Evolution: How could all useful traits evolve simultaneously? I have a basic question about evolution, for which I never found an answer. I understand how evolution works if we focus on one specific organ or trait. With each generation, some organism is more likely to reproduce, so the trait that leads to success gets more frequent. My problem is understanding how all the traits can evolve simultaneously.

Looking back to our ancestors, we evolved many different kinds of adaptations (in unrelated areas like eyesight, kidney efficiency or a healthy fear of predators, digestion of certain nutrients, balanced walking etc.).
Natural selection can only work with what's there, so mutations are important. But if  mutations are rare, it seems unlikely that many (thousands of) properties of organisms get improved in a single generation. You'd need to get very lucky to randomly improve all the genes responsible for it.

So, if we look back to our ancestors again, did they just improve on a single or a handful of traits in each generation? In that case we would need hundreds of generations before we have improved somewhat on each "front". By then, the other properties could "drift" back to a not-so-advantageous version. (This was supposing that each generation improves on a random trait, as opposed to long sequences of generations each improving on the same).
Or were there always some super lucky organisms that randomly got an improvement on almost all different traits? But just having some of those super lucky ones is not enough. The good traits don't guarantee success, just improve the odds. So we'd need many very lucky ones in each generation.

Has anyone calculated or simulated how the adaptation for many different traits can happen simultaneously?

Has anyone calculated or simulated how the adaptation for many different traits can happen simultaneously?

There are a lots of studies on the subject but I don't fully understand what is your issue. So I'll try to give some words hoping that helps a bit but it is possible that I'll totally miss the point you want to make.

The mutation rate in humans is around $1.25 \cdot 10^{-8}$ per base pair per individual per generation. The human genome contains about 3400 Mpb, meaning that you probably carry $1.25 \cdot 10^{-8} * 3.4*10^9 = 42.5$ mutations that none of your parents had in their genome. Now if you consider the population size, you'll see that a fairly big amount of mutations occurs each generation in the human population. So mutations are not that rare! It might unfair to take human as an example though as human's population size is very big. Anyway, the great majority of mutations are deleterious. In consequence, you are right, probably not many beneficial mutations will occur in a given population at one given generation and especially not in the same individual (except if you think of viruses!).

Now, depending on how beneficial is the mutation you are considering (selection coefficient), depending on its dominance, depending on the (effective) population size, your new mutations might take quite a bit of generations before reaching fixation in the population. In this time other mutations might occur. And then, the question is very interesting. Imagine a population of asexual individuals where two beneficial mutations exist (at two different loci [=position on a chromosome]). Because there is no recombination (by definition of what is an asexual population) never these two mutations will be found in the same individuals and in consequence if one mutation reaches fixation, it necessarily mean that the other mutation would have disappear. In sexual population it is different. Recombination allow that the two mutations, once they reaches a sufficient frequency will probably be found in the same organism and therefore, the two mutations can reach fixation.

Hope that helped a bit


Allergic rhinitis vaccine Note : Any answer to this question will not be (and should not be) taken as medical advice.

One of my friends has allergic rhinitis and has been prescribed an oral vaccine. He is allergic to 3 different classes of substances and so, has been given 3 different types of vaccines. He has to place them below his tongue.

I am curious about some of the procedures he has to follow.

1.How does a vaccine of this type work ?

2 He has been given 2 vials for each type of vaccine. First one is labeled SRS and other one as I understand is - it's allergen. So, What is SRS ? What's the requirement of it ?

3 It is written in the instructions that he should not eat anything one hour before and one hour after taking the vaccine. Why ?

Rhinitis is irritation and inflammation of the mucous membrane inside the nose. Common symptoms of rhinitis are a stuffy nose, runny nose, and post-nasal drip. The most common kind of rhinitis is allergic rhinitis, which is usually triggered by airborne allergens such as pollen and dander [1].

Many questions regarding sublingual immunization still remain to be addressed, including the use of proper adjuvant and the optimization of vaccine formulation to further enhance the vaccine efficacy [2].

Sublingual immunization can induce both systemic and mucosal immune responses against a variety of antigens, including soluble proteins, inter particulate antigens, and live-attenuated viruses [2].

Sublingual immunization has been shown to be safe and highly effective in generating robust immune responses against the administered antigen. Moreover, it has been shown to confer protective immunity by simultaneously eliciting systemic IgG and mucosal IgA antibodies as well as cytotoxic T lymphocyte responses in the peripheral lymphoid organs and mucosal tissues. Studies also suggest that sublingual immunization could be a better alternative to the traditional parental route of vaccine delivery against both genital and respiratory pathogens [2].

Although the s.l. mucosa does not allow passage of macromolecules into blood, s.l. immunization with ovalbumin, a model soluble protein antigen, administered
alone or together with cholera toxin adjuvant, induces mucosal antibody responses as well as systemic immune responses in mice. The magnitude of serum antibody responses induced by s.l. immunization was in fact comparable to that seen after intranasal (i.n.) immunization and far superior to that after o.g. (oro-gastric) immunization [3].

Upon stimulation of mucosal surfaces by foreign antigens, dendritic cells among the antigen presenting cells are immediately processed and transport antigen via afferent lymph to draining lymph node for presentation to T cells. Subsequently they induce secretory IgA antibodies. This suggestive link between trafic pattern of dendritic cells and their functions led to the investigation of the chemokine responsiveness of dendritic cells during their development and maturation. It has been observed that type II mucosa tissues (e.g., skin, vaginal, and buccal), which are covered with stratiﬁed epithelia and devoid of
mucosa-associated lymphoid tissues, mainly express CCL20, CCL19/CCL21, or CCL27/CCL28 individually [4].

CCR7 (chemokine receptor) expressed CD8α-CD11c+ cells ferry antigens in the sublingual mucosa, migrate into the cervical lymph nodes, and share the antigen with resident CD8α+CD11c+ cells for the initiation of antigen-specific T and B cell responses following sublingual challenge. The sublingual mucosa is one of the effective mucosal inductive sites regulated by the CCR7-CCL19/CCL21 pathway [4].

References:

Wikipedia, Rhinitis
Byoung-Shik Shim, Youngjoo Choi, In Su Cheon, and Man Ki Song. Sublingual Delivery of Vaccines for the Induction of Mucosal Immunity.
Cecil Czerkinsky, Nicolas Çuburu, Mi-Na Kweon, Fabienne Anjuere and Jan Holmgren. Sublingual vaccination.
Joo-Hye Song, Jung-Im Kim, Hyung-Joon Kwon, Doo-Hee Shim, Nirmala Parajuli, Nicolas Cuburu, Cecil Czerkinsky and Mi-Na Kweon. CCR7-CCL19/CCL21-Regulated Dendritic Cells Are Responsible for Effectiveness of Sublingual Vaccination.


What is the difference between pluripotent and totipotent cells? Both develop into specialized cells.Then how are they different?

Expending on Gerando Furtado link

Totipotent cells can differentiate into three germ layers (endoderm, mesoderm, or ectoderm), into cells of the cytotrophoblast layer or syncytiotrophoblast layer of the placenta.

Pluripotent cells can differentiate into the three germ layers (endoderm, mesoderm, or ectoderm).

So totipotent cells develop into the all the cells of the embryonic body and fetal side of the placenta. While pluripotent cells can only develop into cells of the embryonic body.


How allele is related to trait that is more complex than two cases (ex. height)? Recently I started to learn about evolution and genetics. Simple stuff at the beginning - some videos, some reading. So far, everything seems to be pretty simple and straightforward. I easily grasp the concept of gene, allele and trait as the basic level. What bothers me is, that all of examples shows allele that has two options, sometimes three - peas yellow or green, blood type IA, IB and i - so on and so on.

But traits usually aren't digital in nature, they are analog. They are gradients. You have no people that are 160cm tall or 180cm tall only - you can have one that is 160 tall and another who's 160.1 and another who's 159.95. Height seems to me as a real number which may provide unlimited results.

Is the Mendelian reasoning about alleles and traits still valid in case of height trait? How does it work in such case?

You are absolutely correct that many traits are not "digital", but "analog". In genetics, these are usually called quantitative traits. Such traits generally do not follow Mendel's laws of inheritance, but are said to have "complex inheritance". Most traits (phenotypes) in biology at the level of whole organisms probably have complex genetics; height is a classic example.

It is thought that complex traits arise by the combined actions of many genes (via their encoded proteins), while Mendelian inheritance occurs when phenotypes happen to correspond to the activity of a single gene. For very complex traits like height, many functions of the body might be involved, so the number of genes that may have some effect on the trait can be very large, but the effect of any single gene on the trait is likely small. In general, it is not understood exactly how genes contribute to the trait in such complex traits, so a phenomenological/statistical approach is used where the trait is modeled as some simple function of the genotype which is fit to data.  Wikipedia's page on quantitative genetics has more information on this.

In addition, traits may of course be affected by environmental factors as well as genetics. Height for example is strongly affected by having access to good nutrition. See this article for some discussion.

For traits with complex genetics, the underlying genes are generally difficult to identify, and for along time we have known almost nothing about the genetics of traits like height, obesity and diabetes. Since the early 2000's, massive efforts have been put into mapping the genetics of such complex traits by brute force --- measuring the effect of all genes on the trait in a very large number of individuals, in so-called genome-wide association studies. These have revealed a large number of genes over the past decade, but as expected each has only a small effect on the trait.


From which animal is this derived? I know only that it is not a bird and an insect. I am really interested in from what it is.

That's the gladius (also known as pen) of a cephalopod, probably a squid. The gladius is an internal remnant of the originally external shell of cephalopods.

According to University of California Museum of Paleontology:

  Members of the Coleoidea are probably the best known of the Cephalopoda, as this group contains the squids (Teuthoidea) and octopuses (Octopoda) [...] The majority of coleoids are squid species, and most of these animals are torpedo-shaped, fast moving, and have a thin, flexible internal shell called a pen.

And according to the Tree of Life project:

  Other cephalopods have other types of shell remnants. The gladius lies within a sac, the shell sac, which secretes it and to which various muscles attach. The gladius has a variety of shapes and thicknesses, is composed mostly of chitin and is located in the dorsal midline and generally extends the full length of the mantle.

Here is one similar to yours:

Sources:

http://www.ucmp.berkeley.edu/taxa/inverts/mollusca/cephalopoda.php
http://tolweb.org/accessory/Cephalopod_Gladius_Terminology?acc_id=1955


Problems interpreting gram stain slide My main question is this: when you interpret gram stain results, does the majority color determine if its pos or neg?

We've been given unknowns and now have to determine what the organism is. I'm having trouble interpreting gram staining results. As far morphology they are all cocci and (sort of) in clusters but (this is the confusing part) they are both purple and pink. I understand that purple indicates gram+ and pink is gram-, but there should be one genus of organism not two. So shouldn't there be only purple or only pink, but not both? Should I be looking for the "majority" color and using that to decide whether I have pos or neg? That is, if its mostly purple, does that mean pos, ...but if so, then why are there still pink cocci on the slide?

I also understand why gram-pos appear purple, --that the crystal violet-iodine complex is retained due to thicker cell walls in gram-pos..... and thinner cell walls in gram-neg, so they are decolorized and appear the color of the counterstain.

Also I definitely did not see any rods in my slide, just cocci.

The only reason that it shows both colors is due to imperfect manipulation while staining. You cannot count on the majority to determine the result of the stain.

In your specific case, rinsing or decoloration with EtoH was probably not done enough and safrainin wasn't completely eliminated.

The best way to be sure of the result would be to redo the coloring.

A good tip while staining is to have duplicates or triplicates.

Secondly, to answer what you said here:

  I also understand why gram-pos appear purple, --that the crystal
  violet-iodine complex is retained due to thicker cell walls in
  gram-pos..... and thinner cell walls in gram-neg, so they are
  decolorized and appear the color of the counterstain.

Actually it is not only the thickness of the cell wall that will cause the bacteria to retain or not the crystal-violet. Gram positive bacteria have a plasma membrane then peptidoglycan on top while Gram negative bacteria have a plasma membrane, then peptidoglycan and another outer membrane on top. Crystal violet "sticks" primarily to the peptidoglycan.

Decoloring will remove the stain on the outer membrane of gram negative bacteria. You were right with the fact that Gram positive bacteria will have thicker peptidoglycan.

Gram + vs Gram - cell walls http://www.diffen.com/difference/Gram-negative_Bacteria_vs_Gram-positive_Bacteria


(Rough) Model for DNA evolution in E. coli genes I need a model of in-gene DNA drift. I'm not interested in bacterial phylogenies alone.

Here is what I understand:

Sequences corresponding to genes have both exons and introns, but in bacteria the proportion of introns is low.
Because I'm talking about genes, sequence changes are not very neutral but subject to selection.

I have checked a few papers linked in Wikipedia about this subject, but I notice that they are tuned for entire sequences, and many of them almost predate the genomic era.

What are some current, canonical sources in this area?

Bacterial DNA evolution is like other evolution in the sense that the mutation rates are probably random and biased somewhat by the physical and chemical structure of DNA as well as the presence and activity of DNA repair enzymes.  The mutation protocols for preparing mutant libraries from UV or chemical mutagens are a good place to start I would think - like this reference. Most of this stuff is oriented towards protocols used in the lab, not in the wild.  Like how much UV does E coli get in your gut?  Not much.  Still it does happen and is a typical baseline factor in evolution.

Bacteria also mediate their own adaptation via phage transfer as well as direct lateral gene transfer, chromosomal rearrangement.  The dynamics of this evolution is just as interesting I think as site mutation as the bacteria can use its repair mechanisms and even actively upregulate some adaptation itself, responding to environmental changes.  The fundamental differences between bacterial evolution and say evolution of animals and plants come from the fact that life is relatively cheap - a single well adapted survivor can repopulate very quickly and so that even radical genetic diversity has a benefit even if some of the population dies off every generation from being a bad adaptive experiment.  (BTW animals do this too, but in the short lived haploid gamete phase, not so much as diploid animals).

Well anyway back to bacteria.  Eric Alm's lab at MIT started with his work with operon evolution.  Genes grouped together on a single mRNA leap from one cluster to another across evolution, allowing for coordination of biochemical processes in the cell.  Lately they have been looking more intensely at the evolution of bacterial species, and how the selective environment influences bacterial adaptation.

Its hard to be more specific since I'm not completely clear on your focus and needs here, but this is what I know.


Does a generator potential pass along a nerve the same way an action potential does? I have read that a generator potential is a localized depolarization of a membrane. Does that mean that it does not pass along a neuron the same way an action potential does ? If not, then how do generator potentials from multiple rods in our eyes add up (converge) and trigger an action potential in a sensory neurone ?

Generator potentials (GP) are meant to generate action potentials (AP). An action potential results, whenever the level of depolarisation at a particular place crosses a threshold. This "place" is usually the beginning of an axon of a typical receptor, since it is equipped with all the channels required to begin and propagate an action potential. The purpose of the receptor architecture, then, is to make the threshold go off in a naturally meaningful situation.

There are two possible ways this is done. Say the neuron is transmitting information about the location of a stimulus. Then the "naturally meaningful threshold" would be some spatial cutoff, a minimum area that needs to be stimulated for the action potential to go off. Then, the receptor would have several GP-producing dendrites spread out, each generator potential being summed at the meeting place of the dendrites, which happens to be the cell body and the beginning place of the axon. So the individual generator potential in each dendrite will contribute to the sum, which will be summated and the cellular decision-making process (or a crude example of it) be affected as this summation.

Another way is temporal summation, something which has, for example only one GP-producing dendrite and the axon. Then, for the summated potential at the cell body to cross the threshold, the stimulus must stay, or be summated across, for some time-cutoff. GPs have some decay time, before which if another GP reaches there, it adds up. This would be meaningful in things like the presence or absence of a touch, the cutoff preventing against minor fluctuations.

This said, the situation in the eye in much much more complex. There are several layers of neurons and each neuron performs a lot of different functions and has a specialised architecture for it. The Rods and Cones actually produce hyperpolarizations and not depolarisations (theoretically, both are propagated in the same way, but hyperpolarisations themselves do not initiate AP).

To complicate further, most receptor systems alter the frequency of AP and thus have some basal frequency, this modulation also being important for encoding the message.

An image of GP:


Why do Alu repeats form secondary structures? I've been doing a lot of research on Alu repeats and how they mediate the gene expression. I read the following article "Useful junk: Alu RNAs in the human transcriptome".

And it says that alu repeats embedded in 5'UTR makes stable secondary structure that prevents the assembly of ribosomal subunits, thus blocking the process of translation. I've been reading various articles to find out why Alu repeats form this secondary structure and why only in the 5'UTR and not in the 3'UTR. But haven't been able to find an answer.

Single-stranded RNA can easily form secondary structures, a very important example of this are tRNAs.

From a quick look at the article you read it seems that these Alu repeats work similar to riboswitches in the 5'-UTR. They can form secondary structures that block translation initiation, riboswitches commonly do this by hiding the Shine-Dalgarno sequence in a stable helix.

This kind of regulation of translation can obviously only work in the 5'-UTR as that is the place where the translation starts. The 3'-UTR can't affect translation in this way as the translation starts at the other end of the mRNA.

The Alu repeats still can form secondary structures in the 3'-UTR, and the article suggests that those might have an effect on mRNA stability.


How many phosphates are in the 5' end of a DNA strand? I know that the pyrophosphate of a NTP is hydrolysed so that it can create enough energy for the synthesis of DNA. But if we want to get specific we can know for sure that the 3' end of the DNA strand has got one phosphate because the phosphate is having a bond with another nucleotide. But what could be the reason for the 5' end to have only one phosphate and not 3? Could it be the energy providing or that the structure has to be consistent or something else that I can't think of?

The DNA polymerase can only extend a primer and therefore almost all lifeforms have a primase (which is a type of RNA polymerase) that synthesizes RNA primers at the replication origins that the DNA polymerase can extend.

As you guessed, the 5' end would indeed have a triphosphate.

  Organism            Template Sequence        Primer Synthesized
Herpes simplex-1        3′-GPyPy                 pppPuPu
T4                      3′-TTG                   pppAC
T7                      3′-CTG                   pppAC
E. coli                 3′-GTC                   pppAG
S. aureus               3′-ATPy                  pppAPu
S. aureus               3′-ATPy                  pppAPu
A. aeolicus             3′-CCC, CCG, CGC         pppGG, pppGC, pppCG
B. stearothermophilus   3′-ATPy                  pppAPu
Human                   3′-PyNN                  pppPuNN
Calf                    3′-PyNN                  pppPuNN

  Initiation sites used by primase from different sources. Pu = purine, Py = pyrimidine, N = any base ppp = the triphosphate on the 5′-end of the primer. Those bases that are required but do not code for a base in the primer (“cryptic” nucleotides) are underlined and in bold.

  Kuchta and Stengel (2010)

In the final stages of replication, these RNA primers are removed by RNAseH and DNA polymerase I in bacteria and the gaps are filled by the latter (Cooper (2000) The Cell). In eukaryotes, the primer is removed by the action of Fen1 and Dna2 exonucleases and the gaps are filled by DNA polymerase δ (Burgers 2009).

In PCR, it is quite straightforward: the product will have whatever 5' modifications the primers have (usually none).


Cellular respiration — How is the water expelled? The equation of cellular respiration is as follows:
6 O2 (g)  +  C6H12O6 (aq)  $\rightarrow$ 6 CO2 (aq)  +  6 H2O (aq)  +  ATP

How is the water produced expelled from the body (of course, after some of it is used)? Is it expelled in urine? Or is the water vapour we breath out actually the by-product of respiration? Or, is it expelled in both methods/ways?

Edited: I was wrong, the balance varies quite a bit by species. Reptiles and birds are far more water efficient than large mammals becasue they do not lose water through sweat or urine. There are animals that are metabolically water neutral, but humans are not one of them. In humans the water produced metabolically does far exceed the water used metabolically. I should have realized that reptile also produce less water. source 1source 2

In humans there are three main ways water is take in, drinking, injection (food), and a net metabolic production. There are four major losses, urine, sweat, respiration, and feces. so it is through one of these four methods.


Beetle Identification - Oregon My dad found it so I don't have a lot of good information, but it was probably about 2.5 inches, somewhat west of Portland, and was found on a sidewalk. I don't know the area so I can't say what habitats are there that it might have come from.

I think this may be a male of Trichocnemis spiculatus (Cerambycidae, subfamily Prioninae). This species is known from Western USA/Oregon, based on this key: Screening Aid for the Cerambycidae of the Western U.S.A. (from Oregon Department of Agriculture). By overall appearance, this species fits well. However, females have more pronounced spines at the sides of the pronotum, which points to a male for the individual in your picture.

(picture from http://cerambycidae.org/taxa/spiculatus-(LeConte-1851), also more pictures at bugguide.net)


Are Italians genetically separated from other Europeans? I was reading this Wikipedia article about the genetic history of Italy, and I found it interesting.

There are however a few things that puzzle me, because they seem to contradict each other. For example it states that because of the Alps forming a natural barrier Italy is, along with Finland, a genetic island in Europe. Does this mean Italians and Finns are genetically separated from all other Europeans, and to what extent? Later in the same article it says that "In Italy as elsewhere in Europe the most common haplogroup is haplogroup H", which would seem to contradict the genetic island theory. After all, Italy has been colonized by countless populations throughout its history, which might suggest the Alps didn't really stop the gene flow from neighboring countries (not to mention that other European countries are equally separated by mountains, like Spain).

I have no background in genetics whatsoever, so excuse my ignorance, I'm just trying to understand an article that seems very confusing and throws lots of different information together.

EDIT: Thanks for the quick reply! I've found another link (which seems to be more reliable than Wikipedia's unverified claim), though it still sounds like a weird theory to me.

I'm afraid that the "genetic island" idea is almost certainly wrong because

The wikipedia page offers no evidence for this claim:

  Following scientific research carried out by Dutch geneticists, Italy has proven to be one of the last two remaining genetic islands across Europe (along with Finland), this due to the presence of the Alpine mountain chain that, over the centuries, has prevented large migration flows aimed at colonizing the Italian lands.[citation needed]

Remember that any random idiot person can edit a wikipedia page. If there is no supporting reference for a claim you find in wikipedia, you should treat it as suspect.
As you point out, the Alps only block entry on the north of Italy. Italy, however, is a pretty large peninsula, completely open to the sea along its entire length. For example, here is a map of Greek and Phoenician colonies circa 530bc (source):

As you can see, significant parts of the coast of what today is Italy were colonized by Greeks and Phoenicians. There were many subsequent waves of migration and/or invasion by various tribes such as

The Lombards (image source):

The Visigoths who sacked Rome in AD410
The Ostrogoths whose kingdom in its prime contained most of modern Italy

The many Jewish communities in Italy that go as far back as the Roman era.

An article by Brisighelli et al. (which is actually quoted at the very top of the Wikipedia page you linked to) mentions that (emphasis mine):

  A total of 583 individuals were sampled from across the Italian Peninsula, from ten distant (if homogeneous by language) ethnic communities — and from two linguistic isolates (Ladins, Grecani Salentini). All samples were

  [...]

  Italy shows patterns of molecular variation mirroring other European countries, although some heterogeneity exists based on different analysis and molecular markers. From North to South, Italy shows clinal patterns that were most likely modulated during Neolithic times.

  [...]

  Before the Roman conquest, ancient Italy was characterized only by the presence of Indo-European populations living in the Italian Peninsula since the second millennium BC, corresponding to the period between the Iron Age and Romanization. During all this period there were also increasing contacts with the Phoenician and Greek colonists: the former being largely present on the coasts of Sardinia and western Sicily and the latter in Southern Italy.

  [...]

  At the beginning of the first millennium BC the following native tribes could be distinguished on the Italian territory: the Ligures, on the coast that bears their name, in the northern Apennine valleys, part of the pre-alpine valleys and the western Po Valley; the Sicani, in the interior of Sicily; and the Itali, in present-day Calabria (from whom comes the name ‘Italy’, which was to be extended to all the territory of the peninsula). Besides the already mentioned Terramare tribe, on the southern edge of the Po Valley, and the Villanovans, probably from Eastern Europe who settled throughout Central Italy, there were also the Umbrians to the east of the upper basin of the Tiber. The Veneti, who occupied the territory that still bears their name, originally came from Illyria as did the Messapii (now modern Salento or South Apulia) and Iapyges, who settled in present-day Puglia (Apulia) 5. Many other populations of Central-Southern Italy were created by the mixing of local and foreign elements dating back to the previous millennium; it is the case of the Sabines and Latini who settled in Lazio together with Falisci, Aequi, Volsci, Hernici and Ausones. The interior of Abruzzo was dominated by the Vestini, Paeligni and Marsi, while the central Adriatic coast was populated by Picentes, Marrucini and Frentani. The Apennine area of Molise and Basilicata was peopled by the Samnites and Lucanians. In Calabria and Sicily there were also the Bruttii and Siculi.

  [...]

  Molecular indices indicated that most of the Italian samples show diversity values that are comparable to other European populations. However, some differences were shown to exist, especially in isolated Ladin populations.

References

Brisighelli F, Álvarez-Iglesias V, Fondevila M, Blanco-Verea A, Carracedo Á, et al. (2012) Uniparental Markers of Contemporary Italian Population Reveals Details on Its Pre-Roman Heritage. PLoS ONE 7(12): e50794. doi:10.1371/journal.pone.0050794


Does the Abbott ID NOW coronavirus test return a positive result if you take it while you're still in the incubation period? It seems like Abbott's ID Now test works by detecting the virus directly as opposed to checking for antibodies? If the test result is negative does that mean you don't have the virus? Or does that not rule out a recent infection with the virus that has not yet reached a level high enough to be detected?

This is a great biological question! It asks a lot about how empirical science is done in the field of modern biology! I'm glad we encourage such questions from curious people who want to learn more.

  It seems like Abbott's ID Now test works by detecting the virus directly as opposed to checking for antibodies?

Yes, the ID NOW test performs a quantitative real-time RT-PCR assay to amplify reverse-transcribed viral RNA, specifically targeting the SARS-CoV-2 RdRp gene.

The product insert for the COVID-19 test for the Abbott ID NOW product describes the "analytical sensitivity" or "limit of detection" (LOD), which describes the true positive rate.

The LOD described in the product insert is the lowest amount of viral genome in the collected sample that you need to get a true positive in 95% or more of administered tests, in units of "genome equivalents per mL".

This is effectively the minimum number of copies of viral genome per mL of assayed sample needed to give a true positive in 95% or more tests. Its LOD (125 copies/mL) is comparable with other tests (example).

A false negative can result if there is insufficient virus copies in the sample, or if there is test material contamination or the test is not performed correctly.

This assay includes positive and negative controls, which help to identify potential problems with how the assay was performed. Controls are important, given the many millions of tests that will be done to identify infected carriers of SARS-CoV-2 — the assay must be done correctly and without contaminants, in order to give the best statistical odds for the correct diagnosis of those who will be tested.


Which part of human eyes is getting tired? It's a thing of common sense that if you read, drive or look at computer screen for too long your eyes will get tired. They burn, itch and try to close all the time.

But I was wondering which part(s) of them need rest so much... Blinking muscles? Lense muscles? Or the eyeball is drying out?

These symptoms have a name: Computer vision syndrome.
Basically our eyes are made to look at longer distances from 1-6 meters without much accommodation. Typically computer screens are located at a much closer distance (30-50cm), which requires constant accommodation by the eye. This leads to high stress on the muscles in the eye which subsequently get tired. Additionally less blinking leads to drier eyes.

One of the common recommendations against this is to regularly focus further located objects to give the eye the chance to relax. This is sometimes called the "20-20-20" rule, every 20 min focus on a 20 feet (about 6 m) far object for 20 seconds. See the article in the Wikipedia and here for more information (and probably also the linked references in the articles).


Estimation of species range fragmentation While discussing species distribution patterns along spatial, temporal or functional gradients one often finds a hump shaped species richness pattern.
This is well documented in many taxa and spatial scales and known as the   mid-domain-effect (e.g. Colwell & Lees 2000 ).

These patterns also arise stochastically (depending on the species range frequency distribution). So random distribution of species ranges midpoints are used as null models to test for these mid-domain-effects.

However, these models assume unfragmented species ranges. With a highly fragmented species range the pattern would look quite dissimilar.

So I don't want to start a discussion on the validity of this concept but rather ask:

Given a gradient and known species occurences on that gradient.
Has anyone read an article about (or has an idea) what would be a good/unbiased* estimator for species range fragmentation?

Thanks

*e.g: One that doesn't over- or underestimate fragmentation for rare or abundant species

Very interesting question +1. I don't know the literature on the subject very well but I did not find much by looking for it. I know that a number of methods exist when you have genetic data (STRUCTURE or some of the work of J. Novembre probably).

Here are two possible solutions

Fitting $x$ distributions

You could be fitting 1, 2, 3, ...., n normal (or uniform) distributions to the observed data. Each time, compare their maximum likelihood (for which you might need a MCMC with 2⋅x parameters, where $0≤x≤n$ is the number of distributions you're fitting) and select the "best" model with some information criterion such as AIC or BIC.

The number of fragments is just the $x$ value associated with the lowest AIC.

Logistic regression

Another (faster and simpler) solution would be to fit a logistic regression to your data.

Iteratively fit a logistic regression of degree 1,2,3,...n and then again use some information criteria to select the 'best'.

To find the number of fragments, you can then either use the number of degrees in the model or even better use some threshold on the the probability of getting a zero (which you could compute with the package effects in R).

Notes

It will probably takes you a day or so if you're at ease with these methods and have intro knowledge in programming.

You might want to get opinions from stats.SE as well.


What happens to colloidal particles in a liquid medium? And how to stabilize it? Definition

    Colloid is a dispresion of small particles of one material in another.

  Definition 2 (Wikipedia)

    A colloidal system consists of two separate phases: a dispersed phase (or internal phase) and a continuous phase (or dispersion medium) in which the colloid is dispersed. A colloidal system may be solid, liquid, or gas.

I am trying to answer problem 2:

  Question

  "Colloidal particles: What are colloidal systems, give an example, what happens to colloidal particles in a liquid medium. How to stabilize colloidal systems in a liquid medium."

My lecture slides mention this about gel: "a continuous network extending throughout the sample formed by association of colloidal particles or molecules in a liquid", "formed in concentrated polymer solutions" and "formed by association of sol-gel particles". Next lecture slides is about "liquid crystals", now I am confused -- not sure whether gel or "liquid crystals" is something to look here.

"Colloidal particles: What are colloidal systems, give an example,--"

  Milk, bear foam, paste, blood, ---

"what happens to colloidal particles in a liquid medium."

  I understand the q as solid in liquid so a gel. Examples about gel are "agar, gelatin, jelly and opal" according to my lecture slides. The electrostatic forces are in some sort of middle phase: not enough to repulse into liquid form but not strong enough to form liquid either.

"How to stabilize colloidal systems in a liquid medium."

  Wikipedia about stability (here)

    "The stability of a colloidal system is the capability of the system
    to remain as it is. Stability is hindered by aggregation and by
    sedimentation phenomena, that determine phase separation."

  Now different things to consider are:

  Electrostatic stabilization

    "In a stable colloid, mass of a dispersed phase is so low that its buoyancy or kinetic energy is too weak to overcome the electrostatic
    repulsion between charged layers of the dispersing phase."

  steric stabilization

    "particles in polymers which prevents the particle to get close in the range of attractive forces."


Length of dispersal flight of European spruce bark beetle? I'm interested in length of dispersal flight of Ips typographus. I can barely find some information about dispersal distances, height of dispersal flight, but not at all information about how many days does it takes for one beetle to find suitable host in average? The only information I found is that it is highly variable (Forsse, E., & Solbreck, C. 1985. Migration in the bark beetle ips-typographus duration timing and height of flight. Z. Angew. Entomol. 100 (1). 47-57). I also know that it is weather dependent but this won't help me... thank you !!

The number of days may still be unknown, and it is probably a large variation when they find a suitable host tree. The "pioneer males" might use "random-walks", when they try several trees before they chose the right one. Its also a large difference between endemic and epidemic periods regarding dispersals.

Anyhow, the flight distance of I.t. has been shown to be more than 8 km (see Botterweg, 1982), but during outbreaks when it can be pheromone sources everywhere most of them may disperse less than 500 m and maybe even less than 100 m. See:

Kautz. 2011. Quantifying spatio-temporal dispersion of bark beetle infestations in epidemic and non-epidemic conditions.

Whichmann and Ravn. 2001. The spread of Ips typographus (L.) (Coleoptera, Scolytidae) attacks following heavy windthrow in Denmark, analysed using GIS

and as mentioned above, the dissertation by Kärvemo and articles within.

I hope this helps.

cheers

Simon


What is the purpose of THC for a Cannabis plant? Why does a Cannabis plant produce THC? This question is brought up drawing an analogy to nicotine in tobacco, where nicotine is developed by tobacco plants as a pesticide. Is THC a pesticide as well? I'm imagining that marijuana plants don't have rheumatoid arthritis.

Apparently it is used by Cannabis sativa as a type of sunscreen as it absorbs UV light
https://www.reddit.com/r/trees/comments/2v79dv/science_sunday_13_wait_why_does_cannabis_have_thc/

https://en.wikipedia.org/wiki/Tetrahydrocannabinol


How bad is ethidium bromide in your plasmid for downstream applications? I want to transfect Adipose Derived stem cells using a clone of my own. My problem is that I get a lot of contamination (not only genomic, but due to the nature of the technique, I get undesired products I haven't been able to get rid of).

So I was thinking about running a gel with my plasmid DNA samples and gel purify my desired bands. I don't know, however, if Ethidium Bromide contamination in my sample would be a problem or if a regular gel extraction kit gets rid of it.

Purification and isolation of DNA bands by cutting them from agarose gel is commonplace (Lee et al., 2012). The purification step after excision of the band gets rid of most of the EtBr and other impurities. E.g., see the websites from Isogen and Sigma-Aldrich.

Reference
- Lee et al. J Vis Exp (2012); 62: e3923


Enzyme kinetics: Effect of immobilization on kinetic parameters What is the typical effect of enzyme immobilization on the kinetic parameters of an enzyme's activity?

Can one assume that they'd stay approximately the same or is there a gross change? Any way to estimate the effect?

The native parameters are as follows:

kcat    0.5 1/min
Km      0.6 microM
[E0]    5   micro M
[S]     60  micro M

Could I expect to retain them after immobilization? Or are these too high for an immobilized enzyme?

If it matters, it is a 500 residue enzyme with a MW of approx. 65,000 Da

The main factor influencing the kinetics of immobilized enzymes is thought to be the rate of diffusion of substrate and product towards and away from the enzyme, respectively.

This has been discussed on ResearchGate and an article in Process Biochemistry from one of those in the discussion quotes figures for effects on immobilized laccase: approx. 100x increase in Km and 2–5x reduction in Vmax (as noted in the poster’s comment).

There are several theoretical treatments of the question:

http://www1.lsbu.ac.uk/water/enztech/summary3.html
http://link.springer.com/article/10.1007%2FBF02460071#page-1
http://www.amazon.co.uk/gp/search?index=books&linkCode=qs&keywords=9780849369872


Do we know the physical-nature of "senses" or qualia? We have a peculiar property/ phenomenon called  having 'sense' or qualia, also sometimes called as consciousness.

Such as, if we see a red flower; we perceive a particular colour, "red". That is an example of sense.

Now scientists could tell, what was the wavelength of red light, which group of cone-cells responded, what group of nerve-fibres were sent message to which part of brain; and how the informations are being computed in brain, what gene-expression-pathways are working. They can describe the chemical reactions and other molecular interactions, even molecular-orbitals taking part.

But could science yet tell; what was that "red"? and why it was not perceived-as blue but was perceived-as red? Similarly, hot, cold, pain, tickle, joy, fear, hunger... whatever we "sense" in our mind; what are they made up of? Are they simply flow of information? doesn't seem.  Could chemical-reactions make-up sense? or what else they could be?

To avoid the answer from being too-broad; I can simplify it in following  alternatives:

qualia does not exist. It is just a myth.
qualia exists, but it is nothing more than information and computation.
qualia exists, but we do not know its nature.
qualia exists, we know its nature, and that is more than information and computation.

Which one is true on present scenario?

I'll try my best to give you my answer. But I maintain that this is still somewhat subjective.

Firstly, I think the short answer to your question as stated:

  Do we know the physical-nature of “consciousness”?

Is no.

I would personally say that our notion of 'sense' - that is, our ability to perceive stimuli, is not the same as consciousness (whatever "consciousness" means at this point). To me, and I think many others, the concept of 'consciousness' is simply being self-aware.

Science understands most if not all sensory pathways very well in terms of the electro-chemical and/or mechanical pathways involved.

To pick from your 4 options:

  Consciousness does not exist. It is just a myth.
  Consciousness    exists, but it is nothing more than information and computation.
  Consciousness exists, but we do not know its nature.
  Consciousness    exists, we know its nature, and that is more than information and    computation.

I think we can rule out 1 - we know we have something that we call consciousness - else we wouldn't be having this conversation!

We can certainly rule out 4 as well because we also wouldn't be having this discussion if it's nature was understood by now! :)

My own opinion steers me toward 3. Though I think understanding it might actually be impossible.

To run with your example of perceiving the colour red, I concur that we understand the physical processes that have occurred to enable us to see, and understand that we saw, red.

However...this puts me in mind of a kind of brain-teaser people sometimes mention: how do I know that what I consider to be red, is the same thing you consider to be red. Now, I don't personally think there's much to this, as colour is a physical property, but it does raise the possibility that the 'concept of red' is not immutable between individuals.

Some more food for thought is whether we actually possess a consciousness. By which I mean, it is an extant, natural phenomenon, like energy for instance, and you either have it or you don't. The alternative is similar to the debate about free will vs. the illusion of free will (I personally fall on the side of thinking the latter). That is to say, do we merely have the illusion of consciousness?

Taking the discussion from the comments about pain and expanding further; just because I feel pain, I do not believe equates to consciousness. How far down the evolutionary tree do you have to travel before you would decide a creature has no 'consciousness'. Sure, we probably agree dogs are conscious, but are they self-aware? Do they exist any further than to satisfy their biological needs? Even if we say yes... how much further do you need to go? Are sharks self-aware? Are hag-fish or nematodes self aware? And yet, we know that all these organisms are capable of sensing pain. So it's clear that simple sensing pain is not enough.

The last thing I recall reading about the basis of consciousness (and the closest thing I think we have to an answer as to what the physical basis of consciousness is) is that it is an emergent property of a complex system like our brain. The degree of 'inter-connectedness' in our brains is what makes us intelligent (not just size), and current thinking is that it's the density and number of networks inside the brain that is key.


Recommendation of a comprehensive book on the history of medicine I was wondering if somebody could recommend a book on the history of medicine, be it comprehensive or an introduction to the history of medicine. I know there are a lot of medical books that cover this subject, but given that I have a limited amount of time for reading I was wondering which book would make the best use of my time.

While it's not meant to be a history of all of medicine, I thought the The Emperor of All Maladies touched on a good deal of the history as the author took us through how cancers were diagnosed and treated since long ago.

Great book, that was.


I'm 20. Can I still grow taller? I'm 20, in about 6 months I turn 21. For some time I've been wondering whether there are natural, non-surgical and non-pharmaceutical ways that humans can continue to grow after reaching adulthood.

Please answer only if you are certain about this or you can reference any
trustworthy source.

Thank you a lot friends.

The answer is probably No.

"Long" bones - like the tibia, fibula, femur, humerus, etc. grow at the ends during childhood via a special formation called the Epiphyseal plate (also known as "growth plates"). The plates are composed of a special cartilage that grows, and slowly calcifies as a person reaches adulthood.

When the growth plates completely stop expanding is left to genetics, but generally happens 2 years after puberty finishes - about 16 for women and 18 for men. So after those ages there's little, if any, significant growth - though it can happen in very rare cases.

To date there aren't any exercises you can perform that will elongate bones. It doesn't make physiological sense; stretching puts stress on muscles and tendons - not bones. Weight lifting will compress bones, making them more dense and will make you shorter in the long run.

While there's been some success in getting chondrocytes to grow cartilage in vitro, there has yet to be significant gains in vivo, thus there aren't any medications available that would cause growth.

The only widely practiced way of gaining height after adulthood is with very painful surgery that involves a lot of braces. The bones are systematically broken, held in place, and allowed to heal. The setup looks like this:

While we get closer and closer to being able to control such things every day, for the time being (and I wouldn't count on this changing anytime soon) everybody is stuck with the height they were genetically programmed with.

As an aside: Being tall isn't all it's cracked up to be. At ~197cm I can tell you it is hell finding pants that fit.


Why are there only 6 molecules of water produced in the synthesis of the fatty acid, palmitate? The equation for biosynthesis is

1 Acetyl-CoA + 7 Malonyl-CoA + 14 NADPH + 14H+ -> Palmitate + 7 CO2 + 14 NADP+ + 8HS-CoA + 6 H2O

I really don't understand how there is only 6 H2O produced... and not 7?

Every cycle, there is the condensation of one molecule of water.

The first turn yields a 4 carbon molecules. Since palmitate is a 16C fatty acid, and two carbons are added each turn, there should be 6 turns remaining, for a total of 7 turn.

All the other numbers seem right. At first I thought my teacher could have made a mistake but everywhere I look on the net, it say 6 H2O.

Someone has an explanation for this?

Thank you :)

Edit: I found the answer in Voet & Voet yesterday. I add it here in case it can help someone else!

At the end of the biosynthesis, the palmitate is bonded with the Acyl-Carrier Protein (ACP) and it takes an hydrolysis to separate it, hence the missing H2O.

I found the answer in Voet & Voet yesterday.

At the end of the biosynthesis, the palmitate is bonded with the Acyl-Carrier Protein (ACP) and it takes an hydrolysis to separate it, hence the missing H2O.


What kinds of light attract moths best? On average, do we know what kind of lights attract moths best?
LED, filament bulb, candle...?

And what about colour? Does that matter?

Multiple studies have found moths along with most other insects to be significantly more attracted to lamps that emit smaller wavelengths such as ultraviolet (UV). Some species of moth appear to be more attracted to shorter wavelengths than others. The visibility of the light to the moth, the distance between the moth and light, and the brightness of the light are also contributing factors in whether the moth will be attracted to light.
Why Moths are Obsessed with Lamps | Nat Geo Wild

Langevelde et al. found that actinic lamps with a mean weighted wavelength of 382 nm (lamp type a) were the most attractive to moths in both abundance and species richness when compared to other lamps that emitted longer wavelengths. The lamp types used along with the data they collected are displayed below:

References & Further Reading
Hsiao, H. (1972). The attraction of moths (Trichoplusia ni) to infrared radiation. Journal of Insect Physiology, 18(9), 1705-1714. doi:10.1016/0022-1910(72)90100-x
Google Scholar | Crossref
Owens, A. C., & Lewis, S. M. (2018). The impact of artificial light at night on nocturnal insects: A review and synthesis. Ecology and Evolution, 8(22), 11337-11358. doi:10.1002/ece3.4557
PubMed | Google Scholar | Crossref
Somers-Yeates, R., Hodgson, D., McGregor, P. K., Spalding, A., & Ffrench-Constant, R. H. (2013). Shedding light on moths: shorter wavelengths attract noctuids more than geometrids. Biology Letters, 9(4), 20130376-20130376. doi:10.1098/rsbl.2013.0376
PubMed | Google Scholar | Crossref
Truxa, C., & Fiedler, K. (2012). Attraction to light - from how far do moths (Lepidoptera) return to weak artificial sources of light? European Journal of Entomology, 109(1), 77-84. doi:10.14411/eje.2012.010
Google Scholar | Crossref
Van Langevelde, F., Ettema, J. A., Donners, M., WallisDeVries, M. F., & Groenendijk, D. (2011). Effect of spectral composition of artificial light on the attraction of moths. Biological Conservation, 144(9), 2274-2281. doi:10.1016/j.biocon.2011.06.004
Google Scholar | crossref


Neuronal membrane resting potential for large cells I'm reading Medical Physiology by Boron and Boulpaep (a really terrific book). In the chapter Electrophysiology of the Cell Membrane, section Membrane Potential Is Generated by Ion Gradients, Not Directly by Ion Pumps, the text reads:

  It may seem that the inside negative Vm originates from the continuous pumping of positive charges out of the cell by the electrogenic Na-K pump. The resting potential of large cells -- whose surface-to-volume ratio is so large that ion gradients run down slowly -- is maintained for a long time even when metabolic poisons block ATP-dependent energy metabolism. This finding implies that an ATP-dependent pump is not the immediate energy source underlying the membrane potential.

I totally get the main takeaway, that Vm results from the net accumulation of ion gradients, rather than the immediate consequences of the ion pumps. But I'm unclear on the phrase large cells -- whose surface-to-volume is so large that ion gradients run down slowly.

Presumably a cell with a large surface-to-volume ratio, like a long thin neuron, would have many ion channels which leak constitutively. So I'd expect the net ion conductance to be high, and gradients would run down quickly. But that contradicts the book's run down slowly point, so I'm confused.

Does passive diffusion play a role here? A long, thin cell would have slow passive ion diffusion, so is that why Vm would run down slowly?

Am I overthinking this?

What is the authors' point here?

In a typical neuron at rest, potassium is high inside the cell and low outside, with the opposite true for sodium. The membrane is mostly permeable to potassium. Let's ignore the other ions.

The resting potential in this situation will be something like -70 mV. Rest means that the net current flow is zero; however, there is still current: potassium is flowing out of the cell and sodium is flowing in. Therefore, if we turn off the sodium-potassium pump, over time, the concentration gradients will slowly equalize.

The authors are making an assumption that the current is roughly a function of membrane surface area: more membrane = more current. However, the "reservoir" of concentration imbalance is a function of volume: a bigger cell has more total potassium ions than a smaller cell.

Therefore, in a large cell, if the membrane potential is mostly driven by the concentration gradient, and it takes a long time for the concentration inside to equalize with the outside because the current is small relative to the volume, the membrane potential will only change slowly if you use a toxin to stop the sodium-potassium pump.

I don't think the authors are really intending to say anything special about large cells versus small ones, they are just setting up some assumptions under which their argument about the resting potential is going to be most evident. This is a bit like in a physics textbook where you read something like "assume a uniform spherical baseball."

The claim they are making: "the membrane potential is because of the concentration gradient, not the action of the pump itself" is true for all cellular membranes, not just in large cells. This particular piece of evidence they are referring to, however, is going to be most obvious in a large cell. That's all.

If you tried to do this experiment in a very small cell by turning off the pumps and watching the membrane potential, you might erroneously conclude that the pump was responsible for the membrane potential, but this would be a false conclusion caused by the concentration gradient equalizing too quickly. Instead you should test it in a big cell to see the effect more clearly.

In my personal opinion, this is not the best evidence to explain this feature, but it's a hard concept for many people to grasp and I suspect the authors of your text approach it in several different ways to find one that sticks.


Do goosebumps always appear in the same spots on the skin? Often one gets goosebumps when one is cold. I am curious whether the precise location of the goosebumps on, say, one's leg changes from occurrence to occurrence or not? In case if their precise locations are always identical is there anything particular about those locations that differentiate them from other parts of one's skin?

Thus the question: do goosebumps appear at the same spots on one's body every time or their exact location changes?

Goosebumps are caused by the contraction of the arrector pili muscles, which are attached to hair follicles. Accordingly, they appear at the same spots on one's body every time.


Help understanding cell replication animations I often come across these animations about molecular biology showing for example how cell replication works, how virus infection works etc. Take this video as an example

https://www.youtube.com/watch?v=odRyv7V8LAE

HIV virus infects T helper cells using receptors on the cell surface which are cd4 molecule, it binds to the receptors using envelope protein. But the video shows you a little ball with some hooks that attaches to another little ball with other hooks.

I understand this is an useful abstraction, but could someone recommend a book or other materials to a novice like me who would like to understand how this really works? Question is probably too general but I am really interested in basics only. Hopefully someone could help

Thanks

When these animations are made by experts, they are actually not abstractions. Animations like this one [https://www.youtube.com/watch?v=X_tYrnv_o6A] actually don't show you an "idea" of how this looks but the actual shape of the individual molecules involved.

The reason we can now for many proteins draw pictures of how the molecule looks on the tiny scale that it is, is the field of structural biology. The scientists working in this field use techniques like X-ray crystallography, nuclear magnetic reconance spectroscopy and cryogenic electron microscopy to determine the structure of a protein at resolutions down to 2.7 Å (Angstrom, 1Å = 0.1nm). Once they manage to get a reliable picture of how a protein molecule looks, they publish their work and submit it to the world-wide protein data bank, which you can access freely using one of three websites: PDBe, PDBj and RCSB.

I tried searching for the proteins in your animation (CD4 and the HIV envelope protein gp120). Some structures do exist for them (e.g. http://www.ebi.ac.uk/pdbe/entry/pdb/2ny1) but they seem to contain only part of what's shown in the animation. Often certain parts of proteins can't be identified by structural biology for technical reasons, but we know they must be there based on the genetic information we have, and we can make some educated guesses about what those bits of the protein might look like. It seems in this animation, there was quite a bit of educated guessing involved.

A lot of biological science nowadays goes by the paradigm "seeing is believing". Many modern animations are reproduced from actual recordings where the process shown in the animation can be seen happening in reality. Cell divison for example is an intensively researched process that has been filmed using many different microscopic techniques and focussing on many different parts of the cell, figuring out what each protein or other molecule does during the process. Putting together knowledge from many different teams, you can generate a full picture of what everything is doing at the same time.

As far as reading recommendations go, any basic molecular biology textbook like Molecular Biology of the Cell by Alberts et al. (pick it up from a library), or lectures freely available online should allow you to gradually wrap your head around it.


Sterilize/disinfect sugar for lab use How do I sterilize/disinfect ordinary table sugar for lab use?
I'm using the sugar in an agar and I want it to be as clean as possible. Are there any effective, conventional ways of doing this?

Autoclaving media with carbohydrates (or sugar solutions on its own) is not a good idea for two reasons:

The Maillard reaction: This occurs when you heat mixtures of amino acids and sugars. The amino group of an amino acid reacts with a carbonyl group of a sugar, fusing the two molecules together. This is a common reaction in the kitchen which is for example responsible for making the bread crust brown. It also changes flavors.
Caramellization: This is the heat induced breakdown of sugars - also leading to brown products, but much more undefined than the Maillard reaction. What products arise depends on pH, temperature and other reactands.

Both reactions may lead to products which can be inhibitory to microbe growth and should be avoided. There is also a paper which analyzed the effect of autoclaving on sugars which might be interesting to read in this context (see reference below).

So prepare a higher concentrated stock solution of your sugars, which can then be added under sterile conditions to your autoclaved and cooled down media or the agar solution (still warm enough to pour).

Sterilize this solution by filtrating it through a 0.2µM filter - depending on the volume either through syringe filters or through bottle top filters.
Make sure to maintain sterile conditions.

References:

Sugar degradation during autoclaving: Effects of duration and
solution volume on breakdown of glucose


In C. elegans, why does knock-down of cco-1 in some tissues increase lifespan, and knock-down of cco-1 in other tissues decrease lifespan? Full question: In C. elegans, why does knock-down of cco-1 via RNA interference in specific tissues like body wall muscle decreases life span, whereas knock-down in the nervous system and intestine increases life-span?

http://www.wormbase.org/db/gene/gene?name=WBGene00000371;class=Gene

Also from paper 'The Cell-Non-Autonomous Nature of Electron Transport Chain-Mediated Longevity'

Supposedly, it's through hormesis. But why is there a differential effect from tissue to tissue?

Let us first answer the question: what is the effect of cco-1 knock-down in C. elegans. Durieux J., Wolff S. and Dillin A. in their paper "The cell-non-autonomous nature of electron transport chain-mediated longevity". Cell 144:79-91 (2011) provide the following explanation:

  The life span of C. elegans can be increased via reduced function of
  the mitochondria; however, the extent to which mitochondrial
  alteration in a single, distinct tissue may influence aging in the
  whole organism remains unknown.

So, by slowing-down the mitochondria function you manage to slow-down the normal wear-and-tear of the mitochondrial enzymes, which are normally responsible for the so-called respiratory chain -- one of the fundamental biological process for storing energy in cells (despite the common belief, ATP is rarely to store energy, but mostly to transfer it to the target!).

If we group the tissues where the knock-down leads to similar effects we will get muscle cells opposed by neurons and intenstine cells.

This is just my suggestion, but if we approach those groups with the idea of energy storage and re-use in mind, we'll see that muscle cells have much higher turnover of energy (for contraction and even more for dilation), whereas nerve and intestine cells are not that dependent upon energy and have much lower baseline of energy consumption and turnover.

Now we can suggest that cco-1 knock-down decreases the functions of mitochondria in muscle cells below the acceptable level and the decreased life span is due to depletion of mitochondrial energy storage under light stress conditions which would have been easily coped with under normal conditions. And vice versa, nervous/intenstine cells requiring a constant energy source at a much lower level just help the animal to cope with stress more effectively even during old age, leading to increased life span.


Are all protein composed of all the amino acid (in animal) or are there less diverse protein? I have a question about amino acid composition of proteins: Are there proteins in animals that are made up only from a small subset of amino acids? So instead of all 20 amino acids let's say only 6-14 ( or any arbitrarily small subset) amino acids are used in a particular protein. Could you give me an example (or maybe a few examples) of such protein(s).

Trp-Cage is a protein found in Gila monsters, and it is only 20 amino acids long and there are plenty of repeated amino acids so this does not use all 20. But there must be plenty of other examples, there is no reason why physically a protein must use all available amino acids.


Looking for good reference book in molecular biology I am starting to work in molecular biology/ molecular genetic and I am looking for a really good book containing the main concepts and mostly the more recent techniques.

I would be interested in a book that has also protocol examples and examples on how to apply the different techniques.
My focus is on bacteria and fungi.

Any suggestion?

These always have a place at my library

HF Lodish, Berk, Arnold, and S. Lawrence Zipursky. Molecular cell biology. Vol. 4. New York: WH Freeman, 2000.

Alberts, Bruce, et al. "Molecular biology of the cell." Garland Science, New York 4 (2002)(the first few editions had James Watson himself as the editor)

Brown, Terence A. Genomes. Garland science, 2006.

For basics. I would recommend staring with Brown, and going on to Bruce Alberts and then Lodish. That's the way I learnt it.

For a really nice book with pictures (yes, we all like those) you might want to look into Lippincotts illustrated reviews (biochemistry, cell and molecular biology and the like). They are also quite good.

For a specific emphasis on techniques, I'd  recommend this:

Sambrook, Joseph, Edward F. Fritsch, and Tom Maniatis. Molecular cloning. Vol. 1. No. 7.58. New York: Cold spring harbor laboratory press, 1989.
(You can read the contents here http://www.molecularcloning.com/)


Why are semi log graphs used in drug Dose response curves? Why are Dose response curves, as well as most biological graphs shown in semi log graphs and not normal graphs? What is the advantage of semi log graphs over regular graphs? I still haven't gotten an intuitive sense of the answer, can someone explain, maybe with a diagram?

The reason is to make it easier to determine a suitable dose from the graph.
Normally, using a arithmetic scale, the response curve is a hyperbolic, with most of the information squished together in a small section of the graph. By using the log the function usually becomes somewhat sigmoid, with a relatively linear section in the transition from low-high response. This means that this dynamics in this section can be studied more carefully.

See e.g. this example (with data from https://www.idbs.com/media/396649/dose-response-comparison-example-hr.jpg), where I have reversed the x and y-axes, and used a secondary y-scale to show the log dose (so the graph is flipped compared to a normal dose-response curve). Here, the orange line shows a semi-log dose-response curve, and the blue line shows the same data using a normal arithmetic scale. Note that the orange line (log dose) should be read against the right scale and the "normal" dose against the left scale):

Here it is obvious that the normal scale doesn't give any possibility to interpret the region where the dose is effective, while this is obvious in the log graph.

The statistical modelling of these data is to some extent a separate issue though, where probit model or logit models along with data transformations are often used to analyse the data. Note also that the "usefulness" of the semilog-plot only lies in the visual presentation, and whether it will add anything depends on the dose series used in an experiment. If the doses used are not exponential (as in this example), the semilog-plot will not add much. In the statistical test of an effect the log dose is also usually not important, and I suspect (as someone not working in pharmacology) that the semilog plot is to some extent a historical artifact from the time before computer analysis of results, when the appropriate dose was determined in  a more manual way (e.g. linear analysis of the middle portion of the semilog graph).

Example data:

dose (conc.)    response
0.00001         0.993
0.0001          1.02
0.001           3.12
0.01            6.36
0.1             31.97
1               51.2
10              75.96
100             89
1000            97.932
10000           98.8


Why is pepsin able to operate at low pH? Pepsin is a protease that operates in the acid pH of the stomach. Many proteins are denatured at low pH, and most enzymes — whether or not they denature — require a higher pH for activity.

Why is pepsin not denatured at low pH, and has catalytic activity at low pH, but not at higher pH?

A good question. As you have accurately described, pepsin is indeed a protein, more specifically, a protease enzyme - a catalyst which assists the break-down of protein at certain amino-acid markers such as tryptophan and phenylalanine. As you are likely aware, proteins are composed from approximately 20 amino-acids, as shown below.

However, the chemical properties of a protein are constituted by its folding - its three-dimensional shape. This answer describes some superficial differences between protein families and the mechanism and function whereby pepsin is capable of functioning at a low pH.

Disregarding any post-translational modifications - the alterations made to a protein following translation from mRNA - proteins are made from a determined sequence of amino-acids, named its primary structure. Different classes of proteins shall have a different sequence and proportion of various amino-acids. For example, collagen fibrils are composed from a greater proportion of the amino-acids glycine-proline-hydroxyproline.

A sample of pepsin extracted from a pig (Porcine pepsin) demonstrated a higher yield of asparagine.

Secondary structure - the inter-molecular bonding between amino-acid side-chains including hydrogen-bonding and disulfide bridge. As you correctly described a protein denaturing, it is these bonds which are broken, thereby altering the protein's shape.

Although there be four principal protein structures - primary, secondary, tertiary and quaternary - the first two are most critical to understanding the ability for pepsin to withstand low pH. Pepsin is originally secreted into the stomach as a proenzyme - an inactive precursor to an enzyme - called pepsinogen. When food is ingested, both pepsinogen and hydrochloric acid are released into the stomach. Returning to our primary structure, pepsinogen possesses 44 additional amino-acids compared with the active enzyme. During acidic conditions, the pepsinogen auto-catalyses its own cleavage from the additional strand, folding into the correct form.

Therefore, other proteins in high acidic conditions lose their unique three-dimensional structure due to the breaking of these inter-molecular bonds. In a sense, denaturing only specifies a transformation into an inactive protein but could be stated for pepsinogen which is 'denatured' into pepsin which attains its activity in this 'denatured' form.

For more information regarding pepsin, I would advise the following Wikipedia page as an initial resource: https://en.wikipedia.org/wiki/Pepsin
For information regarding collagen and porcine-pepsin composition, the following sources respectively may help: https://www.ncbi.nlm.nih.gov/books/NBK21582/ and https://www.ncbi.nlm.nih.gov/pmc/articles/PMC427253/?page=2

I wish you good digestion!


What are these caterpillars eating a potato plant? I saw these caterpillars rapidly consuming a potato plant in Central Texas:

They have thin, dark green-blue bodies with yellow-white longitudinal stripes and a bright rust-red head. Their body seems to be covered in fine hairs which may be difficult to see in the photo. They are about 1 cm long.

On some leaves of the same plant I saw what appear to be eggs - little black balls 1-2 mm in diameter, with a shiny appearance reminiscent of black caviar (well, I suppose they are black caviar). They seem to cover only a handful of leaves, in groups of about 100 or so (rough guess). Some can be seen in the photo.

Curiously enough, nearby there were tomato and strawberry plants, but they were not affected, while the potato was extensively predated (a few dozen leaves consumed).

What are these caterpillars? How do you kill them?

I believe this is the middle instar of a Southern Armyworm (Spodoptera eridania) larvae. Or some closely related species in the Spodoptera genus (family Noctuidae).

 © 2016 Wings, Worms, & Wonder

The larvae undergo six instars as they grow to attain a length of about 35 mm.

You can see a series of life stage pictures from Mississippi State.

Armyworms are so called because you typically find 100s at a time on a single leaf or plant. According to here:

  Armyworms strike in the blink of an eye, and there are so many in their army that you will be finding them for weeks after the primary attack.

Behavior: larvae are mostly active at night and hide on leaf undersides, in curled leaves, or in leaf litter during the day.

This University of Florida site claims

  Young larvae feed on under surface of leaflets leaving upper epidermis intact ("windowpaned"). Older larvae consume foliage and eat large holes in fruit.

Range: native to the American tropics (occurs widely in Central and South America and the Caribbean). Also found in US (principally in the Southeast but extends West to Kansas and New Mexico). It also is reported from California.

Here's a map showing some confirmed sightings [source]:

Host Plants:
This species has a very broad host range including important crops (including potatoes).

I would be concerned for your nearby tomatoes, because thy too are a favorite food of these insects.

See here for more information including management suggestions.

Defecation vs. Eggs??

The picture in the question shows S. eridania's feces.

This Mississippi State site includes a great zoomed-in picture of S. eridania's feces:

 © Lee Ruth
Note: caterpillars don't lay eggs. Only adult moths/butterflies lay eggs.

Eggs: large masses of 100-200 eggs covered with moth body scales, found on underside of leaves, hatch in 3 days.

 © 2016 Wings, Worms, & Wonder

Here's a picture of inside the seed casing of closely related S. exigua [source]:

 © 2016 Wings, Worms, & Wonder

Finally, here's a picture of the nocturnal adult:


How exactly does sensory substitution work? Sensory substitution, when one of sensory modality changes into another sensory modality to help someone restore the ability to perceive defective sensory using a working sensory modality. For example, blind people who have improvements in their other senses like auditory system or olfactory system compared to normal people. Or deaf person who have enhanced vision ability than normal people.

Questions :

Does this work the same way as Alternative Sensation ?
Is there any pattern of which senses will probably improve according to which kind of senses someone's lacking ?
Is there actually any method to train which senses someone would like to improve ?

Tot start of with your definition:

  Sensory substitution, when one of sensory modality changes into another sensory modality to help someone restore the ability to perceive defective sensory using a working sensory modality.

I personally like to use a more subtle definition of sensory substitution (Stronks et al., 2015):

  [T]he process of obtaining information about the world through an alternative intact sensory channel [] that would normally be obtained by the deficient [sensory] system.

In other words, the information is not changed into another modality; it is simply processed by a sense normally not used for that purpose. Your definition seems to imply that the information stream is swapped. Although this is not strictly true, and hence the reason I like the second more subtle definition better, it is nonetheless true that cross-modal plasticity results in the deafferented cortical regions being taken over by other senses; for example in the blind, it has been shown that tactile and auditory information is processed in the visual regions, even down to the V1. The primary visual cortex is normally strictly associated with low-level visual processing, being the first central brain area where visual information enters the brain. Although this view is contested(V1 is also activated by tactile grids for example), in blind folks there are gross rearrangements where the somatosensory and auditory cortices take over the visual system (e.g., Pascual-Leone et al. (2005)).

To your questions

  Does this work the same way as Alternative Sensation ?

'Alternative sensation' is unfamiliar to me, it doesn't pop up in a Google search, and its nonexistence is backed up by this answer.

  Is there any pattern of which senses will probably improve according
  to which kind of senses someone's lacking

Yes. It depends on which senses are used most extensively to substitute for another sense. Training is an important factor in improving alternative sensory capabilities. In fact, it is the determining factor; the loss of a sensory system in itself does not propagate compensatory mechanisms (Stronks et al., 2015). Compensation being

  partial compensation for [the] loss of [a sense] by developing enhanced abilities with [] remaining senses

For example, training with the BrainPort Artificial Vision Device (Fig. 1), which projects electrotactile 'images' onto the tongue using 400 electrodes, gradually improves performance in the blind, all the while the somatosensory information is funneled progressively into the visual system (Stronks et al., 2016).

  Is there actually any method to train which senses someone would like
  to improve?

Pick your sensory substitution device of choice and train away; popular ones include, as said, the BrainPort (improves tactile-to-vision substitution), but also visual-to-auditory techniques like the vOICe (Striem-Amit et al., 2012). Also don't forget the guide cane, which funnels tactile information to the brain. especially the visual-to-auditory sensory substitution devices require a lot of training (Stronks et al., 2015). You can try the vOICe out yourself on an Android. However, I have tried the BrainPort myself and it is really difficult!

References
- Pascual-Leone et al. Annu Rev Neurosci (2005); 28: 377–401
- Striem-Amit, et al. PLoSONE (2012); 7(3): e33136
- Stronks et al., Brain Res (2015); 1624: 140–52
- Stronks et al., Exp Rev Med Dev (2016); 13(10): 919–31

Fig. 1. The BrainPort converts camera images into a 'grayscale' 400 pixel electrotactile image on the tongue. It partially restores visual function in the blind. Picture source: Midday Daily


Can humans transdermally absorb minerals from ocean water, and if so how much? According to several studies quoted here, chemicals can be absorbed by the skin transdermally, at least under certain conditions.

When it comes to elements in seawater like sodium, magnesium, potassium and iodine, is it possible for a human to absorb them transdermally in this instance?

If it depends on various conditions, (such as length of time spent in the ocean, physiological factors (e.g. intense swimming vs. gentle bathing), temperature of the water and their respective effects on skin porousness or other factors affecting transdermal absorption), what would be they be?

And if it can indeed be absorbed (e.g. from open water swimming), are the amounts significant to even measure alongside that of recommended levels for human dietary intake by advisory bodies such as FDA for those mentioned elements, or is it an extremely small amount much smaller than dietary levels of mineral intake?

There is not very much transport of ions or water through the upper layer of the skin, mainly responsible for that is the stratum corneum (SC). Through this layer you will get only with small lipids and also substances which are able to penetrate the lipid layer of the cells like chloroform or DMSO. I think therefore that it is pretty unlikely that you can take up noteworthy amounts of ions (which would have to pass through the lipid layer of the cells which is highly hygrophobic) through the skin. Have a look at these publications:

Routes of ionic permeability through mammalian skin
Skin permeabilization for transdermal drug delivery: recent advances
and future prospects.

Interestingly this is different for other animals. The pacific hagfish is able to resorb organic nutients through his skin, see this article or this publication:

Adaptations to in situ feeding: novel nutrient acquisition pathways
in an ancient vertebrate


Characteristics of Araneus hui (an orb-weaving spider) What are the characteristics of Araneus hui? Neither thematic literature nor photos was found.
Mentioned in RU Wikipedia, reference wasn't found.
https://ru.wikipedia.org/wiki/%D0%9A%D1%80%D0%B5%D1%81%D1%82%D0%BE%D0%B2%D0%B8%D0%BA%D0%B8

These pages cite papers that mention A.hui:
https://www.gbif.org/species/2160156
https://wsc.nmbe.ch/species/2910/Araneus_hui
The World Spider Catalog (WSC) offers papers to their users for free, and it is a free registration.
Browsing through the second pdf on the WSC, here is a sketch of the dorsal (top) view of the species:

The paper is primarily written in a language I cannot read.
The specific paper (book?) is:
Hu, J. L. (2001). Spiders in Qinghai-Tibet Plateau of China. Henan Science and Technology Publishing House, 658 pp.
658 pages is quite volumnous. The title of the paper suggests we limit our search to Tibet. Searching for Araneus images on iNaturalist in Tibet, there is a picture of one Araneus that has not been identified to species level, but it resembles the abdominal shape as in the drawing in the paper:
https://inaturalist.ca/observations/51273647
But the abdominal markings do not match at all. If you expand the geographical bounding box of the search around Tibet, you can browse a gallery of hundreds of possible pictures.


Increasing/decreasing signal intensity in Western blotting So I was in class and my professor was explaining western blotting. It seems as though there's more than one way to increase or decrease the signal intensity. He presented us the challenge to discover different ways this can happen. As hard as I look all I can find on the internet or even in google scholar is just certain chemicals like 'signal enhancer' and that's it, nothing remotely specific. Legitimately I do not propose this as actual homework, in fact it's just a curiosity I have. Therefore I ask the scientific community what, if any, are conditions that one could increase or decrease the signal intensity in western blotting? I understand what western blotting is, anyone can find this on wikipedia, but conditions that could increase or decrease signal intensity?

There are several different places in a typical Western blotting protocol where conditions can be altered to modulate signal intensity. The first is the amount of protein loaded - more protein will give a stronger signal, less will give a weaker signal. However, too much protein can result in indistinct bands, increased background, lane distortion, and other issues.

The next condition to change is the amount of primary antibody and the incubation buffer. More primary may lead to an increased signal, but too much can give higher background. Some antibodies give a better signal when diluted in BSA, others when diluted in nonfat dry milk. Generally, milk will give you a cleaner blot, but may reduce the signal. Incubation time can also affect specificity and signal intensity - some antibodies will fully bind with a 1-2 hour incubation at room temperature, others require an overnight incubation at 4°C.

The third condition to alter is the amount and type of secondary antibody. Increasing the amount of secondary may increase signal, but again may result in increased background. There are also different types of secondaries, depending on your detection system - HRP for chemiluminescent detection, AP for colorimetric, fluorescent tags for imaging systems, etc. These have different sensitivities, but can also result in increased background, depending on the other conditions of the protocol.

Finally, the type of detection system can affect sensitivity. For example, when using standard HRP-conjugated secondaries, there are numerous different ECL substrates with widely varying sensitivities. Here is a list of different systems available from Thermo/Pierce, ranging from standard ECL to Femto.

So, while Western blotting seems like a fairly straightforward procedure, there are many places to optimize the conditions to get the results you're looking for.


Relationship between toxicity of drugs and negative effects on brain Are psychoactive drugs with lower lethal doses more neurotoxic (more damaging to the brain)? For example, tetrahydrocannabinol (one of the active components of cannabis) has a much higher lethal dose than benzoylmethylecgonine (cocaine), so could we deduce that cocaine is more damaging to the brain?
Moreover, is a mathematical relationship between neurotoxicity and lethal doses known?

Short answer
The causes of death after heroin, cocain or cannabis overdose are mainly due to cardiac and respiratory arrest, and not to neurotoxic effects.

Background
The cause of death after a lethal overdose of your mentioned drugs are the following :

Cocaine (lethal dose: 30 mg - 5 g via mucus membrane (EMCDDA)): Cocaine-related deaths are often a result of cardiac arrest followed by an arrest of breathing (NIH). Cardiac effects are mediated via increased sympathetic output and a local anesthetic effect (Schwartz et al., 2010);
THC: (lethal dose: ~1000mg/kg i.v. in primates (Drug library)): No known cases of human fatalities. Toxicity appears as achypnea (rapid breathing), tachycardia (fast heart rate), ataxia, hyperexcitability, and seizures (Fitzgerald et al., 2013), but death seems mostly associated with respiratory arrest and cardiac failure (Drug library);
Heroin: (lethal dose 200 - 2000 mg i.v.(EMCDDA)): overdose often due to respiratory arrest (Anoro et al. 2004) caused by mu-opiate receptor activation in the brainstem (Karch, 2006).

Hence, heroin, THC and cocain are lethal mainly due to peripheral causes (i.e., cardiac and respiratory arrest). Although these effects are mediated, at least partly, through central mechanisms (i.e., occurring in the central nervous system and specifically the brain), the drugs themselves do not cause death because of neurotoxicity.

And a closing comment, with credits to @MarchHo - In general, neurotoxins do not cause death due to neural toxicity per se. Most notably even botulotoxin, being one of the most potent neurotoxins known, causes death due to respiratory failure (CDC).

References
- Anorro et al., Rev Esp Salud Publica (2004); 78(5): 601-8
- Fitzgerald et al., Top Companion Anim Med (2013); 28(1):8-12
- Karch, Drug Abuse Handbook (2006)
- Schwartz et al., Circulation (2010); 122:2558-69


Any tool to align whole genome sequence data to another genome and give exon regions a higher mark? I want to align WGS data from several mammals to one reference such as the human genome sequence. Since in most cases exons should be conserved and spliced in the same way and introns should vary, I want to use a tool that is aware of the annotation of exon and intron.

That is to say that matches in an exon region should have be given a higher weighting than matches in intronic regions.

Also, when a read pair maps to 2 exons, the insert size should be more flexible as the intron length can be vary among different mammals. Since the library insert is less than 2kb for short libraries, the more common situation should be one read on exon and another on intron.

This is different from RNA-seq as I am using WGS data of a whole genome, so both exons and introns are in the reads. And I want to align them to a human reference sequence.

If you are not trying to assemble but just to align each read to the genome, you can use exonerate. On a Unix/Linux platform, once you have installed it run something like:

exonerate -m genome2genome WGS.fasta genome.fasta > out.txt

From the exonerate manual:

          genome2genome
                 This  model  is  similar  to  the  cod‐
                 ing2coding  model,  except  introns are
                 modelled on both sequences.  (not work‐
                 ing well yet)

What I would recommend though, is to align against a reference cDNA dataset, not the whole genome. In that case, you should use this instead:

exonerate -m cdna2genome genome_cdna.fasta WGS.fasta > out.txt

From the exonerate manual:

          cdna2genome
                 This   combines   properties   of   the
                 est2genome and coding2genome models, to
                 allow modeling of an whole cDNA where a
                 central coding region can be flanked by
                 non-coding UTRs.  When  the  CDS  start
                 and  end  is  known it may be specified
                 using  the  --annotation  option   (see
                 below)  to permit only the correct cod‐
                 ing region to appear in the alignemnt.


Excluding the Exon, What Does the Rest of the Genome Do? The exon is the portion of the genome that encodes protein synthesis, if I understand correctly.

But, this exon is apparently less than 5% of the genome.

So, what does the rest of the genome do?

A few percent codes for RNA, like microRNA, long non coding RNA, shRNA ect. These RNA while not translated into protein do have a function.

Some RNA are ribozymes, catalytically active in their own right, but they do work with proteins. An example of such complex is the ribosome, where the catalytic peptidyl transferase activity that links amino acids together is performed by the ribosomal RNA
https://en.wikipedia.org/wiki/Ribosome

Then there are miRNA, that control gene expression by RNA mediated silencing.
https://en.wikipedia.org/wiki/RNA_silencing

Then there lncRNA... these long RNA can regulate gene activity by binding to transcription factors. So a cell can maintain a high concentration of transcription factor in an inactive state that can rapidly go into use once a signal is received. This is rather recent discovery.

About 45% of the human genome is composed of what is essentially viral parasites. While some of these viral genomes are full functional and encode endogenous viruses (this is why there is come concern about xeno tissue transplant). Most of these viral parasites have degraded somewhat, having accumulated mutations that either render unable to leave the cell, but still able to replicate and multiple in the genome (we call them transposable elements), or are completely inactive (repeat elements).
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4124830/

Examples are
Alu element make up 10.7% of the human genome. It is rather old parasite... youngest expansion is about 30 million years old. Mostly inactive, although some Alu elements are still active.
https://en.wikipedia.org/wiki/Alu_element

Line repeats. ~17% of the human genome.

Some DNA is structural. The centromeric repeat array which may be several Mb long per chromosome (exact length is unknown due to variation between people and difficulty to clone and maintain for analysis). Here the DNA serves as a pad over which the kinetochore forms. This DNA tend to be transcriptionally quiet, few if any genes.

And there are pseudo genes... genes that are no longer active due to mutations.


How do antibiotics create drug-resistant strains I've heard for years that low-level use of antibiotics causes the spread of drug-resistant strains of bacteria, but the explanations always fall short.  I understand mutations and natural selection, and that a bacterium can randomly mutate into one that is more resistant to the antibiotic than the wild-type.  I understand that the antibiotics kill off the less resistant strains and leave the more resistant ones, but those more resistant strains would be there even without the antibiotic use, right?

Do the more resistant bacteria compete somehow with the less resistant ones and the antibiotics kill off the competition?

(Edited: previously used the terms "strong" and "weak" which apparently have unintended connotations, and was unclear about the role of mutation).

There is no such thing as a "stronger" or "weaker" strain until the bacteria are treated with antibiotics.

It is true that potentially antibiotic-resistant mutants will still occur whether or not treated with antibiotics.

However, the mutants would not be "stronger" without the antibiotic use, so there is no selective pressure for them to survive to any greater degree than the wild-type. Without the antibiotic, something else will kill that mutant bacteria, meaning that the mutation ultimately did not make it any stronger.


Hardy Weinberg principle The principle is that sum total of all allelic frequencies is 1.

Individual frequencies for example can be named p,q.In a diploid cell , p and q represent the frequency of allele A and a respectively . The frequency of AA individuals in a population is p2  as the probability of an allele A with a frequency of p appear on both the chromosomes of a diploid individual is simply the product of the probabilities. Similarly for aa it will be q2.Can anybody explain that how it will be 2pq for Aa?

I am getting it as pq.

You almost said it all! Here are two ways to think of this problem

Finding the missing probability

Let's denote the fraction yz genotype in the population with $f(yz)$. The sum of of fraction of all genotypes must be equal to 1. In equation it means

$$f(aa) + f(aA) + f(AA) = 1$$

Here, of course I don't make a difference between $f(aA)$ and $f(Aa)$ (whether A is inherited from the mother or from the father). Knowing as you said

$$f(aa) = p^2$$

and

$$f(AA) = q^2$$

and feeding this value back to the first equation result into

$$p^2 + f(aA) + q^2 = 1$$

Solving for $f(aA)$ yields to

$$f(aA) = 2pq$$

Directly calculate the probability

Another to reach this result is to ask the following questions

  What is the probability that the maternal allele is A?

The answer is $q$

  What is the probability that the paternal allele is a?

The answer is $p$

  What is the probability that the maternal allele is a?

The answer is $p$

  What is the probability that the paternal allele is A?

The answer is $p$

Therefore, $$f(aA) = pq + pq = 2pq$$