monitor? Suppose that I take a picture of an object illuminated by an incandescent light bulb and I choose the daylight white balance setting. The picture I then get will display a white object as looking yellow, which is how the object would look had my brain not processed the image according to the ambient lighting conditions.

The question is then why the way the picture looks doesn't change depending on the ambient lighting conditions. If a white piece of paper continues to look white when illuminated by an incandescent light bulb, then why would that same piece of paper displayed on a computer monitor look yellow when I'm viewing it in a room illuminated by incandescent light bulbs?

The phenomenon you are referring to is color constancy: The apparent hue of a reflective surface remains constant even when changes in the spectral power distribution of the illuminant alter the wavelengths reflected from it (Mather, 2008). In other words, despite substantial changes in illumination, we usually experience the color of an object as being constant.

The spectrum of wavelengths that enter our eyes is jointly determined by 1) the spectrum of the illuminating source (a variable), and 2) The spectral reflectance properties of the object (a constant).

To achieve color constancy, an object's spectral reflectance is the constant color parameter that needs to be evaluated.

Any information that better characterizes an object's spectral reflectance is a cue to colour constancy. This includes (Mather, 2008):

Local color contrast. Cone excitation levels of one surface relative to another remains constant when both surfaces experience the same change in illumination. Relative cone excitation levels are invariant ratios useful for achieving colour constancy.
Color adaptation. Adaptation reduces the contribution from the source illumination by lowering activity in the most highly active cone classes.
Global contrast. Global spectral changes generally represent changes in the illuminant; localised differences usually correspond to reflectance differences.
Luminance highlights. Glossy surfaces offer near-perfect reflections of the illuminant, which can then be factored from the rest of the scene.
Mutual reflections. The pattern of reflections that arise from different surfaces, under the same illumination, carries valuable information about the reflectance properties of each surface.
Range of reflected spectrum. This gives an indication of the breadth of the illuminating spectrum.

A graphical example of the effect of lighting conditions is found below (Fig. 1.)

Bowl of fruit photographed under artificial daylight (left), hazy day light (middle) and clear blue skies (right. Source: Mather (2008)

The most powerful cue to constancy is thought to be local color contrast (Mather, 2008). In other words, the relative contribution of the different cone classes stays constant, despite differences in the spectrum of the illuminant.

In your example, the object (paper) is not represented by a reflectance, but as an image; a representation taken out of its context, and it will appear yellow. Even if the ambient lighting is the same, as in your example, the monitor displays a 'real' yellow color, which has a different spectrum, because it is not a reflectance, but it is generated by a light source: your monitor; as mentioned in the excellent comment of @AMR. The real sheet of paper will have a different reflectance spectrum. Hence, both photo and real sheet will be interpreted as a function of ambient lighting by your visual system and they will appear different.

Even when your image was printed as a photo, the color is obviously different from the white sheet of paper. So the ambient light has a different effect on the reflectance spectrum of the photo and the real sheet.

Also the global contrast is different: the photo with a different spectral content than the real sheet is re-placed into the context of ambient lighting. Hence, the photo it is out of context and will be re-interpreted.

Reference
- Mather, Foundations of perception and sensation 2nd ed. Psychology Press 2008


During the process of correcting mutations via gene therapy, is the defective gene removed? Just recently started learning about gene therapy, many websites explain that the corrected DNA can be added to the genome using a vector and all that. I just don't understand what happens to the other sequence of nitrogenous bases that codes for the incorrect protein.
Thanks in advance for any answers :)

To be specific: I am talking about adult, somatic gene therapy here, and germline gene therapy experiments is still a landmine when considering ethical reasons.

The defective gene codes for a defective protein, that usually plays a part in pathways. Since the protein is also defective, that pathway is also rendered defective because of this protein, and usually when pathways go defective, bad things happen.

There are three target approaches to gene therapy:

Gene silencing by Antisense Oligonucleotide Therapy
Genome Surgery by ZFN, Crispr/Cas9 etc..
Gene Replacement by viral vectors

The only method that corrects the defective gene here is the genome surgery method. By using Zinc Finger Nucleases, or Crispr/Cas9s, TALENS or other methods like that, the defective protein is corrected at the genome level, which automatically corrects the mRNA and protein, and everything works as it should.

Other methods like Antisense, just prevent the incorrect protein from forming. This is really useful if the defective protein is itself toxic to the body, and a replacement protein can be achieved by masking the defective region to produce a truncated but functional protein.

Gene replacement usually puts in a healthy copy of the gene in, that functions along with the defective copy, and this solves majority of the problems as the affected pathway is no longer rendered inactive, as the healthy protein takes over the defective pathway. The defective protein is still produced, but doesnt do anything (or rather, is rendered moot as the healthy protein takes over) and gets removed during regular maintenance of the cell.

Now depending on the type of disease the individual has, gene replacement may also take place along with gene knockout (depending on if the defective gene is toxic), but obviously many considerations have to be thought about before the combinatorial therapy can be used (toxicity of treatment itself being the primary concern, followed closely by efficacy).

Now obvious question with gene replacement, antisense or any other form of gene therapy is how we get the therapeutic agent to all cells, and yes that is a major challenge, and that's why gene therapy is expensive. And no, the therapy doesn't correct all the cells in your affected tissue, but it aims to correct majority of the cells, and that should restore function (atleast in myopathies like the muscular dystrophies)

As you can see here, in DMD, dystrophin gets muated due to a mutation We can either mask the mutation by Antisense therapy at the level of the RNA (which leads to a functional protein forming), put in an alternative form of dystrophin (mini or micro dystrophin) that takes over the function of dystrophin in majority (if we are so lucky) of the cells, and the overall phenotype of the individual improves. Recent advances in genome surgery are also being investigated for ameliorating disease symptoms. The reason I concentrated on DMD is that, gene therapy for DMD is my PhD. So apologies for the bias.


How to compare SNP from genotyping results for multiple people with a known phenotype? I'm looking at different genotyping profiles available at opensnp.org and am trying to compare profiles for people with different phenotypes.

For example, given 10 profiles of people who can roll their tongue and those who cannot, I am trying to identify what is different between these people and what's similar.

A typical record is in this format:

Rsid, chromosome, Position on chromosome, actual 2 letter mutation

How can such records be compared to identify similarities for a given phenotype? Does RSID uniquely identify a mutation, or is it a combination of rsid and position?

In other words, if one user has rsid 123 at position 555 and another one has rsid 123 at position 666, and the mutation is the same, is this a similarity, or does position matter?

Each rsid identifies a unique SNP in the genome. Thus there should not be any entry in the files that have the same rsid but different chromosomes and/or positions. If you do find this, it is likely that you have data from different versions of the assembled genomes.

To find genetic variants associated, i.e. correlated, with your trait, you need to focus on the genotype at each of the SNPs. For example, SNP rs3094315 is an A/G polymorphism, i.e. an individual can either have the genotype AA, AG, or GG. To find if it is associated with tongue rolling, you would count the number of AA, AG, and GG individuals (alternatively you could sum the number of A and G alleles) in the group that can roll their tongue and compare those numbers to the group that cannot. You would then repeat this for each SNP that you want to test. For most SNPs, there will be no difference in proportion.

That being said, this is not a modest undertaking as this a cornerstone of human and statistical genetics. There are many issues that could strongly bias your results (e.g. population stratification, genotyping error, linkage disequilibrium, multiple testing). To learn more, you can read about the Cochrane-Armitage Trend Test and the PLINK software. If you are really serious I recommend Applied Statistical Genetics with R by Andrea S. Foulkes.


Why do the two hemispheres of the brain control the opposite sides of the body? Why does the left hemisphere control the right and the right hemisphere control the left? I googled it but didn't find a good answer regarding this. Could someone explain?
Does this adaptation help in the speed of transmission of nerve impulses?

Just to get the ball rolling here.  This particular aspect of brain evolution is very old. The cross wiring of the hemispheres of the brain seems to be as old as the right and left hemispheres itself.  It predates lizards - i.e. hundreds of millions of years ago. It  possibly predates right/left dominance and the organ asymmetry which puts the heart on the left side of the body.

Digging back deeper, we can see that worms have bilateral brain structure, but as noted in the comments below, the nervous systems do not cross.  I would guess that this means that the phenomenon appears sometime before lizards - putting the development having been done by the early Carboniferous period when the first animals came to the land and the first reptiles appears, which is the perhaps 350 million years ago.

Echinoderms (like starfish) are 'missing links' in bilateral symmetry as their larval stage has bilateral symmetry even though the adult has radial symmetry.  Such wiring may be so embedded in the way most animal body plans develop that it hasn't changed in evolutionary history. If that is related to other animals trait, it could be a billion years ago. Some argue this is not the case.

One might guess that the cross over of neurons in brain control is good for integrating the signals from both sides of the organism. There are quite a few theories.


Exactly what kind of spider is this in Louisville, KY? I took this photo many years ago, but I guess the year doesn't really matter. It was here in Louisville KY, on the outside of a window, on a web it built. It was a couple hours after sunset in the summer. It was about the size of a silver dollar.

Some people said it's a Garden Orb at first, while recently others say it's a Wood spider. Either way, I'm not entirely sure.

What species of spider was this?

It is an Orb Weaver (Neoscona crucifera). It is found from Maine to Florida in the east, to Minnesota in the Midwest, to Arizona in the southwest, and in Mexico.

Females are about 9.5–19 millimeters (0.37–0.75 in) long, while males are somewhat smaller. The upper surface of the abdomen is brown and hairy. The legs display alternating light and dark brown bands. The undersurface of the abdomen is black, with two white spots.
This species is relatively variable in color and sometimes pattern, but is most commonly seen sporting a rusty-red or golden orange color. The orb-shaped web is very large and is often constructed on buildings and other man-made structures, especially near outdoor lights. This species is most conspicuous in late summer and early fall.

For many years, this kind of orb spider would build a very large web every night just outside the back door (near a light.) While fascinating to watch, if was a lot less fascinating to forget it was there in the morning and walk face first into it. But I prefer to live and let live, so... :)


Is it possible to Breed an Animal to have more Females than Males? Minute Earth talked about environmental factors that cause animals and humans to have more male or female children: https://www.youtube.com/watch?v=3IaYhG11ckA

Presuming that is accurate, I was wondering if you could artificially select for people or animals who have more children of a certain gender?

As far as I know, there are no animals that do produce notably more males than females, or vice versa, except maybe some insects.

Yes.
 What you are looking for is a meiotic drive, it's a genetic factor that favors its own transmission. Sex linkage is very common in these due to sex chromosomes not undergoing recombination. Once such driver, R2D2 (I shit you not) is a Y linked gene that drastically increases the number of male offspring in a mouse that carries it, to the point it can cause a population collapse from lack of females.
Several such drives are known, none quite as drastic as R2D2.


Stabbing muscles when flexed and when relaxed Just a random question, would a sharp object pierce your muscle more(stabbed with the same amount of force) when the muscle is flexed or when relaxed?

Well, if we look in very basic detail at how muscle contraction works within a myofibril of the sarcomere:

N.b. this isn't on a loop and only plays through seven times

The red lines represent actin filaments whilst the blue lines represent myosin filaments.  During muscle contraction the filaments move over each other:

As shown in the above diagrams the "more contracted" a muscle is then the smaller the size of the H zone (the area where there are just myosin filaments).

So if we consider a penetrating impact that went through a plethora of identically aligned sarcomeres (obviously this is not the case in nature) then we could presume that (et ceteris paribus) the object would not penetrate as deeply into a contracted muscle as it will hit more tissue on its route than in a relaxed muscle.


Why can action potentials not be initiated at dendrites? Why are action potentials not initiated at dendrites, although dendrites are the first to receive input from the presynaptic cell?

In fact, excitatory postsynaptic potentials (EPSPs) at the dendrites are smaller than in the cell body and axon.

Considering the fact that dendrites have enough voltage gated ion channels, why is it that cation influx through these channels is not able to depolarize the dendrite above threshold and generate an action potential?

The exact site of action potential generation is debated, as is the underlying physiological mechanism (Colbert & Johnsten, 1996). It is generally agreed upon that the initiation site is beyond the soma, at the axon hillock, or even further in the initial segment of the axon.

The reason for the distal axonal initiation site of action potentials is, according to the classical view, that the density of Na+ channels is not high enough in the soma, while the density in the axon initial segment is substantially higher and sufficient. However, it has also been proposed that the threshold of action potential generation is lower at the initial segment (Kole et al., 2008).

Regarding your questions in the comments:

So can't action potentials be initiated at dendrites and soma with the help of VGCCs?
Answer: No. Channel density is too low;
What are the channels required for AP?
Answer: Basically Na+ and K+ channels;
How is it that action potentials are initiated at axon hillock, although the input is at dendrites? Why can't enough depolarization happen at dendrites and soma?
Answer: Either due to a low density of Na+ channels, and/or a higher action potential threshold (e.g., due to the presence of K+ channels in the soma counteraction depolarization);
As a corollary,if enough depolarization cannot occur at dendrites and soma,how then is it propagated to the axon, which is further down anatomically , in the neuron?
Answer: If the EPSP reaches a region with sufficient Na+ channels, depolarization becomes sufficient to activate a critical amount of Na+ channels that causes a sufficient increase in the membrane potential to sustain a full-blown action potential. Along the way, leaky K+ channels decrease the depolarization so a critical amount of channels is necessary, otherwise the EPSP dies out.
What about backpropagating APs from axon hillock to dendrites ? How is that possible?
Answer: the soma and dendritic region are believed to represent too big an electrical load to ensure action potential propagation in both the orthodromic and the antidromic direction. This impedance mismatch can be overcome for an action potential propagating from the axon back into the somato-dendritic region when the initial segment and axon hillock provide additional current. This can be achieved with a high density of sodium channels in that region (Lüscher & Larkum, 1998).

References
- Colbert & Johnsten, J Neurosci (1996), 16(21): 6676–86
- Kole et al., Nature Neurosci (2008); 11: 178-86
- Lüscher & Larkum, J Neurophysiol (1998); 80(2): 715-29


Why do bacteria use formylated methionine in the initiator tRNA, while eukaryotes do not? Could anyone suggest an explanation for the evolution of this trait in bacteria? Does it confer any advantage?

It is also exploited by immunity receptors of some eukaryotes for the recognition of bacteria.

In the literature I was only able to find a paper suggesting a possible role in signalling for protein degradation.

Summary

The question is posed in terms which imply that the formylation of the initiating methionine (Met) of protein synthesis was a relatively late evolutionary development for some purpose not concerned with translation, such as allowing regulation of protein degradation.

My answer takes the quite different view that this was an early evolutionary development in translation, arising as part of the system for initiating at a specific codon — AUG. With time, the initiating system became more sophisticated, with the specificity of initiation residing more in a separate initiating Met-accepting tRNAf which evolved to have a distinct structure from the elongating Met-accepting tRNAm allowing it to be distinguished from the latter and other elongator tRNAs.

I postulate that in the line leading to eukaryotes and archaea a mutation subsequently occurred that resulted in a loss of ability to formylate Met-tRNAf, but that individuals with this mutation were viable as initiation had ceased to be dependent on the formylation for discrimination.

Contemporary systems for initiating translation

I constructed the diagram below for an answer to another question, but it shows some of the common features of initiation of protein synthesis in contemporary eukaryotes and prokaryotes. (The reader who wishes more detail on translation is directed to standard text books, e.g. chapter 29 of Berg et al.)

The common features of initiation in eukaryotes and prokaryotes are:
1. The use of  a Met-accepting tRNA with an anticodon that recognises AUG to insert the first amino acid in a protein.
2. That this tRNA, here designated tRNAf (but also designated tRNAi) is distinct from the Met-accepting tRNA used for inserting Met at other points in the protein during elongation.
3. That the (f)Met- tRNAf is recognized by an initiation tRNA-binding factor (I-TBF in the diagram — a non-standard abbreviation) and not by the elongation tRNA-binding factor (E-TBF in the diagram).
4. That the (f)Met- tRNAf is delivered to the P site of the ribosome (otherwise occupied by the growing peptidyl-tRNA), rather than the A site, to which elongator-tRNAs are bound.
5. In many cases the N-terminal Met is removed by proteolysis after translation.

The features of initiation that differ between eukaryotes and prokaryotes are:
1. That the initiating amino acid in eubacteria and mitochondria and chloroplasts  is N-formyl-methionine (fMet), rather than methionine, as is the case in eukaryotes and archaea.
2. The selection of the particular AUG codon for initiation is different in the two cases. In eubacteria and archaea the 16S rRNA binds to a polypurine, Shine and Dalgarno, sequence; in eukaryotes the normal method involves a complex of the small ribosomal subunit and the Met-tRNA ‘scanning’ from the 5ʹ-end of the mRNA (the secondary structure of which is first unwound.

Argument

As the question about the function of the formylation is posed in evolutionary terms, and fMet-tRNA is involved in the initiation of protein synthesis, it seems valid to consider the evolution of this latter process, however speculative that may inevitably be. The following formulation is my own, although I suspect it represents the orthodoxy in this field. This, of course, does not mean that it is necessarily correct.

It seems likely that initially translation lacked signals for start and stop (and probably also protein initiation factors). I will not deal with termination, other than to say it is probably an easier problem, but initiation would seem to require the introduction of two new features:
(i) The designation of a specific initiation codon AUG†, which, for whatever reason, corresponded to one of the existing amino acids, methionine.
(ii) Given that this initiation codon also served for incorporation of Met internally, the development of a system to select one particular AUG for initiation.
It seems simpler to suppose that (i) preceded (ii), and that is what I shall assume, although the following arguments do not depend on this.
In contemporary initiation the problem of competition between initiation and elongation factors for (f)Met-tRNAs has been solved by the evolution of two separate tRNAs that accept Met — one for initiation and one for elongation. These share certain structural features — their amino acylation is catalysed by the same amino acyl-tRNA synthetase — but they differ in recognition by the protein synthesis factors that bring them to the appropriate P or A site on the ribosome. Despite the lack of formylation of Met-tRNAf in eukaryotes, the structural similarity to the eubacterial tRNAf is such that it can be methylated by E. coli transformylase (reviewed here). However, I imagine that this structurally different tRNA took time to evolve, as, indeed did the protein synthesis factors.

My argument is that the formylation of Met-tRNA was the basis of the initial discrimination between initiator and elongator Met-tRNAs, and this could have arisen even before the gene duplication that led to separate tRNAs.

Why would fMet-tRNA bind preferentially to the P site and Met-tRNA to the A site? The amino acyl tRNAs that bind at the A site all have a free α-amino group that attacks the linkage of the peptide to the tRNA in the peptidyl-tRNA in the A-site at the peptidyl transferase centre. The peptidyl-tRNA, of course, lacks such a free α-amino group. In this respect fMet-tRNA, with a blocked α-amino group, resembles peptidyl-tRNA (see diagram below). One can imagine how structural differences in the P site could hinder binding of Met-tRNA, but allow binding of fMet-tRNA. And, of course, fMet-tRNA would not be able to react if bound at the A site, which might also have structural features to hinder its binding.

If subsequently the discrimination became magnified by gene duplication and evolution of a structurally distinct tRNAf, the need for formylation would be diminished, and one could envisage that its subsequent loss in eukaryotes may have had no adverse effects, or was easy to accommodate.
The question does arise why formylation has persisted in eubacteria, even though it is possible to obtain viable mutants lacking the transformylase. This is what the work alluded to in the question addresses. There is a 2015 paper by Piatkov et al. which suggests that N-terminal fMet can be a degradation system in E. coli. Presumably this arose after the divergence of the line leading to eukaryotes and archaea, which developed other systems for regulating protein turnover.
However I would suggest that, assuming that the foregoing is correct, it is an explanation for the persistence of the formylation of Met in eubacteria, and not the reason for its initial appearance.

Concluding Remarks

At present I know of no convincing evidence that proves my arguments and rejects the proteolysis idea regarding the reason for the evolution of fMet-tRNA. This is the problem with ideas about early evolution. It is compounded here by the facts that suggestion of a role in proteolysis only came up recently and that this is no longer the ‘hot’ field it was 50 years ago.

Nevertheless, I find it hard to imagine a system as crucial and sensitive as protein synthesis incorporating a feature like formylation of methionine if it only had a secondary function. In this case it would seem easier to formylate the N-termini of proteins post-translationally, as for other N-terminal modifications like acetylation. Furthermore, the finding that the eubacteria-derived mitochondria still use fMet can hardly be to control protein turnover, as the vast majority of mitochondrial proteins are translated in the cytoplasm and lack fMet.

†Footnote

I am aware that, in bacteria especially, there are other possible initiation codons, notably GUG, although the initiating amino acid is always (f)Met. (This attests to the importance of the tRNA structure in contemporary initiation.) It is simpler just to refer to AUG in the argument.


Why do some Brown Pelicans have orange or reddish parts on their bills? I am doing research on Brown Pelicans and have photos/descriptions of the breeding and nonbreeding appearances of adults, esp. the California and eastern subspecies here on our southern Pacific, Gulf of Mexico, and southern Atlantic coasts.

One question is really puzzling me:

The birds are described as having long pale bills, some with some brown on them. The bill of the California subspecies is described as acquiring some orange or red during the breeding season (along with the gular pouch which turns bright red/orange/pink). But I see photos of nonbreeding birds (with completely white necks) with either a little or quite a bit of orange on their bills, usually on the lower half.

There are so many pictures like this that the orange cannot be just a breeding color.

Do some Brown Pelicans just have some or quite a bit of orange on their bills, even when they are not breeding? I have looked at just about every link that comes up under Brown Pelicans and no one explains the presence of orange in some of their bills (except during the California subspecies' breeding season). In the official descriptions of the appearances of nonbreeding adults, orange in the bill is never mentioned. I would like to know the answer to this detail in the appearance of some of them!

After doing some reading at the Birds of North America webpage on Brown Pelicans.
It does mention orange on the bill outside of the breeding season.
Brown Pelicans have a greenish gray bill once they are older than 24 days which becomes gray-brown in their first year. At around 12 to 14 months of age, yellow will begin to appear at tip and on the sides. At 16 to 19 months of age, the bill becomes gray-green-yellow with some orange, the orange becomes more distinct at 29 to 37 months.
It is difficult to define the plumage of a Brown Pelican during their first 2 to 3 years; they acquire definitive plumage between the ages of 3 to 5 years old.
Here are the descriptions of their bill in Definitive Basic and Alternate plumages:

In Definitive Basic plumage, proximal end of upper mandible pinkish
orange, distal end buff yellow over pinkish orange, and nail at tip
buff yellow. Lower mandible pinkish orange, except middle section gray
or mottled gray. Proximal end of gular pouch reddish orange (P. o.
californicus) or green-gray (P. o. carolinensis); distal end dark
gray-green. As breeding season approaches, colors intensify; bill
becomes brightest 4–6 weeks before pouch.
In Definitive Alternate
plumage, upper mandible bluish pearl-gray and pinkish on proximal end,
buff-yellow-orange-red over bluish pearl-gray on distal end, and
bright buff-yellow on nail. Lower mandible pale yellow on proximal
third, bluish pearl-gray elsewhere; yellow at maximum intensity when
young being fed; may serve as target for begging nestlings.
Colors
fade with onset of incubation through prebasic molt; upper mandible
gray proximally, buff-yellow and orange over pearl-gray distally, and
buff-yellow on nail; distal two-thirds of lower mandible gray;
proximal end of gular pouch faded yellow-gray (P. o. californicus) or
gray-green (P. o. carolinensis); distal end dark green.

It appears their bill does retain the orange after breeding although it may begin to fade and it does mention how the colour intensifies during breeding.
Reference:
Shields, Mark.(2014).Brown Pelican (Pelecanus occidentalis), The Birds of North America (P. G. Rodewald, Ed.). Ithaca: Cornell Lab of Ornithology; Retrieved from the Birds of North America: https://birdsna.org/Species-Account/bna/species/brnpel


How is 16s rRNA used to identify unknown bacteria? How is 16s rRNA used to identify unknown bacteria?

With PCR the 16S rRNA is amplified and sequenced, but how can you identify the bacteria with this 'piece of knowledge' if the 16S rRNA is conserved and so the same in all bacteria?

It is not conserved, its sequence is not the same in all bacteria. Indeed, it has a slow rate of evolution (mutation) that make it perfect to build phylogenetic trees.

As correctly suggested by David in his comment, here are some references about the 16s rRNA and on how it is used to identify known and unknown bacteria.

http://www.sciencedirect.com/science/article/pii/S1369527499800526

http://nar.oxfordjournals.org/content/38/22/e203

https://www.ncbi.nlm.nih.gov/pubmed/18828852

https://www.ncbi.nlm.nih.gov/pubmed/27388368

https://www.ncbi.nlm.nih.gov/pubmed/27659439

https://www.ncbi.nlm.nih.gov/pubmed/18353221

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760787/


What is the basic structure of the nuclear lamina What gives the nucleus
  its shape is a mesh of intermediate filaments called the nuclear
  lamina. It forms an interface between the chromosomes and the inside
  of the nuclear envelope. If these large protein fibres were to be
  temporarily separated into their component nuclear lamina, the nuclear
  envelope would pull away from the chromosomes and withdraw into the
  endoplasmic reticulum. Problem solved.

I am confused by the last sentence starting with "If these large proteins..." Could someone explain this in another way? I would appreciate any response. Thanks!

Watch this animation and you'll understand the general process of mitosis:

http://www.sumanasinc.com/webcontent/animations/content/mitosis.html


Is there a scientific explanation for male and female fragrance preferences? The following is only anecdotal evidence, but in my experience it's very consistent.

When products have added fragrance (cosmetics, soap, air freshner, candles, etc), women often seem to enjoy the fragrance whereas men's reaction is normally something from indifference to outright revulsion.

I've tried googling this but the results are all about sexual attraction, which I'm not asking about.

One could speculate that this pattern is because the folks in marketing have worked out that adding fragrances will make women buy things and that as far as men are put off by fragrances, that doesn't have a net negative sales impact. But such theories don't answer the underlying question:

Why is there a difference in experience between men and women reacting to the same fragrances in the first place? Is there a "hard science" explanation for this phenomenon?

The idea that males and females react differentially to various smells in the context of “hard science” alludes to the concept of sexual dimorphism in olfactory signaling, which has been investigated:

  Stowers & Logan. Sexual dimorphism in olfactory signaling. Current Opinion in Neurobiology. 2010. 20,770-775.

    What makes males and females behave differently? Although genetic master-regulators commonly underlie physical differences, sexually dimorphic behavior is additionally influenced by sensory input such as olfactory cues. Olfaction requires both ligands for signaling and sensory neural circuits for detection. Specialized subsets of each interact to generate gender-dimorphic behavior. It has long been accepted that males and females emit sex-specific odor compounds that function as pheromones to promote stereotypic behavior. Significant advances have now been made in purifying and isolating several of these sex-specific olfactory ligands. In contrast, the neural mechanisms that enable a gender- dimorphic response to these odors remain largely unknown. However, first progress has been made in identifying components of sexually dimorphic olfactory circuits in both Drosophila and the mouse.

You’re right that most research in humans (like this paper) on this subject includes elements relating to sexual orientation or sexual selection, but I did find one article that is more relevant to your question:

  Lindqvist. Preference and Gender Associations of Perfumes Applied on Human Skin. Journal of Sensory Studies. 2012. 27,490-497.

    Abstract

      The perception of fragrances has been a growing field of interest, where perfumes classified as either typically feminine or typically masculine primarily have been used as stimuli. The current study explored gender associations and preferences of more “unisex” perfumes found in the middle of a gender continuum of fragrances, both when the fragrances were applied on humans, and when they were presented in glass bottles. Blindfolded participants indicated if they wanted to use the fragrances themselves, if they wanted their partner to use the perfumes, scaled gender associations (femininity and masculinity) for each perfume and tried to guess the gender of the person each perfume was applied on when not presented in a bottle. Results show that the gender of the person that the perfume was applied on did not affect the participants' preference or their gender scaling. Moreover, the preference did not differ between female and male participants, indicating that the commercial gender categorization is less important to the perfume consumers.

    Practical Implications

      On the commercial market, most perfumes are classified as either feminine or masculine, although the odor quality of feminine and masculine odors are overlapping and constitute a continuum rather than two separate clusters of odors. Earlier research has shown that participants tend to prefer perfumes positioned in the middle of this gender continuum. The current study investigates gender associations and preferences of perfumes from the middle of the gender continuum while these are applied on humans. When blindfolded participants evaluated their perception of the perfumes in this study, it became clear that neither the gender of the humans that the perfumes were applied on, nor the commercial gender labeling of the perfumes were important to their perception. Consequently, the commercial gender categorization does not seem to be sufficient for all perfumes. Instead, the classification of perfumes could be according to other aspects, e.g., according to odor quality.


How do crickets get away with being so loud without getting eaten? How do crickets get away with being so loud without getting eaten? There are a number of bugs that reproduce by blatantly advertising their location. For instance fireflies advertise their location with physical light and are extremely easy to catch.
How is this evolutionary selected for?

They don't always 'get away with it'!  A study by Pascoal et al. (2014) found that field crickets (Teleogryllus oceanicus) on Oahu and Kauai islands of Hawaii have lost the ability to produce sound after an invasive wasp that is acoustically oriented to prey was introduced to the islands within this century. There are a few mutation to the crickets' wing morphology that produces "flat wings" that cannot make sound. Ordinarily, this mutation would reduce fitness through a reduction in competition for attracting mates. However, the selection pressure from the wasp caused independent mutations for flat winds to sweep through the island to the point that the Kauai population was 96% flat wing.
This example illustrates that the deciding factor between 'getting away' with producing so much noise comes down to the selection balance of attracting more mates or attracting more predators.
Reference:
Pascoal, S., Cezard, T., Eik-Nes, A., Gharbi, K., Majewska, J., Payne, E., … Bailey, N. W. (2014). Rapid convergent evolution in wild crickets. Current Biology: CB, 24(12), 1369–1374.


Can you help with insect identification? (Outback Australia) This was in my child's shoe that was left outside. They got it out of the shoe and it went on the wall where they measured it. The body is approx 3 cm and from head to tail it's 6 cm. Any help would be greatly appreciated!

We are in central Australia in the Outback.

This is a member of the family Anostostomatidae, but given its sex is unlikely to be placed further (many Orthoptera are best identified on the basis of males, including this family).  There don't seem to be internet-based identification tools for the group (but the page http://bie.ala.org.au/species/urn:lsid:biodiversity.org.au:afd.taxon:a8042a0a-f34e-4ae3-ab86-5306b9176774#gallery shows a number of specimens and living examples, the latter usually taken only to family); Chapter 5, "Australian king crickets: distribution, habitats and biology (Orthoptera: Anostostomatidae)" in the book The biology of wetas, king crickets and their allies appears to be the best option I've seen that might allow a further identification.


How is incomplete dominance different from codominance? Ok let me start with the definitions of incomplete dominance and codominance.

incomplete dominance - The situation in which the phenotype of heterozygotes is intermediate between the phenotypes of individuals homozygous for either allele.

codominance - The situation in which the phenotypes of both alleles are exhibited in the heterozygote because both alleles affect the phenotype in separate, distinguishable ways.

It is the standard textbook example of incomplete dominance to show a cross of red and white Snapdragons of pure bread. Which yields the phenotypic ratio of 1 red : 2 pink : 1 white. The standard text example of codominance is AB blood type where the A glycoprotein and B glycoprotein together produce a distinguishable phenotype apart from AA or BB.

I really don't understand the distinction between intermediate phenotypes and distinguished phenotypes. How is pink not distinguished from white and red. Consider a hypothetical example of some insect that interprets red, white and pink as distinguishable signals where perhaps red is a safe flower, white is ignored, and pink is dangerous. Say these signal recognitions have evolved based on the insects contrast against the flower pigment and the probability of being eaten by a predator because of increased exposure while getting nectar from the flower. I suppose I have a misunderstanding but wouldn't the red, white, and pink phenotypes be distinguishable rather than intermediates in that case?

So I'm probably just being an idiot but how is incomplete dominance different from codominance?

Certainly if you are talking about signals, red, white, and pink phenotypes are distinguishable rather than intermediates...

But inheriting a character is far away from the concept of distinguishing signals. As genotype of an organism decides its phenotype, you should know that in a hybrid both the paternal and maternal traits would exist. If one is dominant then it is expressed and the recessive is not.

However if the dominant gene is unable to express itself independently in presence of the recessive and if the recessive is partially expressed, then both the dominant and recessive give rise to an intermediate phenotype which "only one of them cannot produce"

This is what we call blending. In case of Snapdragons, pink is a phenotype that allele responsible for red or white alone could not have produced.

In case of co dominance you can notice multiple dominance. i.e., no recessive character is there. All alleles are expressed "independently of one another" in an organism.

Eg:- AB blood group.

Also consider cross between black coat coloured cat and white cat. The offspring produced has black and white patched coat colour. i.e., Black and white didnt blend to give rise to grey. I mean, alleles responsible for these traits are independently expressed.

Hope that clears your doubt. :-)


where to buy DNA sample kit? why isn't it easy to find online? I guess you can say that it's a hobby of mine to research my ancestry and gather as much information from my family's history as I can. Being a student I can't afford to pay for mtDNA or Y DNA test of my relatives. For the first time I'll be doing it for myself fortunately :)
Now I came up with the idea of storing saliva samples of my oldest relatives just in case they pass away. I'm afraid that can happen at any time since they are getting very old. I guess it's a good plan for now. It still depends on how much a DNA sample kit costs. I'm not going to say any brand names here, but it'd be very nice if someone pointed me out where I can buy self-collecting saliva sample kits on the internet. I've found producers, but no online store.... I also wonder why this is the case.

Most people using these tools for research and diagnosis have long-established connections and providers of industry standard tools. Most companies that provide these tools need a steady, reliable source of income, and historically demand for those tools comes from facilities such as hospitals and labs, not DIY biotechnologists (who typically can not afford the tools), so they focus on getting their products to the population demanding them most. There is budding interest in providing research and development tools to the general public such as this startup's stated goal:
http://www.the-odin.com/about-us/

But generally you have to go to a company's website, select the product you desire, and request a quote based on how many kits you'd like to order. The process isn't as easy or accessible for DIYers simply because the demand has not been great enough until recent technological advances such as CRISPR and DNA sequencing technologies made it cheap enough to run these tests on home equipment. It's similar to how not every computer geek could afford a CPU of a certain speed 20 years ago, but now CPU's of that speed are wide spread.

Salimetrics has some swab kits available for under 100 USD here
http://store.salimetrics.com/saliva-collection-methods/

Oragene offers saliva collection kits and this link details some storage options.
http://blog.dnagenotek.com/blogdnagenotekcom/bid/40944/Best-Practices-for-Long-term-Storage-of-Oragene-DNA-Samples

A list containing price per sample of oragene sample kits can be found here:
http://genomics.pitt.edu/pricing/price/HSCRF%20Genomics%20Research%20Core%20Price%20List.pdf

Some issues with collecting a saliva sample for DNA testing are neutralizing the enzymes and materials present that will degrade the DNA, and then isolating, storing, and testing the DNA. These techniques are usually used by trained professionals, once again highlighting the reason companies do not focus on selling to individuals, but to professional organizations.

An overview of the process of saliva collection and links to a few providers of the tools required to acquire your sample can be found here:
http://www.the-scientist.com/?articles.view/articleNo/43347/title/Tools-for-Drools/

This is a handbook detailing some tips on techniques used for collection and storage:
https://www.salimetrics.com/assets/documents/Saliva_Collection_Handbook.pdf

I am not affiliated with any of the companies mentioned above but if linking them is a no-no here on Stack Exchange the links will be removed and I will mention the companies only as examples. Hope this helps!


Species identification; clusters of big plump red bugs in Taipei I saw these red insects in Taipei near XinBeitou MRT station in the last week of April 2017, around lunch time. They were fairly active and would keep checking each other out with their antennae for a moment and then move on to the next. What struck me was the wide range of sizes and development in the groups. I didn't notice any feeding or mating that I could recognize, just a lot of walking around and checking each other out.

There are plenty of birds around (this is quite a green area) but I didn't notice any interest by birds in eating them.

I've also included a screenshot from google maps so you can see the location and the trees growing in these concrete structures.

The body of the largest individual is probably 2.5 centimeters long.

I'm fairly certain these true bugs belong to the species Leptocoris vicinus, and carry the nickname of "soapberry bugs", which is specific to the subfamily Serinethinae. They're quite common in urban areas of Southeast Asia, which coincides nicely with where you encountered them.

Also, you had mentioned,

  There are plenty of birds around (this is quite a green area) but I didn't notice any interest by birds in eating them.

Soapberry bugs, as well as many other types of insects, are able to freely congregate in large numbers, and in such exposed places, due to their bright coloration. Having such a bright color may indicate to some predators that the prey in consideration is toxic, a phenomenon referred to as aposematism.

 source

 source

And then, here's a map of their distribution, with Taipei holding marker #37. (source)

An interactive version of this map can be found here.


Which biological kingdom comprises the greatest biomass on Earth? Which of the five biological kingdoms - animalia, protista, plantera, monera, or fungi - has the largest biomass?

To clarify, if the biomass of every species in each of these kingdoms was added up, which kingdom would have the greatest sum?

Probably Eukaryotes. Specifically, plants.

This is a very fundamental question of life that is often overlooked. It goes without saying that plants and animals are the strongest contenders. However bacteria may also rival them. Be aware though that this is a contentious claim given more thorough estimations that take into account fluctuations in bacterial presence. This EMBO Reports science and society article claims that plants account for 99% of Eukaryotic biomass.

For further reading the Wikipedia page on biomass doesn't seem too shabby for more details on tonnage and methods of calculation.

The most numerous organisms could possibly be viruses or bacteriophages depending on if you count viruses as "living".


How do we know if the folding@home project results are right? Some of us are involved in the folding@home project, spending time, money, and resources.

I would like to know the answer to two main questions:

How do we know we fold it right? I mean, these models used in folding calculations. Is it probable that in a decade we will find that all these results are nil and void?
Do we have any example that these calculations were practically applied anywhere?

in silico modelling of anything in biology is an active field of research. It's very useful for making predictions and developing hypotheses, but any findings need to be confirmed experimentally.
From the Folding@Home website:

Folding@home has been a success. In 2000-2001, we folded several small and fast folding proteins with experimental validation of our method. We are now working to further develop our method, and to apply it to more complex and interesting proteins and protein folding and misfolding questions. Since then (2002-2006), Folding@home has studied more complex proteins, reporting on the folding of many proteins on the microsecond timescale, including BBA5, the villin headpiece, Trp Cage, among others. In 2007, we crossed the millisecond milestone by simulating a protein called NTL9, and the 10 millisecond barrier in 2010 with ACBP.
More recently (2006-present), we have been putting a great deal of effort into studying proteins relevant for diseases, such as Alzheimer’s and Hunntington’s Disease. You can learn more about our results and peer-reviewed scientific achievements on our Papers Page.

As they say, you should check out their research contributions for how it's being practically applied.
You may also be interest in this article for the science behind and prospects of protein folding prediction: Bowman GR, Voelz VA, Pande VS. 2011. Taming the complexity of protein folding. Curr Opin Struct Biol 21(1):4-11. At least try reading the conclusion for a less technical overview.


What causes XYY Syndrome? It's obvious how a misdisjunction can result in klinefelter's syndrome (XXY) but I don't see how this can result in XYY syndrome. Your parents have a collective total of only one Y chromosome so how can any misdisjunction result in a child with two Y chromosomes?

It comes from a Y nondisjunction in the father. Anaphase nondisjunction of the Y yields a YY, which goes with one X from the mother to give XYY.


Can antibiotic resistant bacteria compete with normal one in an antibiotic free environment? The question is based on an intuition that antibiotic resistance can't come along. This mutation will probably make bacteria less tenacious. Is there any research how AR bacteria compete with normal one in an antibiotic free environment? Because if them generally lose to normal bacteria then AR bacteria is not a big threat and they can't spread to much.

The antibiotic resistance adds to growth cost. In an antibiotic free medium the antibiotic-susceptible strains will outgrow the resistant ones. See this


What evolved to produce sweetness, plants or consumers? I couldn't find an existing answer on this site, although I may be wrong.

What evolved to produce "sweetness", a pleasant reaction to the presence of sugar?
(A) Plants, using it to lure in consumers and spread seed
(B) Animals / consumers, which used sugar as a vital nutrient, to identify nutritious food, or
(C) Neither of the above; something else?

None of the above.

Seeking sugar evolved long before animals, before multicellular organisms even.
Plant evolved a strategy to exploit it much much later with the evolution of fruit and nectar.

Animals evolved to like the taste of sugar since it is the primary fuel almost all life metabolizes to live in an easy to digest form, literally a simple carbohydrate. plants use sugar substances as lures becasue that's what animals already wanted and plants were already making it. Also a lure is not going to evolve before the seeking behavior that would actually make it a lure. fruit and nectar are new sugar is one of the oldest metabolic compounds in existence.

Metabolizing glucose is one of the shared characteristics between Eukaryotes and Bacteria and is present in nearly all life,source. Meaning it is was likely present in their common ancestor. This means plants and animals have been eating sugars since before they diverged into plants and animals. . Chemotaxis  of motile bacteria towards glucose is well understood, and likely predates the existence of eukaryotes. source

The production of sugar by photosynthetic bacteria predates the merging of Eukaryotic cells and chloroplast ancestors. It was present in the Cyanobacteria that gave rise to chloroplasts, meaning sugars were produced long before plants existed. source the attractive aspect was only exploited later with evolution of nectar and fruit.


What is the meaning of "leukemic cell recovery" in an abstract? An article abstract:

  Significant predictors of treatment outcome are poorly defined for patients with T-lineage acute lymphoblastic leukemia (T-ALL). A high WBC at diagnosis, which has traditionally been a predictor of poor response in T-ALL, has considerably weakened prognostic significance in the face of modern, more intensive chemotherapy. To test the hypothesis that bone marrow stroma-supported leukemic cell recovery might identify children at high risk for relapse, we measured the ex vivo recovery of T-ALL lymphoblasts from 29 newly diagnosed patients using a stromal cell co-culture assay. In all cases the T-ALL lymphoblasts showed an increase in recovery of T-ALL cells (RTC), ranging from 4 to 343%, in comparison to samples maintained without stroma. Since we were blinded to patient outcome in this case-control study, we then correlated patient outcome with RTC. The RTC for 18 patients in complete continuous remission (CCR) for greater than 4 years was stochastically larger than for the 11 patients who eventually relapsed (P = 0.011, by the two-sided Wilcoxon test). Furthermore, 100% of patients with an RTC of more than 26% had a CCR greater than 4 years while 78% of the patients with an RTC of less than 25% relapsed within 4 years. This is the first report to show that higher lymphoblast recovery may predict a more favorable outcome for children with T-ALL. A prospective study is needed to test whether stroma-supported leukemic cell recovery might serve as a basis for assigning risk-adjusted therapy.

What is the meaning of recovery here? It puzzles me as a non-native speaker of English. Do the authors simply mean "the number of cells that survive"? Or is there some "recovery process" - if yes, what is the nature of this process?

P.S. The question arose from a question asked by a fellow translator. She translates a text in which T cells transduced with gene for a receptor against leukemic cells are co-cultured with such cells, after which

  "T cells transduced with the receptor markedly reduced leukemic cell recovery".

The translator has trouble understanding how to put it in Russian, because translating "recovery" verbatim would imply some process in which a cell recovers, say, from injury.

Is "recovery" just "the percentage of cells that survived, relative to the overall number of cells"?

TL;DR: Yes, it's just percentage of cells that survived. With the caveat that the assay doesn't give information on how much the number of cells is influenced by survival, dying, or growth rate.
"Recovery" in this context means "cells found after X amount of culture time". Generally speaking, recovery often refers to putting something in a program/dish/liquid/organism and seeing how much is still left after some processing/treatment/culture. For example, if I give a 1-year-old child 10 porcellain plates to play with, I might be interested in what percentage I can recover after 2h of play time. Of course in the context of cell culture, that percentage can be above 100% if the cells multiplied in the meantime.
As the methods of the article describe, the culture assay consists of first growing a single layer of stromal cells (HS-5 cells) on a culture plate for 24h. These cells provide support for the actual cells of interest. The researchers then spread 5.0 × 105 viable T-ALL lymphoblasts isolated from a patient sample on the stromal cell layer. They do this twice* for each sample, in one case collecting the cells after 1h (which isn't usually enough time for human cells to do anything), in the other case collecting them after 72h of culture (which is enough for healthy cells to grow substantially). Then they use flow cytometry to quantify how many T-ALL cells are now in the culture after that time has elapsed.
This helpful graphic is from the paper. The word "cells" in the formula refers to T-ALL cells.

The percentage of recovered T-ALL cells (RTC) was calculated by:

Essentially, what the authors here studied is whether the likelihood of a T-ALL patient to relapse might be related to the ability of their cancerous cells to survive or grow in a culture dish coated with stromal cells.
The quote from your colleague would mean that the T cells were surviving/growing less or dying more if they were transduced with the receptor.
*rather, four times. Twice for 1h and twice for 72h collection. At least this is what "in duplicate" implies.