Is sexual selection evolutionarily advantageous?

What does "evolutionary advantageous" mean?

First note that is sexual selection evolutionarily advantageous? is a question that makes no sense. An allele or a trait can be evolutionarily advantageous if it increases the fitness of its carrier. If an allele, an evolutionary process or an environmental change decreases the risk of extinction for a species, then you cannot talk about evolutionary advantage. Selection (whether natural, sexual, artificial or whatever) does not (necessarily) minimize the risk of extinction of species.

This post is very related to your question and is definitely worth reading.

I hope your teacher didn't really say that! Assuming he did say that, then know that it is really not as easy as he's suggesting.

There are a number of studies that address the question on whether Sexual Selection (SS) and Natural Selection (NS) have opposite or antagonist effects. The subject is not easy and as SS is not my field of expertise my answer will not be complete. I will talk about two possible hypotheses for explaining the existence of SS and what they mean in terms of probability of extinction.

Good Genes

Under the "Good Gene" hypothesis, females' preference (we'll assume that females are choosy but there are many species where males are choosy) of some traits evolve because those traits are correlated with the global health of the male. In consequence, by choosing a male carrying some trait, the female makes sure that her offsrping will receive good genes from their father. This hypothesis assumes that poor males cannot produce fancy phenotype, while good males can. This is called Zahavi's Handicap Principle.

Under this hypothesis, if a trait become too costly for a given male, the male will just die, therefore limiting the evolution of secondary sexual traits. As a result, the population will no get extinct. Furthermore, under this hypothesis, SS may actually increase the effect of NS making sure that only the best male reproduce. In results the mean absolute fitness of the population should increase faster in a population where "Good gene"-SS occurs.

Sexy Son

Females preference for some trait may also evolve because mating with a sexy male means having sexy sons. This is called the "sexy son" hypothesis.

Under this hypothesis, again if a sexy male has a low enough survival, then a female has better to mate with a less sexy male (even though her offspring won't be very sexy) so to increase the survival of her offspring. After a bunch of generations, all females will end up preference mating with non-sexy male, changing the concept of what we call sexy in this population and therefore reversing the effects of SS.

You may also want to read about Fisher's runaway processes.

Just an article among others

Aneil Agrawal has some nice articles on SS that may interest you. This article for example discusses how sexual antagonist genes influence whether SS has an antagonist or parallel effect to NS.

Is SS really different from NS?

Your question Why natural selection did not eliminate sexual selection? assumes that NS and SS are two different things! This is a very old-style point of view. Charles Darwin coined these two terms thinking of two, unrelated processes. Today, most authors see SS as being part of NS (if a chestnut tree is a type of tree, SS is a type of NS). And many of the processes that are termed SS has actually not much to do with "competition to access a mate" but only has to do with NS. For example, many people talk about SS when talking about sexually antagonist genes or sexual conflicts. In short, the concepts are kind a mixed up. You may want to read about the work of Hannah Kokko about the semantics of terms related to SS.


Use of progesterone in preventing ovulation?

When progesterone alone is used as a contraceptive it is assumed that the oestrogen level is endogenously maintained by the follicular cells.

Yes mainly oestrogen and only little does progesterone inhibits LH or FSH secretion.

LH surge is the principle stimulator of ovulation.

  However,experimental work has suggested that immediately before the LH surge occurs, there is probably a sudden depression of estrogen...and this might be ...that leads to LH surge
  [source: Textbook of medical physiology A South Asian Edition- Guyton & Hall]

If progesterone or progesterone-oestrogen combinations be given before ovulation then feed back inhibition of LH surge occurs.This would lead to contraception by anovulation.

Progesterone is only known to proliferate the endometrial lining.

However, administration of progesterone or oestrogen -progesterone combinations after ovulatory phase helps to achieve high concentration of these hormones ,much before the normal time required to attain peak levels due to endogenous secretions alone.

This helps to depress the FSH -LH secretion by feedback inhibition very quickly causing involution of the corpus luteum and early shedding of the endometrium termed as breakthrough bleeding

REFERENCE:

reference site
Textbook of Medical Physiology A South Asian Edition-Guyton & Hall


Looks like Jewel Fish, a cichlid that has been kept for a long time. Hemichromus bimaculatus , native to west Africa a bit different from "African Cichlids" which are from east Africa. Source : Exotic Aquarium Fishes by W. T. Innes ( the guy neon tetras are named after), 1937 ; But I don't think you can find it online .


Fracture healing occurrs in several steps:

haemorrhage: blood and surrounding cells fill the space created by the fracture.
fibrous callus: chondrocytes colonize the fracture space, with neovascularization.
bony callus: osteocytes colonize the fracture space and rearrange in woven bone
remodelling: in long bones, woven bone is remodelled into lamellar bone and creates a new haversian system

If the fracture is not immobilized enough (not enough rest), several things can happen that are mutually exclusive:

normal healing: luckily, the bone is not too much mobilized and is able to heal normally
fracture displacement: the bone heals, but in an incorrect alignment. This gets partially corrected over time, but the correction mechanism is limited, especially in adults.
pseudarthrosis: the worst case. instead of normal healing, cartilage grows to protect the bony extremities that are mobilized and prevents further healing. This causes pain, and will require surgery in most cases.


Is feeding birds only after a snowstorm helpful or harmful?

Feeding for a short period should be helpful, not harmful to the birds, particularly if it is during or following a cold storm.  (Ground feeding birds, such as the Junco or Towhee shown in your picture have particular difficulty after a storm covers the ground with snow.)  A concern people have with feeding is that feeding will create a dependency of the birds on the artificially supplied food.  The worst case of this would be expected to occur during fall migration, where an unusual supply of food might delay birds from migrating, which may be detrimental if they cannot survive the colder weather they may encounter because of the delay.  Other than that period, short term feeding should not be problematic since the birds will not develop a strong visiting habit over a short period.

Dependence on human feeding was studied by Brittingham and Temple in an article "Does Winter Bird Feeding Promote Dependency?".  This study evaluated chickadees in two areas, one which had supplemental food available for a year.  The next year, without food available for either area, showed no difference between the resident birds of the two areas.  Although they didn't test suddenly discontinuing food in midwinter, they do comment on that scenario:

  We did not test what happens when feeders are removed unexpectedly from a site in the middle of winter, but we suspect that this would not be as detrimental as is typically thought. In winter, a natural food patch may disappear suddenly as a result of a winter snow or ice storm or the foraging activities of other flock members. As a result, chickadees apparently track a number of food patches at all times and sample a number of areas continuously no matter how abundant food is in any one patch. This strategy is necessary for surviving in an unpredictable and fluctuating environment. People consider bird feeders to be a very predictable food source, but in terms of evolutionary time, they have only been available for a very short time. For birds, they are probably no different than any other food patch.


Can the mating of a couple with Rhesus positive and negative blood types result in miscarriage?

I want to know can +ve and -ve blood group of a couple could be a cause of miscarriage in pregnancy?

Yes. In extreme cases, it can. You are talking about Rh Incompatibility, and can become a big issue when the mother has Rh(-) blood and the father has Rh(+) blood (such as the case with your cousin and his wife).

What could have happened (but definitely won't say for sure) is that your cousin's wife had a natural miscarriage which exposed her to the Rh proteins of the child, and then the subsequent pregnancy had complications due to the previous exposure and mother's development of antibodies which lead to the second miscarriage. However, I am not a licensed physician and you should consult a physician before pursuing any sort of treatments!!!

Rh factor is the presence of surface proteins on Erythrocytes (Red Blood Cells or "RBC"). If Leukocytes (White Blood Cells - most commonly reported as "T-cells") encounter Erythrocytes that do not share the Rh factor of their host, then they can develop antibodies to it - which help identify Antigens (foreign proteins and molecules). Once the Antibodies have been generated the Immune System can attack any foreign Erythrocytes.

In this way, the mother's Immune System can actually attack the RBCs of her child.

You can find out more here: http://kidshealth.org/parent/pregnancy_center/your_pregnancy/rh.html

And a few select quotations:

  Rh incompatibility usually isn't a problem if it's the mother's first pregnancy because, unless there's some sort of abnormality, the fetus's blood does not normally enter the mother's circulatory system during the course of the pregnancy...

  ...Other ways Rh-negative pregnant women can be exposed to the Rh protein that might cause antibody production include blood transfusions with Rh-positive blood, miscarriage, and ectopic pregnancy...

  ...Rh antibodies are harmless until the mother's second or later pregnancies. If she is ever carrying another Rh-positive child, her Rh antibodies will recognize the Rh proteins on the surface of the baby's blood cells as foreign, and pass into the baby's bloodstream and attack those cells. This can lead to swelling and rupture of the baby's RBCs. A baby's blood count can get dangerously low when this condition, known as hemolytic or Rh disease of the newborn, occurs.*

And you are correct that there is a treatment via injection, but the Doctor is also correct in that administering it past the first pregnancy does little for future fetuses:

  Today, when a woman with the potential to develop Rh incompatibility is pregnant, doctors administer a series of two Rh immune-globulin shots during her first pregnancy. The first shot is given around the 28th week of pregnancy and the second within 72 hours after giving birth. Rh immune-globulin acts like a vaccine, preventing the mother's body from producing any potentially dangerous Rh antibodies that can cause serious complications in the newborn or complicate any future pregnancies.

And the ultimate effects of missing the shots and having very unfortunate luck:

  Rh incompatibility rarely causes complications in a first pregnancy and does not affect the health of the mother. But Rh antibodies that develop during subsequent pregnancies can be potentially dangerous to mother and child. Rh disease can result in severe anemia, jaundice, brain damage, and heart failure in a newborn. In extreme cases, it can cause the death of the fetus because too many RBCs have been destroyed.

Is there a cure? No. Once the antibodies have been developed, the Rh(+) protein is known to the mother's Immune System. Nothing short of wiping out the mother's Immune System would act as a cure.

However, in extreme cases, there are treatments:

  If a doctor determines that a woman has already developed Rh antibodies, then the pregnancy will be closely monitored to make sure that those levels are not too high. In rare cases, if the incompatibility is severe and the baby is in danger, a series of special blood transfusions (called exchange transfusions) can be performed either while the baby is still in the uterus or after delivery.

But don't fret yet!

Rh surface proteins are determined by genetics, and each time a child is conceived there is a chance that the Rh protein will be (-) if the exact genotype of the (+) parent allows it. So if your cousin's wife were to get pregnant again (and each time she does) it's a chance that the Rh Incompatibility (aka - "Hemolytic Disease", aka - "Rhesus Disease") won't show up.

So there are some reasons to stay positive.


Why analyse transcriptome instead of proteome?

Q: Why not just extract the proteins…

A: It’s not just a question of extracting the proteins, you would need to separate them and then isolate each of them. There is currently no practical way to do this for say, 10,000 proteins, which in any case may have multiple forms. The beauty of the RNAseq method is that it does not require physical separation or isolation of transcripts.

An approach more likely to be useful is to identify and quantify the proteins in situ, but this is still some way off having the comprehensiveness and sensitivity required.

  Q: …sequence them…

A: Protein sequencing is slow and difficult. It cannot be applied on a mass scale, unlike sequencing of DNA copies of RNA transcripts. Other methods of identification based on physical behaviour (migration or elution position) are more promising, and the direction that is likely to be followed.

  Q: …quantify them…

A: Even that is difficult, when you are eluting proteins from gels, for example. In contast, RNAseq methodology just counts transcripts. (But the likely direction this will go is quantitation by peak height, without separation or isolation, as with metabolomics, or by the intensity of some signal from the protein immobilized in the gel, staining of something more sophisticated.)

So, in general, you do protein analysis on particular individual proteins of interest to you, whereas you can do RNAseq analysis on all the transcripts in a biological sample, and then go fishing (among the results, and afterwards on the lake if that’s your thing).


From this article:

  Researchers found that when the virus productively infects the few permissive CD4 T cells present, death occurs through apoptosis mediated by an enzyme called caspase-3. But when HIV abortively infects nonpermissive CD4 T cells, death occurs by pyroptosis, which depends on the activation of caspase-1. It turns out that the vast majority—roughly 95 percent—of CD4 T cell death in lymphoid tissues is driven by caspase-1-mediated pyroptosis.

When it comes to macrophages, however:

  macrophages are much more resistant to cytopathic effects of lentiviral replication than for example activated CD4+ T cells [23, 24, 25], and HIV-1 has evolved sophisticated mechanisms to prolong the life span of infected macrophages [24, 26]. Especially long-lived macrophages may therefore harbor the virus for long time periods, thus constituting HIV-1 reservoirs and posing a major obstacle to virus eradication from infected individuals.

Source


Difference in length of Okazaki fragments

I have found one more possible reason from Bruce Alberts' The Molecular Biology of the Cell: (Ch. 5 page 254)

  Nucleosomes are spaced at intervals of about 200 nucleotides pairs along the DNA strand , which may explain why new Okazaki fragments are synthesized on the lagging strand at intervals of 100-200 nucleotides in eukaryotes, instead of 1000-2000 nucleotides as in bacteria.

As already discussed by me and @SatwikPasani in the comments, increasing telomere longevity in eukaryotes by reducing the length of okazaki fragments, and consequently reducing the part of telomere cut-off after every division might be another reason for having shorter fragments in eukaryotes as compared to prokaryotes which do not contain telomeres.

EDIT : Having thought over it again, the relation between Okazaki fragment length and telomeres do not seem logical as only RNA primer length is important when considering telomere length.

Balakrishnan and Bambara (2013) explain the regulation of (and differences between) prokaryotic and eukaryotic Okazaki fragments in detail.


I-cells produce the normal functional lysosomal hydrolases, however they are secreted outside of the lysosome.

The Hurler cells lack a functional lysosomal hydrolase to degrade the certain oligosaccharides.

When the two cell lines are mixed together in the same media, through non-specific endocytosis, the Hurler cells will simply arbitrarily want to endocytose things such as nutrients from the media into the cell, and some of the times, the Hurler cells may endocytose the functional enzymes secreted outside of the extracellular matrix / membrane from the I-cell.

Thus, the Hurler cell's lysosomal contents can then be degraded to some extend and restore the defect exhibited in normal Hurler Cells.


What does it mean to protect RNA polymerase?

By "protection" the authors mean that in the presence of NusA, some proteins are less prone to aggregation after heat shock. "Protection", in general, could also refer to stabilization i.e. reduction in the degradation rates of the protein.

To detect the influence of NusA on heat-induced aggregation, we used
lactate dehydrogenase (LDH). LDH was incubated at 48°C in the absence
or presence of NusA. As shown in Fig. 2b, LDH slowly aggregated at
48°C without the protection of NusA. However, when this experiment was
performed in the presence of NusA, aggregation was visibly reduced.
These results suggest that NusA also protects unfolded proteins from
irreversible aggregation during thermal stress.
...
...
In E. coli, RpoA and RpoB, the major components of RNAP, are prone to
aggregation under heat stress in vivo. They were reported to interact
with GroEL and DnaK, mainly for the protection from aggregation or
refolding into a nonnative state48,49. However, based on the strong
interaction between NusA and RNAP, we propose that the chaperone
activity of NusA could provide more direct and concentrated protection
for RNAP under stress, i.e., NusA could simultaneously act as a latent
protector of RNAP during transcription elongation and termination.


Revised answer summary

My original answer provided evidence that the trp repressor is a dimer, and that conclusion stands, especially as regards its functional form. I still regard the statement in Wikipedia that it is a tetramer as incorrect, although I now see how it might have arisen. It seems to be a misinterpretation of results in vitro that show an equilibrium can exist between dimer and tetramer (not tetramer only). I have expanded on this in an additional section.

A functional dimer

The functional form of the is certainly a dimer, as originally reported by Schievitz et al. (1985). The summary of this paper includes the statement:

  “The crystal structure of the Escherichia coli trp repressor has been solved to atomic resolution. The dimeric protein has a remarkable subunit interface in which five of each subunit's six helices are interlinked.”

It was crystallized in combination with the operator DNA, and the structure deposited in the Protein Database (PDB) as 1TRO. I reproduce an image from the PDB entry below. Many other DNA-binding proteins also have dimeric structures.

A dimer–tetramer equilibrium observed in solution

The statement in Wikipedia probably arises from a report by Fernando and Royer (1992) — subsequently confirmed — that in solution there is an equilibrium between the dimer and higher oligomers (the tetramer predominating). Tryptophan was found to shift the equilibrium to the dimer. The authors claim that this has physiological relevance, although this still seems a moot point.


Could an action potential produce few or more neurotransmitters based on the stimulus received?

Short answer

Widening of the action potential increases neurotransmitter release;
Generally, an action potential results in the release of about one vesicle of  neurotranmitters;
An action potential does not have to lead to neurotransmitter release - the chance being anywhere between 9 - 100%, depending on the synapse under investigation.

Background

Neurotransmitters are released in packets, called neurotransmitter vesicles:

Source: Science blogs

Vesicles are released via a mechanism involving Ca2+. When an action potential reaches the synaptic terminal, voltage-gated Ca2+ channels open, which leads to Ca2+ influx. The increased Ca2+ in the terminal leads to release of vesicles.

A study by Sabatini & Regehr (1997) showed that widening of the presynaptic action potential in rat cerebellar cells resulted in enhanced Ca2+ influx, which in turn greatly enhanced neurotranmitter release.

According to a study in rat hippocampal cells it was shown that, on average, a single action potential releases approximately 0.5% of the vesicle pool from the presynaptic terminal. The presynaptic vesicle pool was estimated to be 100 - 200 vesicles, which hence added up to 0.5 - 1 vesicle released per action potential (Ryan & Smith, 1995).

An earlier study of Rosenmund et al. (1993) confirms these findings in hippocampal neurons, and investigated the variability between different synapses in greater detail. They found that the chance that a single action potential released neurotranmitters was 9 - 54%. They reasoned that larger synaptic terminals, or terminals triggered by long-term potentiation have a higher chance of releasing neurotransmitter. Moreover, such terminals with enhanced release probability may also have a higher chance of releasing multiple vesicles per action potential. They predicted that 54% of release events from such enhanced terminals may release multiple vesicles per action potentials, whereas just 9% of normal terminals may do this.

References
 - Rosenmund et al. Science 1993; 262: 754-6
 - Ryan & Smith, Neuron 1995; 14: 983-9
 - Sabatini & Regehr, J Neurosci 1997; 17: 3425-35


Leaf formation on unknown tree: cocoon or something else?

Based on the location and assuming this isn't a domesticated hazelnut there are two likely hazelnut species.  The lack of the distinctive "beak" seen on the Beaked hazelnut means this is most likely an American hazelnut (Corylus americana):

The hairs along the young branch are also consistent with this (see for example the Plant Guide from the USDA).

Note, however, there are hybrids between American and European hazelnuts so it is beyond my ability to be completely sure by visual inspection alone.


Conservation Genetics - Book recommendations

This book "A primer of conservation genetics" would suit quite well I think. In particular chapter five deals with "Genetics and Extinction" and is preceded by a lot of population genetics based theory. A beginner might also combine it with "A primer of ecological genetics" (Hartl & Conner) but you seem to have enough Pop gen knowledge to not need it!

The landscape genetics is perhaps a bit lacking from this book though. Maybe a better and more comprehensive solution, but slightly more advanced, is this book which does feature some aspects of landscape genetics in chapter 15 along with good population genetics type coverage of extinction.


Measuring optical density with/without re-suspending cells

Definitely (2). Clumps of cells will cause a lot of noise in your absorbance measurements (depending on whether the light beam hits a clump or some empty space).

I don't know what your microbe is or what growth medium you're assaying on, but typically it's very important to maintain the culture well-mixed at all times, not just during measurement. If your cells clump to the bottom, you will not get the same aeration as you will if they're well-mixed, and accessibility of other nutrients could potentially be limited as well. Generally the most controlled condition is to maintain good mixing at all times, but certainly this is organism- and medium-dependent.


What's the difference between the terms "gene map" and "genome"?

This question can be easily answered by reference to reputable sources on the internet, but as it is important to encourage the general use of the term, Genome, I shall cite examples.

Genome

  WHAT IS A GENOME?

  A genome is an organism’s complete set of DNA, including all of its genes

US National Library of Medicine, Genetics Home Reference

Genetic Map

  the arrangement of genes on a chromosome

Merriam Webster Dictionary

This is actually definition 3 of map in the dictionary — i.e. a variant on topological maps. The scientific usage is made clearer in the following:

Mapping

  DNA mapping refers to the variety of different methods that can be used to describe the positions of genes. DNA maps can show different levels of detail, similar to topological maps of a country or city, to indicate how far two genes are located from one another.

Nature Scitable

Distinction in a nutshell

A Genome is an entity — a Genetic Map is a graphical representation of features of that entity.

Hence the following sentence makes sense:

  There is no genetic map for the genome of Bacillus obscurus.

The two terms are certainly not identical. The confusion of the poster may relate to the practical limitations of representation such that often the map of only one chromosome is presented at a time.


How do biologists infer correct ORF of a DNA sequence?

TransDecoder is a commonly used program for extracting likely coding regions from transcriptome assemblies, which does the following to make a call:

  TransDecoder identifies likely coding sequences based on the following
  criteria:

  a minimum length open reading frame (ORF) is found in a transcript
  sequence
  a log-likelihood score similar to what is computed by the GeneID
  software is > 0.
  the above coding score is greatest when the ORF is scored in the 1st
  reading frame as compared to scores in the other 5 reading frames.
  if a candidate ORF is found fully encapsulated by the coordinates of
  another candidate ORF, the longer one is reported. However, a single
  transcript can report multiple ORFs (allowing for operons, chimeras,
  etc).
  optional the putative peptide has a match to a Pfam domain above the
  noise cutoff score.

So in essence, look for the longest ORF, and then use some secondary metric (hidden Markov model, position weight array, database query, etc) to refine your prediction.


Which protein complex is composed of the greatest number of different kinds of proteins, and how many types are involved?

In this paper detailed analysis has been made on spliceosome (U2-type) composition. It should be noted that this complex has dynamic composition. In the paper authors state that up to 170 proteins may associate to a metozoan spliceosome during its course of action. Individual assemblies contain approx 110 proteins (human). Similar complex of the yeast contains approx 60 proteins (precatalytic B complex), while C complexes have 50 proteins, altogether 90 different were identified in yeast. See the linked paper for details.


As someone commented, it seems likely that this was just caused by a piece of fruit that had been accidentally left in the bag. It attracted fruit flies and for weeks they were reproducing.


The directionality of the strands matters, because genes can be encoded on both strands of a chromosome (each strand can be read in 3'-5' direction by RNA polymerase). Therefore someone with the A-T case you described is also heterozygous.


Smooth muscle in the skin actually produces very little motion.  They are found in special places, such as the areolas of the nipple, the tunica dartos of the scrotum, and also around hair follicles.

Smooth muscles that surround hair follicles give you what is known as goosebumps - they contract all together, creating a bump in your skin around the hair follicle.  This can happen when you're cold, scared, or experiencing strong emotion.

Sources:

Skin Tissue Engineering and Regenerative Medicine, Justine Fenner, Richard A.F. Clark, 2016; Chapter 1


A singleton in mathematics is a set with one element.

They are likely referring to variants found in only one individual in their pool. It's possible there are other uses of the word singleton but given the context I think it is most likely.


Yes, double-stranded, helical RNA exists. It can occur naturally, a famous example would be Rotavirus, as well as synthetically in the lab.

Please note, however, that viruses strictly speaking do not qualify as a living organism.

References:

RNA double helix structure identified using synchrotron - McGill University

Double-stranded RNA viruses - Wikipedia

Rotavirus - Wikipedia


Can the shoulder bones grow after the growth plates have fused?

Regardless of growth plates, exercise does not cause bones to get longer or wider than they would have without exercise.
Each bone is like a sponge, it grows to a predetermined size as regulated by your DNA. Exercise makes the bone more dense and stronger. The more you exercise, the more stress your bones are under.  The bones respond by getting denser and stronger.

Like most organs/tissues, skeletal bone is constantly remodeling. Bone remodeling is a lifelong process where mature bone is removed (a process called resorption) and new bone is formed (called ossification). Cells called osteoclasts are responsible for the breakdown (resorption) while cells called osteoblasts handle new bone ossification. When we are young, we make new bone faster than we remove old bone and we increase our bone mass. Through our 20s this starts to shift, and we begin to lose bone mass faster than it is created. Source


Is there a genomic code for nucleosome positioning?

The genome is the complete set of DNA in an organism, including genes and non-gene sequences of base pairs (bp).1 Each codon of three base pairs in a DNA sequence specifies one of twenty different amino acids. There are four available bases in DNA; Adenine (A), Thymine (T), Guanine (G), and Cytosine (C).  Four letters taken three at a time (where order matters and repetition of a letter is permitted) gives 64 possible codes. There are only 20 amino acids necessary in most life on earth, so only 20 codes are needed from the 64 possible. One codon is also used as a start codon (start translation) and three codons are used as stop codons (stop translation). So there are 41 extra codons available. As it turns out, for most of the 20 amino acids several different codons can specify the same amino acid, but each codon only specifies a single, unique amino acid, so there is no ambiguity. The code is therefore said to be redundant or degenerate. This degeneracy allows the same protein (composed of amino acids) to be coded with different base pair sequences, which is important if one base pair sequence is better than another in its mechanical properties of bending DNA around a histone octamer to form a nucleosome.

If the DNA molecules in a typical human cell were lined up head to tail, they would form a string about 2 meters long. The diameter of a cell nucleus is only 5 μm (0.000005 meter), so the DNA really must be packaged or organized to fit. The packing solution eukaryotes developed is to coil DNA around histone proteins to form beadlike units called nucleosomes (packing the DNA also has implications for gene expression, but we will ignore that here).

Each nucleosome constains a 147 bp (base pair) stretch of DNA, which is sharply bent and tightly wrapped in a 1 and 3/4 turn (a left-handed superhelical turn to be exact) around the histone protein octamer. There are many of these nucleosome beads on each strand of DNA. Human chromosome 19, for example, has 58.6 million base pairs, so that makes for a lot of 147 base pair beads, even with streches of unwrapped linker DNA between the beads--about 75 – 90% of the base pairs end up wrapped in nucleosomes.

The bending of the DNA around the histone is made easier or more difficult depending on the geometrical and mechanical properties of the specific two base pairs or dinucleotides at the bend. This is not a trivial mechanical property: Some sequences may have a more than 1000 fold capacity to bend around the histone octamer compared with other sequences; we will say these sequences have an affinity for nucleosome positioning since they make it easy for the DNA to wrap. Conversely, some sequences are very "stiff" and are much more difficult to bend, e.g. poly dA:dT sequences. On average, high affinity sequences have more AA, TT and TA steps at positions where the minor groove faces inward towards the histone octamer, i.e., when more bendable di-nucleotides like AT and TA occur on the face of the helical repeat where it can directly interact with the histones (the helical repeat is about every 10 bp; see below).

What do we mean by "grooves?" Remember that DNA is a double stranded helix (as if you were twisting a flexible ladder) coiling two chains of sugar-phosphate "backbones" around the outside of the helix with the nitrogenous base pairs that connect the strands (with hydrogen bonds between base pairs) pointing toward the center of the helix (if you were twisting a flexible ladder into a helix the rungs would be the connected base pairs beween the two backbones). If you held up a screw you would see the threads as "grooves" in this similar helical structure. The backbones of the two strands are closer together on one side ("minor groove") of the double helix than the other ("major groove"). In undeformed β-DNA, the complementary base pairs of the "rungs" rise about 0.34 nm and twist ~36 degrees around the center axis of the "ladder" from each base pair rung to the next. A "helical repeat" will therefore occur every 10 bp's (10 x 36 = 360 degrees) as the helix completes a full turn around its axis. Don't confuse this helix with the wrapping of the DNA around a histone core; the DNA is a double stranded helix and that is in turn wound around the histone in a nucleosome.

But do nucleosomes in actual living organisms ("in vivo") actually tend to position themselves on sequences of DNA that wrap more easily around the histone core of the nucleosome, i.e., do nucleosomes in vivo actually show an affinity for specific DNA sequences?  If they do, then that could be considered to be a "genomic code  for nucleosome positioning." There are other factors (e.g., remodelling complexes which can move nucleosome positions) and related questions, e.g., do stiff sequences like poly dA:dT inhibit the formation of nucleosomes (and are nucleosome inhibitory sequences more common in DNA sequences like transcription start sites that should be exposed to facilitate interaction with trans proteins), but we will just consider simply the basic question.

By analogy, suppose I had a printer that could only print strips of paper a sentence high (vertical height of the strip sufficient to contain a 10 pitch character, say 0.1 inch high) but of arbitrary length. Imagine the printer is fed with a spool of this strip paper, like an old time printing calculator (or ATM receipt printer). If I printed this answer text page, out would come English sentences (at least I intend this to be recognizable English) on a long, thin strip. This sounds rather like a phylactery (tefillin) printer, now that I think of it, but that is a topic for comparative religion. If there are 66 lines of 7 inch long sentences on my page, then that is 38 feet of 0.1 inch paper strip to carry around for every page of text. I might find it more convenient to wind up portions of that long strip on little wooden dowels (like empty sewing thread spools for example) and then unwind them only when I wanted to read my article again (which I can never do enough). If DNA is kind of like this analogy (it is far more complex actually), then the spools are "histones" and when wrapped with paper strip become "nucleosomes." Does it makes sense that the letters I chose to construct the words in the sentences of my article were chosen to some extent based on some hypothetical capacity for some sequences of alphabetic characters to bend and coil around a spool (say some sequences had less cumulative stiff ink drying on the paper strip)? That gives you one angle on the controversy involving the idea of nucleosome positioning by genomic code. However, consider that, as in the case with degenerate DNA codons, I can choose different sequences of characters, i.e., words, to mean the same thing, so possibly I could still choose my words for meaning, but select synonyms that hypothetically bend easier, making it easier on average to coil my sentence strip up on spools.

A recent study, Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach, demonstrated that the local minima (the easy bending sequences) of a real gene could be repositioned (in computer simulation), that is, the nucleosome moved to another place in a real DNA gene sequence, by substituting equivalent base pairs (remember that a single amino acid can typically be defined by several different codons) to preserve the same protein encoding (a protein being a specific sequence of amino acids). This suggests that nucleosomes can at least theoretically be positioned anywhere on top of a gene, multiplexing the genetic information with the mechanical information as it were.

But do real genomes show any evidence of multiplexing genetic and mechanical information as described above? Experimentally mapped nucleosomes on top of genes do show strong signals in the probability for occurrence of mechanically favorable dinucleotides, but that does not prove the case (since shifting nucleosomes on random sequences may also demonstrate similar signals). The researchers in the study just cited then reasoned that if multiplexing is actually occuring, that is, if actual genomes have to balance the energy benefit of placing nucleosomes on DNA sequences where it is easier to bend the DNA into a coil around the histone, then it must be easier (and a more frequent occurrence therefore) to do that in non-coding sequences of DNA where only the "mechanical preference of the amino acids" need be considered (and not the necessity to maintain a specific sequence of amino acids to encode a particular protein).

Accordingly, they looked at the probability distribution for the amino acid threonine codons along nucleosomes on top of coding and non-coding regions of the S. cerevisiae and S. pombe genomes (high resolution nucleosome maps exist for both organisms). Both spectra showed a peak at the 10 bp (remember our earlier discussion of helical repeat), indicating that the codons for threonine display an overall rotational preference with respect to DNA bending within nucleosomes, but the non-coding peak was significantly higher for both organisms. When the 10 bp periodicity was plotted for all 20 amino acids for coding vs non-coding regions in both organisms the majority of points exhibited higher amplitude outside of genes, i.e., in non-coding regions where only the position preferences were a factor.

These findings (that the local minima, the easy bending sequences, of a real gene could be repositioned using degeneracy; that strong signals in the probability for occurrence of mechanically favorable dinucleotides are found in real genomes; and that the amplitude of 10 bp periodicity is higher in non-coding regions of actual genomes) at least suggest the possibility that nucleosome positions are the product of a mechanical evolution of DNA molecules, i.e., that there is a genomic code for nucleosome positioning in eukaryotes.


Why do we see a different color when we mix two colors?

I am not sure if this is entirely correct, its just a scientific guess. But it might actually play some role in this phenomenon. This is actually the physics part part of answer rather than the biology part.

Rayleigh criterion for angular resolution is the minimum angle which two bodies should subtend on an object so that they can be viewed as distinct bodies by that object.

Suppose there are 2 bodies, (right now) with same color of wavelength $\lambda$. Now, they are viewed from a lens of aperture $d$. Thus, from Rayleigh's equation, the minimum angle which these bodies should subtend with each other on the lens is given by:

$\theta = 1.22 \lambda/d$

Now I'm not sure if this is correct, but if the 2 bodies have different colors, of wavelengths $\lambda_1$ and $\lambda_2$ then the equation becomes:

$\theta = 1.22\times (\lambda_2 - \lambda_1)/d$

$\theta = 1.22 \times \Delta\lambda/d$

Now, putting values in this equation:

$\lambda_2 = 597 nm$

$\lambda_1 = 492 nm$

$d = 5 mm = 5 \times 10^{-3} m$

Answer comes out as:

$\theta = \underline{1.22 \times 105 \times 10^{-9}}$
$\hspace{15mm}5 \times 10^{-3}$

$\theta = 2.56 \times 10^{-5} rad = 1.4 6\times 10^{-3\circ}$

So, if these 2 bodies subtend an angle less than $2.56\times10^{-5}$ radian, then they will appear as a single object with green color.

Now, solving it by a common formula:

$\theta = a/l$

$l = a/\theta$

$l = \underline{\hspace{7mm}10^{-2}\hspace{7mm}}$
$\hspace{8mm}2.56 \times 10^{-5}$

$l = 390.625 m$

It means if yould hold two 5 cm x 2 cm papers together (i.e. total 10 cm2), one with blue color and the other with yellow color, then you would see a single paper of green color if you keep these papers $\approx$391 m away (if my calculations are correct ;).

This, in part, explains that it is not the fault of only our eyes, but of light and physical laws too.

References:

Angular resolution
Wavelengths of different colors
Resolving power of imaging instruments


If this is a topic that really interests you, I'd suggest searching for papers/reviews/opinions written by Didier Raoult.  Raoult is one of the original discoverers of the massive Mimivirus and his work will lead you to some truly fascinating discussions that I couldn't hope to reproduce here.

The main argument for why viruses aren't living is basically what has been said already.  Viruses are obligate parasites, and while plenty of parasites are indeed living what sets viruses apart is that they always rely on the host for the machinery with which to replicate.  A parasitic worm may need the host to survive, using the host as a source for energy, but the worm produces and synthesizes its own proteins using its own ribosomes and associated complexes.

That's basically what it boils down to.  No ribosomes?  Not living.   One advantage of this definition, for example, is that it is a positive selection (everyone "alive" has got ribosomes) which eliminates things like mitochondria that are sort of near the boundary of other definitions.  There are examples on either side of something that breaks every other rule but not this one.  Another common rule is metabolism and while that suffices for most cases some living parasites have lost metabolic activity, relying on their host for energy.

However (and this is the really interesting part) even the ribosome definition is a bit shaky, especially as viruses have been found encoding things like their own tRNAs.  Here are a few points to think about:

We have ribosome encoding organisms (REOs), so why can't we define viruses as capsid encoding organisms (CEOs)?
Comparing viruses to a living organism such as a human is absurd, given the massive differences in complexity.  A virus, really, is just a vehicle or genetic material, and would be more rightly compared to a sperm cell.  Is a sperm cell alive, or is it a package for genetic material that is capable of life once it has infected/fertilized another cell?
The really large DNA viruses often create cytoplasmic features called virus factories.  These look an awful lot like a nucleus.  What is a nucleus anyway?  Maybe it's just a very successful DNA virus that never left.
Viruses can get viruses.

I'll wind down here, but suffice to say that while our current definition may have sufficed for a while, and still does, it is no longer quite solid.  In particular, there is a theory alluded to above that eukaryotic life itself actually formed because of viruses.  I can expand on this if you like, but here are some great sources:

Boyer, M., Yutin, N., Pagnier, I., et al.  2009.  Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms.  PNAS.  106(51):21848-21853 (http://dx.doi.org/10.1073/pnas.0911354106)

Claverie, JM.  Viruses take center stage in cellular evolution.  2006.  Genome Biology.  7:110. (http://dx.doi.org/10.1186/gb-2006-7-6-110)

Ogata, H., Ray, J., Toyoda, K., et al.  2011.  Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment.  The ISME Journal.  5:1143-1151 (http://dx.doi.org/10.1038/ismej.2010.210)

Raoult, D. and Forterre, P.  2008.  Redefining viruses: lessons from Mimivirus.  Nature Reviews Microbiology. 6:315-319. (http://dx.doi.org/10.1038/nrmicro1858)

Scola, B., Desnues, C., Pagnier, I., et al.  The virophage as a unique parasite of the giant mimivirus.  2008.  Nature.  455:100-104 (http://dx.doi.org/10.1038/nature07218)


Why human cannot stand still in one place?

Although at first sight this might seem to be biology rather than physics, maintenance of human posture is an example of control theory. Indeed a quick Google will find many publications on it - I found a good review here.

A standing human is a dynamical system that is not in equilibrium so it requires a (closed loop) feedback system to maintain it. This means sensors in your body detect deviations from your desired posture and muscles contract to return you to it. The problem is that there is a lower limit to the movements you can detect i.e. you body moves a certain distance before your muscles respond and move it back. The result is that even when we try to stand absolutely still we are actually continually moving then correcting that movement.

Some people are better at maintaining posture than others, so some people can stand stiller than others. Plus the ability declines with age, as I can testify from personal experience :-)


Are cryovials really better than regular tubes for cryopreservation?

I do not have data to back this up, but can say that from experience, cryo vials are a much better solution for storing your valuable cells. First, their plastic is thicker, meaning they’re more sturdy and can handle a deep freeze much better. The killer feature is the screw caps, which means that they will never pop open accidentally due to mishandling or temperature changes (which has happened me with samples in microcentrifuge tubes). These screw caps also allow much more efficient storage in expensive cold conditions (liquid nitrogen will be best for cells long term) and easier retrieval from boxes that are freezing cold.

Microcentrifuge tunes may suffice but cryo vials exist for a reason.


For that you would need to understand the dynamical systems theory behind the loop. The point at which the oscillation starts is called the Hopf-bifurcation. I shall explain this in simple intuitive terms. Lets assume that Protein-X activates the production of Protein-Y which in-turn causes inhibition of Protein-X production. This is a negative feedback loop.

X → Y
Y ⊣ X

Situation-1: No/little delay

You switch on the production of X. This leads to rapid production of Y which will in-turn quickly repress the formation of X. This would happen so quickly and all that would be observed is a reduction in the steady-state level of X (compared to an unregulated system). Mathematically, the eigenvalues of the system (jacobian matrix- denotes the slope of the function) evaluated at the steady state would be negative and real.

Situation-2: Some delay

In this case, it will take some time for Y to accumulate. This will cause X to shoot up above its final steady state level. This, in-turn, will cause higher production of Y. Because of higher production of Y, X will start getting repressed strongly when Y gets accumulated and starts acting. This will cause X to shoot down below the steady-state but the magnitude of this shoot-"down", will be less than the first shoot-"up". Finally, the system will settle to the steady state. This phenomenon is called damped oscillation. In this case, the eigenvalues of the jacobian are complex with negative real parts.

Situation 3: long delay

In this case the delay between production of Y and its action is so high that the system does not damp but sustains its oscillations. The eigenvalues of the jacobian are imaginary. These kind of oscillations are generally sensitive to different factors.

More robust forms of oscillations exist, called limit cycles. The network structures responsible for this are more complex than a delayed negative feedback loop. Typically it has a coupled positive and negative feedback. Understanding limit cycles is little bit more complicated and I shall not discuss them here.

Also, check out these reviews:

Tyson, John J., and Béla Novák. "Functional motifs in biochemical reaction networks." Annual Review of Physical Chemistry 61 (2010): 219.

Tyson, John J., Katherine C. Chen, and Béla Novák. "Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell." Current Opinion in Cell Biology 15.2 (2003): 221-231.

and this book:

Alon, Uri. An introduction to systems biology: design principles of biological circuits. CRC press, 2006. ISBN 9781584886426


can you tell me what kind of animal this is?

Looks rather like a boar skull, which would make sense in Mississippi (especially Southern Mississippi), where their population has been growing for decades.


From your bam-file, you can generate a BED(-graph) of per base coverage with bedtools genomecov (use the -ibam, -d and if you want a BEDgraph also the -bg flags).

There are multiple R packages for bioconductor which read and visualise these, including sushi.


Can anyone identify this chrysalis? (Identified)

I've found it - it's a Common Rose Swallowtail (Pachliopta aristolochiae)

A few images on this page.
http://flickrhivemind.net/Tags/aristolochiae,butterfly/Interesting including these two

There is a picture also at http://en.wikipedia.org/wiki/Pachliopta_aristolochiae but this one is upside down compared to mine.

Mystery solved.


Is there selection against long proteins and long genes?

Is there evidence of selection against long proteins and long genes?

I am not aware of any such evidence and cursory googling did not reveal studies that researched a correlation between gene selection and gene size. However,  the larger a gene, the larger the probability of a deleterious mutation within said gene so I expect that there is some limit to the size genes can reach and be stable through evolution.

  Are there proteins that are much longer than Titin in other species?

To date, titin is the largest known protein

  Do I exaggerate the cost it represents, either by not considering that
  an average rate (such as transcription rate) is not representative of
  the actual rate for typically long gene/protein or by assuming that it
  is costly to create tons of mRNAs that won't never be translated?

I really like how you estimated the time cost of producing titin. However, as you already suspect, I believe that you have several flaws in your assumptions.

First of all, the stability of mRNA and proteins varies a lot and depends strongly on their sequences. The half life of proteins can vary from minutes to Years. The Titin protein has a half life of ~70 h.

Similarly, mRNA stability varies from minutes to > 12h. Especially household and structural genes were identified to have mRNAs with long half lifes.

Both protein and mRNA stability is not simply governed by random decay but rather by tightly regulated degradation. For proteins, an example is ubiquitinylation which is a process where certain amino acid sequences are recognized and cause the protein to be ubiquitinylated which in turn triggers the degradation via the proteasome. For mRNA, the secondary structure is crucial since certain loop structures can be recognized by RNAses. Thus average protein/mRNA lifetimes do not help to estimate the actual turnover of a specific protein.


Alkaline denaturation neutralize the charge of acids but also cause hydrolysis of bases upon prolonged treatment. Strong bases will raise pH until the H+ shared between the N-base electronegative centers (N-H and O=) is stripped from the H-bond, effectively breaking them.

Organic solvents such as dimethyl sulfoxide and formamide, or high pH, could break the hydrogen bonding between DNA strands too. Low salt concentration could also denature DNA double-strands by removing ions that stabilize the negative charges on the two strands from each other.

Low pH (less than pH 1): both RNA and DNA hydrolyze (phosphodiester bonds break and the bases break off).

High pH (greater than pH 11): RNA hydrolyzes, DNA will denature but the phosphodieser backbone remains intact.

[salt]
Tm is sensitive to Na+ concentration.
Na+ acts to shield the negative charges of the sugar-phosophate backbone from interacting with one another. The repulsion between the negatively charged phosphate backbones is the major force destabilizing the double helix, therefore increasing Na+ concentration increases helix stability and decreasing Na+ concentration decreases helix stability.

References:

http://faculty.tru.ca/dnelson/courses/biol335/335notes/3recdna/4-hybrization/recDNA3a.html

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1367631/pdf/biophysj00681-0002.pdf


Why only honey bee collects & store honey?

Many different bees also make honey, not just honey bees (Apis species). There are carpenter bees, bumblebees and as Geraldo said, there's honey pot ants.

Only honey bees make any great quantity of honey. The other species make far less and it's a different consistency. Honey bees live in large colonies and honey is stored to feed developing larvae as well as feeding workers and the queen through winter. Other bees are solitary except for a few bumblebee species but their colonies are much smaller - usually less than 50. Bumblebees make far less honey. There's no need to store honey for winter as the queen and workers die in late fall. Only a newly hatched and fertilized queen will survive, hibernating through winter underground. Hence, storing more than the immediate needs of queen, larvae and workers would be pointless.

You mentioned butterflies sipping nectar. A butterfly's lifespan is very brief and only sips nectar to provide energy for fertilization and egg laying. Then, generally, they die. Larvae have been provided for already since the eggs hatch on the appropriate plant leaves as their food.


Where can I find a list of diseases and their incidence?

About diseases in general, that would concern the health dept. of the respective country government, and the govt. is the most probable source for such numbers.

However, orpha.net has two reports with numbers concerning hereditary diseases, have a look at http://www.orpha.net/consor/cgi-bin/Education_Home.php?lng=EN#REPORT_RARE_DISEASES


Chance of child inheriting at least one copy of an allele - heterozygote mother, unknown father

It seems that what you are trying to do is calculate the probability of the child having at least one copy of the "risk allele" which I will denote as "A" (and it's counterpart "a").

First of all you know that the mother is Aa, and the child will get one allele at random. The probability that the mother passes on the A allele is then 0.5.

The tricky bit is the seemingly unknown genotype of the father. However, you do know genotype frequencies, which are the probability for the fathers three possible genotypes.

If the father is AA then it is certain the child will get the risk allele, and the probability of the father being AA is 0.0025.
If the father is heterozygous then there is a probability of 0.5 he will pass on the A allele, and the probability of the father being Aa is 0.095.
If the father is aa there is a probability if 0 that he will pass on the A allele.

Combined these give the probability that the father carries at least one A and will pass it to his child.

$$(1 \times 0.0025) + (0.5 \times 0.095) + (0 \times 0.9025) = 0.05$$

The probability of the child getting at least one A is then the probability of getting it from the mother plus the probability of getting it from the father.

$$0.5 + 0.05 = 0.55$$


Depending on the development cycle of Chlamydia tend to appear in two forms, the elementary body and the reticulate body. As outlined in the excerpt below, the reticulate body can be found as inclusions in a cell's cytoplasm when stained with iodine. So yes, your initial guess of inclusion-forming units (IFUs) being a measurement of how much of Chlamydia spp is present in a sample (cell or tissue) is correct.

It is similar to the concept of Colony Forming Units (CFU) which is a unit used to estimate the number of viable bacteria or fungal cells in a sample. Viable is defined as the ability to multiply via binary fission ("division in half") under controlled conditions.

Applying the concept of CFU to the above an inclusion-forming unit may be understood as a unit to estimate the number of Chlamydia cells in a sample. The difference between CFU and IFU would be as follows, CFU counts are normally taken for bacteria/fungi grown in a controlled environment. CFU counts also only account for viable cells, dead cells are disregarded. This is in contrast to IFU counts as we do not have a controlled environment as such and depending on what staining method you use, IFU counts may or may not account for dead cells too.

  Chlamydia may be found in the form of an elementary body and a reticulate body. The elementary body is the nonreplicating infectious particle that is released when infected cells rupture. It is responsible for the bacteria's ability to spread from person to person and is analogous to a spore. The elementary body may be 0.25 to 0.30 μm in diameter, and it mainly consists of C. trachomatis, C. pneumoniae, and C. psittaci. This form is covered by a rigid cell wall (hence the combining form chlamyd- in the genus name). The elementary body induces its own endocytosis upon exposure to target cells. One phagolysosome usually produces an estimated 100–1000 elementary bodies.

  Chlamydia may also take the form of a reticulate body, which is in
  fact an intracytoplasmic form, highly involved in the process of
  replication and growth of these bacteria. The reticulate body is
  slightly larger than the elementary body and may reach up to 0.6 μm in
  diameter with a minimum of 0.5 μm. It does not present a cell wall.
  When stained with iodine, reticulate bodies appear as inclusions in
  the cell. The DNA genome, proteins, and ribosomes are retained in the
  reticulate body.

Link to Wikipedia page - excerpt was taken from there.


What software do I need to read-write cas9? and .dna files?

You have a long journey ahead. This guy spent about 4 years to learn what he is doing here.

He is using Snapgene software


Two reasons for antibody wash:

To limit non-specific epitope binding. All ABs have specificity.  Washing is usually trying to remove weaker binding to non-intended targets.
For flow, excess AB that is not bound, if also pre-conjugated to a fluorophore, may allow for excitation of the fluorophore while going through flow even though the antibody isn't bound to the cell type of interest.

If you had a very specific AB, and very little excess, you may not notice a thing. I'm sure there are additional reasons; these are the two that immediately come to mind based on my own flow cytometry experiments.


How much DNA of mitochondrial origin is incorporated in main cell's DNA?

Interesting question. I researched this a bit now and the phenomenon is termed "numt" for  "nuclear mitochondrial DNA". This term descrives the transfer of cytoplasmic mitochondrial DNA sequences into the separate nuclear genome of a eukaryotic organism. It seems that most of these sequences are inactive. This list at pseudogene.net has a large number of sequences in a lot of different organisms, for humans insertion between 0,2 and 14,2 kb are listed. Most of these sequences are detected in the deep sequencing projects underway these days and by comparative sequence analysis. An example is this paper, where they found mtDNA on chromosome 1 of homo sapiens, which was still part of the mitochondria in homo neanderthalensis.
For more information you can go to the list of papers I list below, this should be a good starting point:

http://www.ncbi.nlm.nih.gov/pubmed/11369110
http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020273
http://www.ncbi.nlm.nih.gov/pubmed/15014143
http://www.ncbi.nlm.nih.gov/pubmed/18721785

The papers should all be accessible, if not, let me know.


What is the name of this brown, "flat hat", fungus?

Pretty sure (but not 100% certain) that it is a Amanita porphyria bk9845, which in german is called a "Porphyrbrauner Wulstling"

  Cap: 3-12 cm; convex, becoming broadly convex, often with a central bump; sticky at first or when wet; bald; appearing streaked radially; the margin not prominently lined; grayish brown to brown or purplish brown; often with scattered gray to purplish gray warts or patches.

Source:

amanita porphyria


Do blind people learn Braille equally fast as the sighted?

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

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

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

Hope this was helpful!


What are the olfactory chemicals in whiteboard/permanent markers and what do they bind to in the nose, lungs, and brain?

The smell of dry erase markers come from the chemicals ethanol, butanol and isopropyl alcohol. Like all chemicals inhaled through the nose, they bind to the Receptor neurons in the located in the back of the nose. The neurons interpret the chemicals using a 'lock-and-key' model but the specific way its coded and perceived in humans is still being researched and the process is not completely understood.


Strange Black-Brown Insect Identification

This is an earwig, an insect in the order Dermaptera that has notably robust cerci.

 Credit: Ron Yeo

Note that the name comes from an old wives' tale about these insects crawling into people's ears. They don't:

  Earwigs do get their name from the belief that they climb into human ears while individuals are asleep, however, this belief is fortunately untrue

Based on the sexing rules indicated here, your specimen's relatively straight cerci might be an indication that you found a female.

Earwigs are found worldwide, and with about 2000 species (source), it'll be difficult to narrow this down to species. If you can get access to a local dichotomous key or other accurate insect ID guide, you might be able to narrow further.


Are receptors integral membrane proteins or peripheral membrane proteins?

All the receptors I know about are integral, transmembrane proteins. It would certainly be possible for a receptor domain to exist on a peripheral protein that interacted with a transmembrane protein, but I don't know of any examples of this: an extracellular peripheral protein would tend to float away, which is a bit of a problem if they aren't intended for secretion.

There are certainly peripheral proteins that associate with the internal parts of transmembrane receptor proteins and may influence their function, but they are not themselves receptors.

I'm not sure about your question about "which proteins" - those proteins are most often named after their ligand followed by the word "receptor", or based on their function that is triggered by binding their ligand, or both (i.e., the AMPA receptor is a glutamate receptor that is also activated by AMPA; receptor tyrosine kinases are a family of receptors that are tyrosine kinases; the individual members of the family are typically known by their ligand).


Why is Homologous Recombination (HR) more frequent at long sequence repeats?

HR rarely occurs at all in normal somatic cells, because multiple different mechanisms try to prevent this from happening between sister chromosomes during mitosis; the implications of this recombination can be detrimental to the organism. Instead, in eukaryotes, HR normally occurs during Meiosis, in the formation of Gametes, which will recombine anyway. This actually has a beneficial effect because it increases genetic diversity of offspring, thereby promoting evolution.

As for how homologous repeats enhance HR, it is a rather simple mechanism. Basically, you have the two homologous strands side by side, and you have this extensive repeat section in the middle. The thing is, because the repeat section is so long, and because of the fact that it repeats, really any repeated sequence anywhere along that section can cross over with any repeated sequence on the other strand. This increases the availability of HR sites, as well as increases the number of possible outcomes, therefore increasing the probability that HR will occur. Plus, as the number of repeats increases, the number of possible recombinations increases exponentially, making HR on long repeats much more likely than other cases of HR

I hope that satisfactorily answers your question.


How are monocytes larger than capillaries?

They aren't completely rigid and can change shape to squeeze through (see Downey et al).

If they are activated, monocytes can get stuck in capillaries and block them, which contributes to poor circulation following reperfusion after an ischemic blockage (see Engler et al).

Downey, G. P., Doherty, D. E., Schwab 3rd, B., Elson, E. L., Henson, P. M., & Worthen, G. S. (1990). Retention of leukocytes in capillaries: role of cell size and deformability. Journal of applied physiology, 69(5), 1767-1778.

Engler, R. L., Schmid-Schönbein, G. W., & Pavelec, R. S. (1983). Leukocyte capillary plugging in myocardial ischemia and reperfusion in the dog. The American journal of pathology, 111(1), 98.


Your misunderstanding probably stems from the differences of definition of inverse in bioinformatics (reverse) and cell biology/genetics.

What is shown in the picture is chromosomal inversion, in which the segment of DNA gets cut, flipped and ligated. Note that in the DNA, 5' would be ligated to 3' and vice-versa. So the 5' of the bottom strand i.e. T is ligated to the 3' of the top strand i.e. C. Similarly for the other ends. Therefore, you see a reverse complementation.

The sequence of the top strand however should have been 5'-TTAC-TGCCGTCAG-TAG-3' which has been incorrectly shown as 5'-TTAC-TGGGGTGAG-TAG-3'. That is a mistake in the picture.

Have a look at this picture [1]:

[1] Okamura, Kohji, John Wei, and Stephen W. Scherer. "Evolutionary implications of inversions that have caused intra-strand parity in DNA." BMC Genomics 8.1 (2007): 160.


Is Hypericum Perforatum (St. John's wort) a C3 or C4 plant?

It's C3, according to the Illinois plant information network.  (See CO₂ fixation on this page.) This is the best I could find.


Can Omega 3 Fatty Acids prevent chest pain in periodic Atrial Fibrillation?

Omega 3 Fatty Acids cannot prevent the the acute symptoms of periodic A Fib, nor is there a role for vitamin D in the treatment of acute symptoms of periodic AF.

Atrial Fibrillation with the symptom of chest pain is very worrisome and requires urgent or emergent treatment. The most common treatments are heart rate control via IV antiarrhythmics, or cardioversion, either electrical or chemical, usually done in the emergency room.

There has never been a study wherein AFib accompanied by symptoms of chest pain was treated by Omega 3 Polyunsaturated Fatty Acids and there never will be, because N3PUFA does not cardiovert arrhythmias nor does it effect heart rate in AFib.

No medical body of any kind would support such a study.

Finally, there is no convincing evidence that N3PUFAs decrease the incidence of AFib, and this has been studied often, because eating 4-5 servings of fish per week has been shown to have a beneficial effect on A Fib. That gives reason to hope that N3PUFA supplements might be similarly beneficial. However:

  The role of omega-3 polyunsaturated fatty acids in the setting of AF is controversial. Although some studies demonstrate a lower incidence of AF recurrence with omega-3 polyunsaturated fatty acids use, others have shown an increased risk. Further studies are needed to assess the role of N3-PUFAs in the prevention of AF.[1]

If N3PUFAs have not been proven to help AFib long term, there is no hope whatsoever that studies will be undertaken to shown their effect in the acute treatment of symptomatic AFib, which is the scenario you have described.

Atrial Fibrillation becomes symptomatic when the arrhythmia results in decreased perfusion of various organs. If there is decreased perfusion to the heart, the presenting symptoms may be of ischemia (usually chest pain or pressure) or shortness of breath due to decreased cardiac output and decreased oxygenation in the lungs. If it is severe enough, fainting may occur from decreased blood pressure, and decreased perfusion of the brain. If it is not severe, it may result in a sensation of flip-flopping in the chest, or palpitations (irregular, thumping, or pounding heartbeats). There are other symptoms of A Fib but since you mentioned chest pain, I won't elaborate.

[1] Atrial Fibrillation in the 21st Century: A Current Understanding of Risk Factors and Primary Prevention Strategies


What is the role of hippo signalling in oral squamous cells

Mutations in the Hippo signalling pathway cause unusual organ growth in flies.  After a good deal of intensive research, its been shown that Hippo genes are responsible for suppressing organ growth in development, increasing cell death and slowing proliferation.

Given this role, its not surprising that Hippo genes are also important in cancer.  I'm not an expert in cancer, but a quick search turned up an association of cancer with the Yki (YAP in mammals) transcription activator, an oncogene from the Hippo Pathway.  YAP suppression has been linked to cancerous growth.  And its also been shown that YAP is amplified in oral squamous cell carcinoma cells.  This last is circumstantial but consistent with what we know about YAP.


What kind of insect is this and what is it doing?

I think it's a Robber Fly. Those are predatory.


How do the lungs act as a sieve to trap blood clots?

Just as an intro...

The heart pumps deoxygenated blood from the right ventricle, through the pulmonary arteries (pic) which then eventually split into small capillary networks that surround the alveoli. The alveoli are formed by the trachea eventually branching off. So when you breathe in, the alveoli become filled with higher levels of oxygen.

The blood then becomes oxygenated and returns to the heart via the pulmonary veins to be pumped to the rest of the body.

The deoxygenated blood becomes oxygenated because there is a difference in oxygen and carbon dioxide concentration between the capillary network (O2 low / CO2 high) and the alveoli (O2 high / CO2 low) and so gas diffuses across because of the difference in concentrations (pic).

Physiology textbooks explain these mechanisms but for blood clots in particular, you'll need to check out a pathophysiology book.

Blood clots

When a blood clot travels to the lungs, it's referred to as a pulmonary embolus or PE.

Most of the time (90%), pulmonary emboli are formed in deep veins of the lower leg. These then travel to the pulmonary circulation system.

Large emboli block larger vessels - the pulmonary arteries and their branches. The smaller ones travel further into the network.

Patients can sometimes be asymptomatic and the emboli can at times resolve on its own. The extent of the severity of a PE is determined by:

how much blood flow is obstructed;
how long the embolus has been there; and
presence other underlying lung or heart disease.

There are a number of things that a PE can cause physiologically.

Reduced Gas Exchange - alveolar dead space occurs when an alveolus is ventilated, but not perfused with blood. This, along with other factors, cause varying levels of hypoxemia (lack of oxygen).

Pulmonary Infarction - in a small amount of cases loss of blood flow to lung tissue can cause tissue death. This is fairly uncommon.

Right Ventricular Failure - if there is a large enough blockage (> 50 - 60%), the pressure in the pulmonary arteries increase. Subsequently, the load on the right ventricle is higher.
So in acute cases, the ventricle hasn't had time to adapt (hypertrophy) and so the right heart can fail.

At any rate, the haemodynamic balance can be disrupted when a PE is present.

In the elderly or people with underlying disease where their lung function is already decreased, PEs can have a significantly larger effect because they can't compensate. There are many more important points related to this but hopefully this is a useful (very) basic overview.


Guanidium is a chaotrope i.e it increases the entropy in the solution. It doesn't disrupt hydrophobic interactions. Guanidium and urea act by forming hydrogen bonds. They can bond with both the dissolved macromolecule and water. The water molecules are arranged as a shell around the hydrophobic regions so as to contain it, which leads to the reduction of entropy. This containment causes hydrophobic regions to come together and give rise to a pseudo-interaction (hydrophobic interaction. See the figure below). Guanidium interacts with the water shell and disorders it, thereby reducing the hydrophobic effect.
Guanidium can also interact with macromolecules directly, by forming hydrogen bonds. In this process they can disrupt the normal H-bonds in the macromolecule.


What are the benefits of statins in terms of prolonging life?

I suspect I won't be crunching as much numbers as you'd want me to, however here are some basic points:

Statins have shown a clear ability to improve the blood llipid profile.
Their use in primary/secondary prevention for cardiac events is justified by the belief that less blood lipid will leave less lipids to clog the arteries with. This is an old paradigm, and it is debated, even if we nowadays indeed give statins to all (potential) cardiac patients. There is evidence for a positive effect of those drugs, but it is not undisputable.
An enormous amount of money is made from statins, and the pharma pushes very hard for their use.
They do have undesirable effects, but those appear mostly early, so patients are usually well monitored for them and they mostly pose no real threat.

On the subject of women: women before menopause are protected from cardiac events by their hormone profile, and would therefore likely benefit very little from statins at that time. After menopause, women present the same cardiac risk as men do. I do not know if studies have shown a difference in outcome for statins in postmenopausal women. If you want to know more, I advise you to go searching for it on Pubmed

DISCLAIMER: The above does not represent professional medical advice, and is subject to debate.


I know nothing about plant physiology but I googled your question and here is what I found
Vascular cambium
From wiki

The vascular cambium (plural cambia) is a plant tissue located between the xylem and the phloem in the stem and root of a vascular plant, and is the source of both the secondary xylem growth (inwards, towards the pith material at the center of plant, often dead and/or deteriorated, that is composed of parenchyma tissue) and the secondary phloem growth (outwards [to the bark, rough or smooth, of the plant]). It is a cylinder of unspecialized meristem cells that divide to give new cells which then specialize to form secondary vascular tissues.

Intra fascicular cambium
From Biology.easlife

The cambial strip which is present between the primary xylem and primary phloem is known as the intra fascicular cambium. The intra fascicular cambium is also known as the vascular cambium. During the secondary growth the cambial ring is formed by the inter connection of the intra fascicular and inter fascicular cambium. - See more at: http://www.biology.lifeeasy.org/5040/what-is-intrafascicular-cambium#sthash.aY3SPblI.dpuf

What is the difference between fascicular cambium and inter fascicular cambium?
From biology.lifeeasy

The cambium present within the vascular bundle is called intra fascicular cambium or vascular cambium. It is present between the primary xylem and primary phloem. The intra fascicular cambium is primary in origin.
The new strip of cambium which is formed from the permanent cells of inter fascicular parenchyma is called the inter fascicular cambium.  The inter fascicular cambium is secondary in origin since it is derived from the permanent cells of medullary rays.

Need more?
If the above definitions don't help, you should include in your question why these definitions don't help and what is unclear.


First, your assumption is wrong. Bacteria multiplication is not limited by food availability only, it is one of many constraints.

Oxygen availability, water availability and the absence of toxins also play a role. You can easily start a thriving bacterial colony somewhere, but once one of these conditions changes sufficiently, the colony can die off. And it can be the growth itself which changes the conditions. A classic example is found in wine fermenting. The yeast there multiplies freely until it has produced so much alcohol as a waste product that it dies off. This is why wine is always in the 12 to 18% ABV range, anything above is "fortified wine" where the concentration was increased after the yeast's death. Yeast are not bacteria, but bacterial colonies' growth is limited in similar ways.

Second, even if the assumption were true, the spoon wouldn't be clean. Bacteria converting food in waste doesn't result in nothing, nor does it result in something gaseous which would literally disappear into thin air. OK, part of their byproducts are likely to be some gas. But you certainly get lots of bacterial bodies (alive, later dead) and also lots of waste product. Together, it forms some kind of sticky organic goo (frequently a biofilm).

So, about your spoon

it is entirely possible that it never got a thriving bacterial colony, because the conditions weren't right despite food availability
it is also possible that it got some kind of colony (pathogenic or not), and it died off before the food was consumed
in the case of a colony, it doesn't matter how much it got to consume before dying off. The spoon wouldn't have ended up clean under any circumstances, including the very unlikely "death by food going out" scenario
depending on the conditions in which the spoon is held, the colony which dominates the spoon can be bacterial, or fungal (mold, yeast), or you can end up with different species building their colonies in parallel. Still, the previous points hold under the "mold colony" or "multiple colonies" scenarios just as under the "single bacterial colony" scenario.


What does `knee atlas` means in an IEEE's paper?

The knee atlas is an MRI generated with the intent of identifying anatomical features, much like this.


Have there been any macro-evolution experiements?

Issue with the question

The question of what is an evolved phenotype that is "seemingly significant enough to the layman to be called macro-evolution" is very unclear and it makes it hard to answer.

Most experimental evolution are performed on lineages that have very short generation time (for obvious reasons) and on these lineages it is hard to even imagine the evolution of something that a layman would consider to be "significant enough to be called macro-evolution".

The whole issue is that one will probably consider a change in phenotype to be "seemingly significant enough to the layman to be called macro-evolution" if it occurs on lineages that have long generation time and therefore cannot be observed within a lifetime.

The question interesting. However, I think the best one can do is to look at the wiki article for experimental evolution who already offer quite an interesting list of examples. I tried below to highlight a few cases of eventual interest

Long term artificial selection on "large living things"

If one wants to consider artificial on "large living things", then probably artificial selection on crops and cattle will be a good place to look at. I think I don't need to list and make extensive description of how artificial selection has changed their phenotypes (and genotypes). Consider the pigs, banana and corn as examples.

A few evolved features that has evolved in labs in small organisms

We have observed evolution of multicellularity form unicellular organisms, observed new metabolic pathways and change in ploidy level just to cite a few major things that we evolved.

Lenski experiments

The Lenski long term experiments is the longest in lab evolution experiment performed today. They made a lot of different observations and not only the case of citric acid metabolization that you mention. Note that being able to metabolize a new compound is a pretty considerable evolved feature that only those who can't go further than considering evolution of extra legs as something significant would fail to appreciate.

Drosophila and Waddington's experiment

If one must restrict I suppose that looking at experimental evolution on Drosophila would be our best bet.

Change in allele frequency through selection is a relatively fast process. Creation of beneficial variants through mutations is often the limiting process. Cases where very different phenotypes exist in natural population and selection over these phenotypes (change in frequency only) will probably not be considered to be "impressive enough". However, one can consider Waddington's experiments (and further experiments inspired by Waddington's work) as an example of experimental evolution where standing genetic variance existed before the experiment started but was hidden in the environment they experimented (the exact process here might well be too advanced for a layman). Waddington in his experiments showed one can evolve Drosophila to have a double thorax or lose their halteres in only 20 generations.

Other Drosophila experiments

We evolved Drosophila to live in hypoxic conditions. It took about 200 generations that is more than 4 years. We have also selected Drosophila for cognitive abilities and food preference (and many other things).

Note on the term "macro-evolution"

The term "macro-evolution" hasn't been invented by creationists. It has been invented a long time ago, in 1927 by a russian entomologist. T. Dobzhanski and E. Mayr (two famous evolutionary biologist) have used this term without ever quite defining it. Because the term was never correctly defined, the vast majority of evolutionary biologist have either criticized the term.

It is true that the term is now sometimes used by creationist as any poorly defined term is one of the finest solution to build questions that can't be properly addressed due its lack of clarity.


Whether alleles are "codominant" or "recessive" or "dominant" depends on the level at which you look at it.

If you look at it from the organismal "healthy vs sick" point of view, then sickle cell anaemia is "recessive" because the individual is only sick when they have both sickle cell alleles.

If you look at it from again the organismal point of view, but this time looking at the trait as well, then you find that (if we say "A" is the anaemic allele and "N" is the normal allele) AN has a different trait (called sickle cell trait) than NN, so you could say the alleles are codominant because both the A and the N "do something" in the heterozygote.

If you look at the molecular level, again you will find that sickle cell anaemia is codominant. The gene codes for the haemoglobin beta gene. So if you have AN, then one of your alleles will be coding for the defective haemoglobin, and the other will be coding for the normal one. So you would have 2 types of haemoglobin in your blood, which means that it is "codominant."


In human anatomy / biomechanics, what is the motion called when the arm swings sideways so the elbow moves in an arc of 90 degrees?

It’s humeral retroversion at a 90 degrees abduction angle with extended elbow and slightly internally rotated shoulder.


Unlike P and O sequences which are literally joined at their ends, the sequences trpR and P are rather distant. The DNA between them is so long, that the limited space of the page prevents a decent proportional representation. So instead of painting a long line of limited-importance strands, the graphic designer choose to omit the part between slashes.

Note that despite the apparent disconnect possibly suggested by the sign -//-, the intervening DNA is continuous. The sequences trpR and P are still on the same chromosome.


Digging around a bit, I found a few resources:

Design and models for estimating antagonist potency (pA2, Kd and IC50) following the detection of antagonism observed in the presence of intrinsic activity.

and PHARMACODINAMIC on page 30, describes pA2 as:

  indicates affinity of antagonist for receptors

(as Alan Boyd just commented on)


Chili is a common reference to chili peppers in an abundance of countries, but they fall within the same designation as other so-called "peppers" such as bell pepper, cayenne, jalapeno, etc. because they are all of the same genus Capsicum. They differ, however, from traditional real peppers (black pepper for example) of the Piperaceae family. Capsicum actually belongs to the nightshade family (Solanaceae), but so do potatoes.

The word pepper originates from a south Indian term for the long pepper plant which was used as spice at the time and is a member of the Piperaceae family. I think that people have generalized chili as a pepper in this case due to the heat component, but this section of the answer is also off topic for this site.


Are there any mammals in which polyspermy produces viable zygotes?

The short answer appears to be "no".

The longer answer seems to be dependent on what you mean by "viable". Triploid humans do exist that apparently arise from dispermy, but most such fetuses die shortly after birth. Those that do not die soon after birth have a variety of health issues such as intellectual disability; "The few [triploid] infants that do survive to term have multiple severe birth defects." They're almost certainly sterile, though that source doesn't say anything about it.

The existence of elaborate physiological mechanisms for blocking polyspermy in sexual organisms generally, and further mechanical means for limiting sperm number in mammals, argue that polyspermy is something that we spend a lot of effort because it's bad. Here is a recent review of polyspermy in mammals; it has a lot more information about both mechanisms and statistics on the outcomes of dispermy.


Main methods used to predict functional annotations in GO

You can refer the IEA documentation maintained by GO consortium to get an idea about the automatically assigned evidence codes using IEA. Also please note that IEA is different from Computational Analysis Evidence Codes

ISS: Inferred from Sequence or Structural Similarity
ISO: Inferred from Sequence Orthology
ISA: Inferred from Sequence Alignment
ISM: Inferred from Sequence Model
IGC: Inferred from Genomic Context
IBA: Inferred from Biological aspect of Ancestor
IBD: Inferred from Biological aspect of Descendant
IKR: Inferred from Key Residues
IRD: Inferred from Rapid Divergence
RCA: inferred from Reviewed Computational Analysis


Why is the head/neck of the femur at that 120-150 degree angle?

The answer to this great question lies in understanding the "Hip Index". I am afraid I will have to go into some technical details to explain this:

When we stand on one leg, the hip abductor muscles on that side have to work hard to keep the pelvis stable and prevent it sagging. In this case the femur is static and the hip abductors are actually working on the pelvis that tilts up or down around the hip centre of rotation. The abductors are represented as "Fm" in the diagram.

In order to do so, the hip abductors have to exert more force than the actual person's weight. This is because the length of the effective lever arm of these muscles "distance h linking H1 with the hip centre H" is shorter than the opposite lever arm "distance D between H and G representing the vertical line down from the centre of gravity".

The hip index represents the mechanical disadvantage of the abductor muscles and is around "2/1" in normal individuals. Therefor if the person's weight is 70kgs, then when they stand on one leg, the hip abductor muscles on that side are contracting at 140Kgs to stabilise the pelvis, and the person's own weight is pushing down at 70kgs from the other side, resulting in the head of femur coming under 210kgs of weight.

If the neck of femur angle becomes more straight as in your question (approaching 180 instead of the average 135), then the hip index goes up towards infinity due to the reduction in distance "h" which approches zero. This is a deformity called "Coxa Valga". If the opposite happens and the neck of femur angle becomes less straight (less than 120), then although the mechanical advantage of the abductor muscles improves, this is offset by the reduction of the actual length of the abductor muscles "distance from i to T", making the muscles weaker. This condition is called "Coxa Vara". In reality, Coxa Vara in humans is also associated with shortness of the neck of femur, which reduces the length "h" also resulting in an increase in the hip index, and an increase in the forces over the head of femur in spite of the abductor muscles becoming weaker.

Both conditions "Coxa Vara and Valga" result in the hip abductor muscles becoming less effective in stabilising the pelvis. In these conditions, the hip index can go up to 4-6/1. This means that a person weighing 70kgs could eventually end up with over 400kgs on the head of femur, leading to pain and early wear and tear. It also results in the pelvis sagging down when walking, which leads to an abnormal walking pattern called "Trandalenburg Gait".

Therefore, a neck of femur angle of about 135 degrees provides optimum conditions for the minimum possible hip index without compromising muscle length and power. Any variation results in reduced abductor muscle effectiveness, gait problems, increased hip joint wear and tear and eventually pain.


Difference in variance of Cys in protein sequences

No, because it's extremely likely your sets are not a representative sample of the true distribution in proteins.

Your bias might be caused by an effect on the functionality of the protein, but it might as well be a bias in which organisms are sequenced or something caused by the alignment or the way you are searching for your sets.