Why are most transcription factors enhancing the expression rather than repressing? One can classify the effects of Transcription Factors (TF) on gene expression into two types: it either enhance or repress the gene expression.

I have always been told that most of transcription factors functions act to enhance gene expression rather than repress gene expression. Assuming this is true, my question is why are activators more common than repressors?. Is there for example a mechanistic explanation for that (cost less energy to enhance or the enhancement pathway is easier to evolve)?

From wikipedia

  While activators can interact directly or indirectly with the core machinery of transcription through enhancer binding, repressors predominantly recruit co-repressor complexes leading to transcriptional repression by chromatin condensation of enhancer regions.

The mechanisms are different and it sounds a likely cause of the overrepresentation of enhancement function of transcription factors in genomes but it is not obvious to me why activators and repressors have to have use different mechanisms and it is not obvious to me either why these different mechanisms would yield to a ratio of repressors to activators other than $\frac{1}{2}$.

I can answer this question only based on guesses because I am not really sure about your claim that activators are higher in number than repressors. So consider this as an extended comment.

  While activators can interact directly or indirectly with the core
  machinery of transcription through enhancer binding, repressors
  predominantly recruit co-repressor complexes leading to
  transcriptional repression by chromatin condensation of enhancer
  regions

Not really true. A repressor can simply sit on the the promoter and prevent RNAP from binding the to the latter.

  Abstract

  Transcriptional repressors are usually viewed as proteins that bind to
  promoters in a way that impedes subsequent binding of RNA polymerase.
  Although this repression mechanism is found at several promoters,
  there is a growing list of repressors that inhibit transcription
  initiation in other ways. For example, several repressors allow the
  simultaneous binding of RNA polymerase to the promoter, but interfere
  with subsequent events of the initiation process, eventually
  inhibiting transcription initiation. The recent increase in the number
  of repressors for which the repression mechanism has been
  characterized in detail has shown an amazing variety of strategies to
  repress transcription initiation. It is not surprising to find that
  the repression mechanism used is usually exquisitely adapted to the
  characteristics of the promoter and of the repressor involved.

Some justification on why the number activators would be more:

A network perspective:

Lets assume an that gene-A somehow causes the repression of the gene-B. This repression can be either direct (A being a repressor of B) or indirect via some other genes. In the case of indirect regulation you just need one repressor in the network path A → B to result in repression of the latter.

So all repressive paths would minimally require only one repressor, all other steps in the path can be activation; whereas in an activating path you would need 'n' activators for 'n' steps.

Post-transcriptional Regulation:

Now if you include post-transcriptional regulation then you can find more number of repressors: miRNAs (2588 reported in humans: miRbase-21) and many proteins as well (For an e.g. see here). Most cases of events leading to translational activation are actually derepression. It is logical in a way because an mRNA is a temporary product; it should not by default require an additional signal to start producing proteins.


Is Pars intermedia functional in humans? My textbook says, "Pars intermedia secretes only one hormone called melanocyte stimulating hormone (MSH)."
My teacher says that in humans MSH is secreted by the anterior lobe because the Pars intermedia is poorly developed and almost merged with the Pars distalis. I am confused as to what is correct. I find nothing wrong in both the arguments. So, is the Pars intermedia in humans functional or not?

Both- the textbook and your teacher are right.

The most obvious function of the pars intermedia in lower vertebrates is the secretion of melanocyte-stimulating hormone (MSH) for the purpose of pigmentary control.
In human fetal life as well, this area produces MSH which causes the release of melanin pigment in skin melanocytes.
In adults,

The human pituitary has no distinct pars intermedia (PI). Instead, the proopiomelanocortin (POMC) producing, adrenocorticotropin (ACTH)- and β-endorphin-immunoreactive PI cells are incorporated within the pars anterior, thereby participating in the formation of the pars distalis.

Edit:

POMC is cut (cleaved) to give rise to multiple peptide hormones. Each of these peptides is packaged in large dense-core vesicles that are released from the cells by exocytosis in response to appropriate stimulation:
α-MSH produced by neurons in the ventromedial nucleus has important roles in the regulation of appetite (POMC neuron stimulation results in satiety) and sexual behavior, while α-MSH secreted from the intermediate lobe of the pituitary regulates the movement of melanin produced from melanocytes in skin.

Sources:

https://link.springer.com/article/10.1007/BF02738816
https://pubmed.ncbi.nlm.nih.gov/6912095/#:~:text=Abstract,the%20purpose%20of%20pigmentary%20control.
https://en.wikipedia.org/wiki/Pars_intermedia


How does chest wall compliance affect functional residual capacity (FRC)? The functional residual capacity is made up of expiratory reserve volume (ERV) plus the residual volume (RV) - i.e. the volume of air remaining in the lungs after passive expiration.

Compliance of the lungs is said to affect FRC. For example, if compliance of the lung increases (e.g. in emphysema), there is less elastic recoil and less air is passively expired, resulting in increased FRC. Could one explain this as increased compliance (where compliance = ∆V/∆P) meaning that the same intrapleural pressure at end of passive expiration results in a greater lung volume (FRC) at that time? This seems to explain instantaneous volumes rather than the actual expiration of less air.

How does this translate to compliance of the chest wall? As recoil of the chest wall tends to be outwards, would reduced compliance mean that there is greater tendency to recoil outwards, making intrapleural pressure more negative and reducing expiration of air, leaving greater FRC?

As far as lung is concerned both inspiration and expiration are passive. Lung just responds to intrathoracic pressure by accommodating more air during inspiration and expelling air during expiration. The active processes in the lung as far as air flow is concerned are limited to the bronchial tree smooth muscles which can increase or decrease the resistance to air flow. The compliance of the lung parenchyma is a function of its anatomical composition.

During inspiration the thoracic volume is actively increased by:

Outward expansion of ribs by the intercostal muscles
Downward expansion of diaphragm

This increase in thoracic volume is refected in all intra thoracic organs:

Venous return increases due to the negative pull
Negative pleural pressure causes air to be pulled into the lungs

Normal expiration on the other hand is passive due to relaxation of the above mentioned muscles. Relaxation will cause a decrease in the thoracic volume which will push the excess air and blood out.

An increase in the compliance of the thoracic cavity would mean weakening of the fascia and bones of the thoracic cage. In other words, the structures that the muscles attach to will become weak. This will cause muscle action to cause excessive expansion of the thoracic cage during inspiration and during expiration due to weaker pull by the attached structures, even residual tone of the muscle may cause distortion of anatomy preventing adequate reduction in the thoracic volume causing increased residual volume. Thusb reducing the volume of the air expired.


What is the purpose of co-transport? My current understanding of co-transport is that, first, a substance is actively transported across a membrane, establishing a concentration gradient across said membrane. This same substance then diffuses down the established concentration gradient, effectively travelling back to where it began, but this time travelling via a transmembrane protein that transports another substance also, regardless of its concentration gradient. Thus, this second substance is transported to wherever it is necessary.

Would it not then make more sense for the latter substance to simply be actively transported to its destination, as opposed to involving another substance which has no net movement at the end of the process? What is the advantage of co-transport?

Would it not then make more sense for the latter substance to simply be actively transported to its destination, as opposed to involving another substance which has no net movement at the end of the process?

But where would the energy for the transport come from! Thermodynamics tells us that the universe tends to increase the amount of disorder (Entropy). If we have active transport of a solute, then by definition, this is going against a concentration gradient. So we could end up with a substance being entirely on one side of a plasma membrane, which wouldn't be disordered at all - clearly thermodynamics wouldn't let this happen by itself since we would be reducing entropy.
This is why energy is needed for active transport. We need to put in the leg-work by using some energy to locally reduce entropy, and ultimately move something to one side of the plasma membrane. Think of the concentration gradient like the pent up energy of a spring. We can release this energy when we want, in order to make it thermodynamically feasible to move a solute against its concentration gradient.

  What is the evolutionary advantage of co-transport?

We've established that we need an energy source to drive active transport. But indeed, why would we use a concentration gradient? Couldn't we equivalently use a different energy source? Well yes, we could use ATP (for instance in Na$^+$/K$^+$-ATPase). But a concentration gradient might already be established over a plasma membrane, so its already there as an existing source of energy. Perhaps this is why co-transport evolved with this mechanism.


Can mRNA be used by ribosomes more than once? Can mRNA be used by ribosomes more than once? I mean can mRNA be translated more than one time? If not what will happen to it after translation?

There are a few cases in translation that I can think of where an mRNA is translated more than once: the closed loop model of mRNA translation, translation reinitiation, and translation by polysomes.

Closed-loop model

Here's an interesting paper to get you started: ncbi

Essentially, the theory is that mRNA can form a closed loop with the 3' end held to the 5' end by various factors. The ribosome assembles near the start, runs through the mRNA, translating the polypeptide sequence, then dissociates at the STOP codon. Since the "end" of the mRNA is near the "start" of the mRNA, the ribosome can reassemble soon after dissociation.

Translation reinitiation

See this.

The ribosome dissociates incompletely at the STOP codon, the small subunit keeps moving on the mRNA, then the large subunit reattaches at a downstream start site. This happens when the mRNA has multiple ORFs.

Polysomes

(See the wikipedia article on Polysomes for more details)

This basically means that you have a ribosome train moving along an mRNA. The same protein is being translated multiple times, but by different ribosomes. One really cool thing about this is that it's actually been observed by electron microscopy!

(source: bioninja.com.au)

To answer the 2nd part of your question...
wikipedia

mRNA gets degraded in a process called RNA interference (RNAi). Small interfering RNAs (siRNAs) are also transcribed that are incorporated into a ribonucleoprotein complex (RISC) that has an mRNA cleaving activity. The siRNAs are complementary to segments of mRNAs in order to give specificity to RISC.


Caterpillar resembling a snake I found a very interesting caterpillar. It's 5 cm long and  looks like a snake. I discoved it in a greenhouse on a vine in the Czech Republic.

I found two types: a green one and a brown one, both with same length.

What species is it?

Looks like the larvae of an elephant hawk moth (Deilephila elpenor).

 Green Variant. ©2005 Henk Wallays  (CC BY-NC 3.0)

In the Sphingidae family (like the snake-mimic caterpillar in this post).

Description: typically brown-gray color with black dots along length of body. Young larvae are yellowish-white or green, but some mature larvae also can be green colored. Fully-grown caterpillars reach 7.62 cm in length.

Have a backward curving spine or "horn" on the final abdominal segment.

 D. elpenor color variation. Source: A.R. Pittaway & I.J. Kitching

Range: Most common in central Europe and is distributed throughout the palearctic region.

Habitat: variety: including rough grassland, heathland, sand dunes, hedgerows, woodland, open countryside, and even urban gardens.

Source: Wikipedia


What is the expected number of children that need to be born for every possible point mutation to occur once? I'm reading The Perfect Health Diet, and in it the author says that the probability of a point mutation is (175/3*10^9) per new child. He then goes on to write:

In the Paleolithic, with 100000 children per generation, it would have taken 8000 generations, or 160000 years, for each possible mutation to occur once.
Today, with more than a billion children per generation, every possible point mutation now appears about twenty times per generation, or almost yearly.

Using his probability, I get that you need 1 / (175 / (3 * 10^9)) (which is about 17 million children). But he writes that for the Paleolithic era, you need 10000 * 8000 = 80 million children! Can someone help me reason out how he got that number?
EDIT
My math was wrong :-) leaving up the og calculation. Here's the reference that he cites:
"Estimate of the Mutation Rate per Nucleotide in Humans" by Michael W. Nachman and Susan L. Crowell
In the abstract they write "The average mutation rate was estimated to be 2.5x10^-8 mutations per nucleotide
site or 175 mutations per diploid genome per generation."

I don't think the book's reasoning is correct.

There are about 3 billion base pairs in the human genome, but only ca 25.000 protein-coding genes. From the top of my head, I recall that each child has about 30 mutations. If that's in the total genome and if they were all point mutations and there's 4 options for the base pair, then we have $30$ mutations out of 12 billion options in each child. So that each possible point mutation has a probability of $30/12 \text{ billion} = 2.5 \times 10^{-9}$ or $1/(2.5 \times 10^{-9})$ if you like. The book's number is 23 times larger but in the same ballpark range. Lets call this probability $p$.

Now the probability of a mutation occuring in n children at least once is equal to one minus the probability of it never occuring in n children. In other words:
$$1 - (1 - p)^n =$$
$$1 - (1 - 2.5 \times 10^{-9})^n =$$
$$1 - (0.9999999975)^n$$

If we want the mutation to occur with probability 95%, we have to solve:
$1 - (0.9999999975)^n = 0.9$
This has the solution $n = 1 \times 10^9$

In other words, with 1 billion children, each point mutation has a 95% probability of having occured at least once. Mathematically this is not the same as saying that every mutation will have occured. In fact, this implies that 5% of the mutations will not have occured. But perhaps surprisingly, we only need 4-5 billion to up the chance to 99.999%. That still leaves out thirty thousand point mutations, but is sufficiently close to "everyone".

Compare this to the numbers you mentioned:
n = 17 million gives each gene a 4% chance of occuring
n = 80 million gives each gene an 18% chance of occurring.

Secondly, a mandatory rant. :-) "The Perfect Health Diet" is written by Paul and Shou-Ching Jaminet, an astrophysicist and molecular biologist respectively. This has the potential to marry the physicist's penchance for oversimplification with the biologist's lack of mathematical prowess. We see both in the passage you ask about. A shoddy calculation about an oversimplification of what mutations and evolution is about.
Both the book's dustcover use of a word like "detoxifying" and mention of how diseases spontaneously resolve if you eat right, are both strong crackpot indicators. It's the kind of thinking that killed Steve Jobs because he didn't seek medical help soon enough but tried to eat his way out of his illness.


Can Escherichia coli survive on glucose and water alone? I am novice to biochemistry and biology in general. I am reading Lehninger Principles of Biochemistry, and I found the following sentence at the beginning of the chapter on glycolysis:

  A bacterium such as Escherichia coli can obtain from glucose the carbon
  skeletons for every amino acid, nucleotide, coenzyme, fatty acid, or
  other metabolic intermediate it needs for growth.

Does this mean that E.coli can survive in a medium containing H₂O and glucose alone? E.coli can synthesize any other nutrient it needs?

The minimum requirement for E. coli and other bacteria to grow and survive is called minimal medium.  It's even defined at Merriam-Webster:

  a medium that contains only inorganic salts, a simple carbon source (as carbon dioxide or glucose), and water

Water and glucose are pretty easy, but the source of salts may often change; regardless, you really need some potassium, phosphate, and nitrogen for amino acid synthesis.  This page has a bunch of information on bacterial growth, including some "recipes" for a few bacterial strains.  For E. coli, the classic media is M9, which over at Sigma is made of:

  33.9g Na₂HPO₄.7H₂O
  15g KH₂PO₄
  5g NH₄Cl
  2.5g NaCl

  per litre of solution.

Here are some other recipes.


How do I read a species description that uses both ≡ (triple bar) and "incl." to denote synonymy? I'm trying to understand the relationship of plants formerly classified as Dorstenia crispa with distinct individuals continuously classified as Dorstenia foetida. I would assume that the distinctive phenotype would warrant a var. or forma, if not a subspecies, but I haven't seen it written as such anywhere.

I turned to monographs, which in one case stated:

  incl. Dorstenia crispa Engler (1898); ... incl. Dorstenia crispa var. lancifolia Rendle (1915) ≡ Dorstenia foetida ssp. lancifolia (Rendle) Friis (1983);

Would this indicate that a specimen identified as D. crispa is properly identified no more specifically than as D. foetida?
Does this indicate that a specimen of D. crispa v. lancifolia is properly D. foetida ssp. lancifolia; or simply recognising that D. crispa v. lancifolia and D. foetida ssp. lancifolia would refer to the same individuals, which are properly still called nothing more than D. foetida?
Since these formerly-recognised infraspecific taxa do exist as separately-kept lines in cultivation, would they be properly recognised as cultivars?

My answer may simply be the closing remark in the above-quoted description, "Since the various forms are connected by intermediates, it is impossible to recognize infraspecific taxa." However, that's deeply-unsatisfying if cataloguing a collection that contains several now-synonymous specimens.

According to the Taxon guidelines for authors (pdf, pg 205), a triple-bar (≡) indicates a homotypic synonym:

  Homotypic names are cited in chronological order in a single paragraph with
  the identity sign (≡), followed by the type.

So, in your example, Dorstenia foetida was described on the basis of the same type specimen used by Forsskål in 1775 to describe Kosaria foetida -- or possibly a neotype was designated linking these two names, possibly by Schweinfurth in Bull. Herb. Boissier 4(App. 2): 120 in 1896. More information about the relevant type specimens would help sort this out.


Does a software exist to automatically design antibodies that target a given protein or antigen? I'm looking for software to automatically design antibodies that target a given protein or antigen.

Much easier said than done!

If I had sufficient funds and time to pursue your goal what I would do is comb the Protein Data Bank for all the PDB files of interest. Surely you have some protein that interest you. Might consider doing the following:

Figure out what family your protein belongs in, considering it's number and presence of motifs: coils, helices, beta sheets, etc...
Do a literature review of any protein that has already been studied belonging to this family. So when a protein in this family catalyzes a reaction what are its flexible and restrained regions?
Use a program like Autodock to dock your protein to a protein that its protein family might interact with.
Calculate the interaction energies using Gromacs, NAMD, or Gaussian. You can do a zero time calculation of initial states or pursue a molecular dynamics approach as the proteins move randomly to their most stable configurations, or even a molecular mechanics approach. Which systems are most favorable?
You got this far. Now what? But then none of these steps creates your candidates. It just gives you an idea of the physics involved in already structurally identified compounds. Yes, you can make point mutations in VMD and Pymol. But, if you want to add a new motif to an existing protein structure it will not work because more than 20 amino acids in a peptide do not fold properly.

To do some of the biological statistics, the research collaboratory of structural bioinformatics is right here: http://www.rcsb.org/pdb/home/home.do

You can parse through their folders with wget or curl in bash scripting
at http://files.rcsb.org/

But then assuming you do figure out a candidate protein that doesn't exist yet. How are you going to make it in the lab? It appears that it would be better to do microbial studies. Maybe you can screen for a match with micro-array plates.


Omics integration questions Let's say that I have a population of Mus musculus in the lab. I divide it in a control group and a test group. The test group is constantly subjected to a stress (example: elevated UV radiation). Both groups are allowed to reproduce for 20 generations.
I want to fully characterize and compare what changed in each offspring (control vs test group) by using omics. The objective is then to integrate all these information in a new database with the pathways that change and by what magnitude.

Should I use genomics or/and exomics or/and epigenomics?
If I do one of the above and proteomics, why could I need the transcriptomics for?
Would the metabolomics, which are mainly punctual measures, add any valuable information?

This is a purely didatic exercise.

Should I use genomics or/and exomics or/and epigenomics?

Depends on what you want to look at. Whole genome sequencing will give you all the mutations. If you are interested only in the coding part of the genome then you can go for exome sequencing. Though, exome sequencing will save your time and resources considerably, you may lose out a lot of relevant information from the non-coding and regulatory part of the genome.

Epigenomics is a very broad term. There are several aspects to it. You can go for the DNA methylome, Nucleosome positioning, or ChIP-Seq for Histone modification/variants.

I would suggest that if you can afford it then go for whole genome sequencing. Next choice would be exome sequencing. Once you have these data it might be relevant to add the third layer of DNA methylome.

  If I do one of the above and proteomics, why could I need the transcriptomics for?

Transcriptomics is easier and better standardized than proteomics. There are also many good analysis tools.
There are several ncRNA, which has been shown to play important role in cellular homeostasis and gene regulation. You will miss out those.
You will save money. The reagents used for the transcriptomics experiments are the same as the ones used for the genomics experiments. Proteomics is a different domain altogether. You might need to look for collaborators.

  Would the metabolomics, which are mainly punctual measures, add any valuable information?

Sure, they do add information. Whether of great value or not depends on the study that you are carrying out. For e.g if you are studying the role of stress in diabetes then doing a metabolomics study may be of great value.


Do adult mosquitoes have color preferences? Do adult mosquitoes get particularly attracted or repelled by any colour, or darkness or light? If so, what are they?

"Mosquito" is a quite broad term, since it englobes several Genera and more than 3500 species. But, at least for some Genera, there are indeed colour preferences.

For instance, Aedes seems to have colour preferences. Have a look at this table from Gjullin (1947), from a research in which the effect of different coloured clothing on the biting rate was investigated:

As you can see, black is the new black for Aedes mosquitoes. At least in the shirt of their victims.

Also, in his paper from 1903, Alpheus Packard describes an interesting experience, this time with Anopheles:

  Color-preference in the Mosquito

  In continuation of their researches on the structure and biology of Anopheles maculipennis, the commonest British mosquito and one known to convey malaria, Dr. Nuttall and Mr. A. E. Shipley observed some interesting facts on the preference this species exhibits for different colors and for different shades of color. The experiments were conducted as follows : In a spacious  photographic studio a large muslin tent was set up with one end against the glass window through which the sunlight poured. At the bottom of the tent were some large pans for the Anopheles to breed in, and these were from time to time renewed.

  The mosquitoes were fed on bananas, which, it may be noted, must be kept fairly fresh, otherwise dates or figs are preferable. On one side of the tent seventeen boxes without lids were piled one upon the other, the order being changed each day so as to eliminate any preference due to position or exposure to light. Each box was lined with a cloth having a slightly rough surface — not a shiny or smooth one — to which a mosquito could easily cling. The experiment consisted in counting the number of mosquitoes found in each box on seventeen different days.

  The results obtained are striking. During the seventeen days on which the count was made, 108 mosquitoes were found in the navy-blue box, 90 in the dark-red box, 81 in a reddish-brown box, 59 in the scarlet box, and 49 in the black box. There was at this point a sharp drop to 31 in a slate-gray box and 24 in an olive-green box. Violet, leaf-green, and full-blue boxes had respectively 18, 17 and 14. Pearl-gray had 9, pale green 4, light-blue 2, ochre and white 2 each, orange I, and pale yellow about the color of khaki none at all.

  It is thus evident that color has a marked power of attracting this species of
   mosquito, and that the color which is by far the most attractive is navy-blue. In both services and equally amongst civilians this is a very common, perhaps the commonest, color for male attire. The experiments just quoted show that it is at least equally popular with malaria-carrying mosquitoes. Light colors were avoided, especially those with a tinge of yellow. Khaki-colored garments would seem to have other advantages besides that of invisibility on a light soil.

Sources:

C. M. Gjullin; Effect of Clothing Color on the Rate of Attack of Aëdes Mosquitoes, Journal of Economic Entomology, Volume 40, Issue 3, 1 June 1947, Pages 326–327.
Packard, A. S. “Color-Preference in Insects.” Journal of the New York Entomological Society, vol. 11, no. 3, 1903, pp. 132–137. JSTOR, JSTOR, www.jstor.org/stable/25003044.


Why is there debate about thymus being an endocrine gland? I read on my textbook that there is debate about whether thymus is an endocrine gland. But they do have glandular cells no? Is producing T Cells the only point for thinking it not as a part of endocrine system?

So, Q: What's the reason behind this debate and has it reached any conclusion?

In my mind as an immunologist, there is no debate. In order to be part of the endocrine system, a body structure needs to be a gland that secretes one or more hormones to induce signaling at distal targets. These hormones can have multiple chemical forms. However, the thymus does not do that. It was proposed beginning back in the 1960s that the thymus contained and produced something called thymosin, which was eventually separated in 40 separate substances, none of which acts as a hormone, and most of which are now known to be present in many other tissues. T cell production and maturation occur as a result of signaling induced by cell-cell interactions (ligands and cognate receptors on the cell surface) as well as the action of many cytokines and chemokines. These compounds are not classified as hormones, though.

It is possible that some hormones might be expressed in the thymus in very small quantities; however they are not secreted. This is due to a part of T cell development and maturation known as negative selection, where the thymus can ectopically express proteins typically only found in other tissues, such as the nervous system, pancreas, or lung, for example. This process allows for the removal of potentially auto-reactive T cells, which recognize self antigen.

Basically, knowing what we do about the function of the thymus in human and mouse, and how it does what it does, I honestly don't see how someone today could classify it as part of the endocrine system, even though histologically it may appear similar to glandular structures, and small traces of one hormone or another may be found in thymic extracts.


Which kind of caterpillar is this? Which caterpillar is this? It was found in mid Europe during this time (April). Size about 2cm in length.

Based on the body structure and double pair of legs per body segment, this is a millipede.

Based on the small size and spacing between body segments, it could possibly be in the Paradoxosomatidae family. You could check by examining the specimen more closely:

  Most species possess a groove or furrow ("sulcus") on the dorsal surface between the keels (paranota) on each segment.

Although the color is wrong, this millipede reminds me of the somewhat-cosmopolitan invasive, the Green house millipede (Oxidus gracilis), which is about 1.8 to 2.3 mm long.

 Source: NCSU Plant Disease and Insect Clinic; Credit: Matt Bertone

Due to the color difference, I cannot tell definitively whether this is your species or not. Your poor picture quality makes this more difficult. However, I thought I'd provide this post for you as a jumping off point. good luck!


Digital Genomic Footprinting for ENCODE I'm reading over the ENCODE Nature papers, and one of the papers referred to is "Global mapping of protein-DNA interactions in vivo by digital" by Hesselberth et al[1].

Genomic footprinting is a massively parallel variant of DNAse I hypersensitivity screening, which I feel I have a good handle on, but I don't understand this paragraph from the beginning of the results (the troublesome part is in bold):

  To visualize regulatory protein occupancy across the genome of Saccharomyces cerevisiae, we coupled DNase I digestion of yeast nuclei with massively parallel DNA sequencing to create a dense whole-genome map of DNA template accessibility at nucleotide-level. We analyzed a single well-studied environmental condition, yeast a cells treated with the pheromone α-factor, which synchronizes cells in the G1 phase of the cell cycle. We isolated yeast nuclei and treated them with a DNase I concentration sufficient to release short (<300 bp) DNA fragments while maintaining the bulk of the sample in high molecular weight species (Supplementary Fig.1). These small fragments derive from two DNase I “hits” in close proximity, and therefore their isolation minimizes contamination by single fragment ends derived from random shearing. Because each end of the released DNase I ‘double-hit’ fragments represents an in vivo DNase I cleavage site, the sequence and hence genomic location of these sites can be readily determined by sequencing (Supplementary methods).

There's a reference to another paper by Sabo et al.[2] about genome-scale DNase assays using microarrays in that paragraph that I'm reading, but if someone understands the biology well, I'd really appreciate an answer.

Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S, Kuehn MS, Noble WS, Fields S, Stamatoyannopoulos JA. 2009. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nature Methods 6(4): 283–289, doi:10.1038/nmeth.1313.
Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, Cao H, Yu M, Rosenzweig E, Goldy J, Haydock A, Weaver M, Shafer A, Lee K, Neri F, Humbert R, Singer MA, Richmond TA, Dorschner MO, McArthur M, Hawrylycz M, Green RD, Navas PA, Noble WS, Stamatoyannopoulos JA. 2006. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nature Methods 3: 511-518, doi:10.1038/nmeth890.

After reading the paper cited I think the logic goes like this: DNAse I will create free ends at accessible sites in the genome. However shearing during subsequent DNA isolation is also a source of free ends, and these represent noise in the analysis. You have to put in a lot of energy to shear DNA to very small fragments, so I infer that mild shearing during DNA isolation is very unlikely to create a new end that is near to an existing DNase I-generated end. Therefore, under the conditions used, any small fragments are much more likely to have been generated by two closely-spaced DNase I hits. By limiting the analysis to these fragments the noise from shearing is minimised.

Now that I've written this answer it doesn't seem like much more than a rewrite of the emboldened sentence, but I hope it is helpful anyway.


Does the process of photosynthesis occur in insectivorous plants? Does the process of photosynthesis occur in insectivorous plants?
Can you please give me a clear answer and explain to me how?
and also can you describe the environment in which they grow ?
Thank you

"Carnivorous plants are plants that derive some or most of their nutrients (but not energy) from trapping and consuming animals or protozoans, typically insects and other arthropods. Carnivorous plants have adapted to grow in places with high light where the soil is thin or poor in nutrients, especially nitrogen, such as acidic bogs and rock outcroppings."

Source: https://en.m.wikipedia.org/wiki/Carnivorous_plant


Why isn't Rh disease present in other mammals? I have read about Rhesus D Hemolytic Disease of the Newborn, sometimes called "Rh disease". It's rare, but it can happen when an Rh+ baby is conceived by an Rh- mother.  This raises many questions. I have heard this problem only happens with humans; if so, why doesn't it affect other mammals like Rhesus monkeys?  Where along the evolutionary time-line did Rh disease come about in the first place?

Rh is just a proteinous(antigenic) factor in red blood cells; not a DISEASE.If it is present in blood you are Rh positive. If not Rh negative.An Rh negative person if exposed to Rh positive blood will form specific antibodies against the Rh antigens. In case of pregnancy, Rh antigens of the foetus do not get exposed to the Rh negative blood of the mother during first pregnancyas the two bloods are well separated by the placenta.

However during the delivery of the first child there is a possibility of the exposure of maternal blood to small amounts of Rh positive blood of the foetus.In such cases the mother starts preparing antibodies against Rh antigens in her blood.

In case of her subsequent pregnancies, the Rh antibodies from the Rh negative mother can leak into the blood of the Rh positive foetus and destroy the foetal RBCs. THis could be fatal to the foetus or could cause severe anaemia and jaundice to the baby.A condition called erythroblastosis foetalis arises.

This condition can be avoided by administering ant- Rh antibodies to the mother immediately after her first delivery.

This is not a disease but is just as a result of antigen- antibody reaction.As far as Rhesus monkeys are concerned, it is an innate factor in them, common to all.It is quite similar to the case of Bacillus thuringiensis in biotechnology. When inserted into plant cells these bacterial phytotoxins cause havoc as an insecticidal agent; whereas they seem to have exactly no effect inside bacteria.You may also consider the case of Penicillium notatum.These organisms are capable of causing harm to other living organisms but are not affected themselves.

Similar is the case with Rhesus monkeys.


Why are "itch signals" transmitted so slowly from the skin to the human brain? In the second half of the BBC radio (and podcast) program Cats and Itch;
Discovery, The Curious Cases of Rutherford and Fry Episode 2 of 5 the phenomenon and origin of the "itch" and related sensations are discussed, with input from several specialists, including "Neuroscientist Prof Francis McGlone from Liverpool John Moores University and dermatologist Dr Brian Kim from the Center for the Study of Itch at Washington University. Yes, that is a real place."
Here is an unofficial transcription of a small segment starting at about 17:30:

Until quite recently, the same nerve fibers were thought to transport feelings of both pain and itch, from the skin to the brain. In 1997, a ground-breaking discovery revealed that itch has its own separate nerves responsible for that oh-so-familliar itchy-scratchy sensation. Now, if you accidentally lean on your “hot”, the sensation will travel through your fast pain fibers at 80 miles per hour; you can almost-instantly pull your hand away.
By contrast though, itchy signals crawl towards your brain at a sluggish 2 miles per hour, so once you’ve been bitten, it takes a while for the itching to begin.

Those quoted speeds equate to about 130 m/s and only 3.2 m/s, respectively.
What causes the "itch" fibers to transmit signals to the brain so slowly? Is there thought to be some evolutionary benefit to such slow conduction, considering that the speed of most signals from skin to brain are transmitted so much faster?

What causes the "itch" fibers to transmit signals to the brain so slowly? Is there thought to be some evolutionary benefit to such slow conduction, considering that the speed of most signals from skin to brain are transmitted so much faster?

The interview most likely refers to the findings of Schmelz et al., J. Neuroscience, 1997: Specific C-receptors for itch in human skin

In essence they found tested the sensitivity of unmyelinated nerve fibers (note: myelination also increases transmission speed) towards distinct stimuli. They found that some of those fibers would selectively respond to stimuli which would be perceived as itching (such as histamines). They find that:

  This slow conduction velocities attributable to small axon diameters ...

Note that since they don't need to, they also don't speculate on the physiological reason, why itching should be processed by slower fibers (and some potential explanations will be recognized quite well by readers of their article).

Please also note that the original claim, from 1997, however has been softened with the years, and there appears no strict separation been stimuli like "hot", and itching, in terms of distinct fibers and transmission speeds; e.g.: Davidson et Giesler, Trends in Neuroscience, 2011: The multiple pathways for itch and their interaction with pain


How does menstruation proceed during one period? I'm simplifying things here:

  A. Does a woman bleed constantly, like a drop every 10 minutes? Two hours without pad or tampon and your underwear is dirty?

or

  B. Does a woman bleed suddenly a bigger amount of menstruation fluid? Then hours might pass before it happens again?

or

  C. Both.

Might be a stupid question. I'm sorry. I read all the other information on the internet but no one answers this one for some reason. I read girls should change the pads and tampons a few times a day (like every 6 hours). Does that mean A is correct?

Thanks for any helpful information!

(Well, I guess I'm male.)

Edit:
What I want to know: If I was a woman, how would I experience the days of period bleedings? From what I read in the comments and answer(s), one should expect A (constant bleeding) and should wear pads/tampons all the time (for 2 to 7 days) and sometimes one could also experience an exceptional heavier bleeding (B)? Are there (healthy) women who would experience B most of the time? I visited Wikipedia and other random sites but they all have the other important information without answering my question. (Also I will be glad to accept an answer, which satisfies my need for knowledge.)

The answer is both. Different women experience menstruation differently depending on the levels of different hormones in their body, personal medical conditions, medications, on their age, and the activities they do in their lives. Bleeding is due to the sloughing off of the highly vascularized endometrial lining of uterus which is no longer receiving the appropriate levels of progesterone for its maintenance from the corpus luteum, in the absence of an implanted embryo in the uterus. You can imagine how different this common event would be if a woman was taking warfarin, had a bleeding or coagulation disorder, had polycystic ovarian syndrome, was a runner, or was a 13-year-old vs a 41-year-old. It varies!

Source:

Welt et al. Physiology of the Normal Menstrual Cycle. Last updated Feb 28, 2014. http://www.uptodate.com/contents/physiology-of-the-normal-menstrual-cycle.
http://www.womenshealth.gov/publications/our-publications/fact-sheet/menstruation.html


What is the benefit for cells having the ATP production regulated in mitochondria compared to being from the nucleus? Mitochondria have their own DNA and appear to be loosely connected to the nucleus and it role.

Why are the functions of mitochondria not in the nucleus? Why doesn't the nucleus control the mitochondria's functions as it controls regulation for other chemical reactions?
Are there evolutionary/competitive benefits for this separation?

For starters, see this thread.

My understanding is that the ancient predecessors of mitochondria were free-living unicellular organisms. Supposedly at one point, these mitochondria-like cells developed an endosymbiotic relationship with a larger cell. This relationship was advantageous for both cells: the smaller cell could focus on energy production, leaving tasks like homeostasis, nutrient collection, etc, to the larger cell. Over evolutionary time, this endosymbiosis caused the smaller cell to lose all functions unrelated to energy production, while the larger cell (as we now know it) came to rely heavily on the mitochondria for energy production.

So it's possible that at one time the nucleus encoded machinery for ATP production, but apparently the modularity and separation of function provided by this ancient symbiosis turned out to be successful.


Calculation of Malthusian fertility and mortality from birth and death rates In a simple Malthusian model, the population $p$ grows according to $p = p_0e^{rt}$, where $r = \beta - \mu$, $\beta$ is the "fertility" parameter and $\mu$ the "mortality" parameter. In the case of $\beta$, the closest thing to this parameter is the Total Fertility Rate. Is there a meaningful way to convert from one to the other? An easy formula might be something along the lines of
$$
\beta \approx \frac{1}{2T}\text{TFR},
$$
where $T$ is the reproductive lifetime, but this doesn't account for gender imbalances or a more nuanced way of treating the instantaneous nature of the parameter.

If every member of the population breeds, the mean number of children born from a single individual during their whole life is $\beta$ times the duration of their life. The mean life duration is $1/\mu$. Hence the total fertility rate in the homogenous model you suggest is $$\frac\beta\mu$$ If only some proportion $p$ of the population can breed, the total fertility rate of each breeding individual is $$\frac\beta{p\mu}$$


Help identify these (two) fishes - Netherlands Yesterday my kids caught these two fish. I tried to figure out what kind of fish (species and name, to tell my kids a bit more about them) they are but I was not successful. Today we made a trip to a nearby sea-life exhibition which exhibits native sea animals but I couldn't find similar fishes there :-)

They were caught in Callantsoog (north-western Netherlands) in salt water in shallow water next to a breakwater wall at low tide.

This is the first fish. To me it looks like some kind of catfish.

It is approx. 10 cm long.

This is the second fish. To me it looks like some kind of eel.

It is approx. 20 / 25cm long.

The second fish looks like a rock gunnel (or Butterfish; Pholis gunnellus).

This is an eel-like fish found in the intertidal and subtidal zones of the North Atlantic.

Interestingly, the rock gunnel is capable of remaining above the waterline at low tide and breathing air.

According to Campbell (1984):

  Fully grown adults can reach 30 cm in length. A long dorsal fin spans the body from just behind the head, supported by soft spiny rays. Its anal fin begins roughly midway along the body. The head is rather small with its lower jaw protruding and mouth turned upwards. Coloration is highly variable, ranging from hues of yellow-green to brown to crimson. A row of 9-13 dark spots, each surrounded by a pale ring, lines the dorsal fin

Sources:

1 Campbell, A.C. 1984. The Country Life Guide to the Seashore and Shallow Seas of Britain and Europe. Country Life Books. ISBN 0-600-34396-0


Why is it important to have a restriction point? (G1-S phase control) Why have eukaryotes evolved to control G1-S phase?
Surely if you could control G2-M phase very well, you will not get an excessive proliferation?
Thanks for your help.

The reason you want a check point in the transition from the G1 phase of mitosis to the S phase of mitosis, is that the cell needs to make sure that it synthesized all of the necessary proteins, and accumulated the necessary compounds with which to have DNA synthesis begin AND complete.

The transition from G1 to S is a point of commitment for the cell. There is no turning back at that point. It either needs to faithfully replicate the entire genome or it should die. An incompletely replicated genome would be disastrous for the cell.

If it tried to arrest and go backwards it would likely have too many copies of certain genes and those gene products would likely cause lethality to the cell. You would end up with all sorts of errors and breaks where replication forks collapsed. It would basically be death for the cell. What would be even worse would be if this cell was actually able to avoid the death signals, and at some point enter the cell cycle with all of these damaged chromosomes and you are looking at the possibilities of cancer.

If it arrested and then proceed to G2 and M and somehow got through those checkpoints, then you will have two daughter cells with incomplete genomes. Again if they could survive at all, then likely end up becoming good candidates to proceed down the road to cancer.

That is why G1 needs to be completed properly before the cell commits to replication. It is a point of no return and needs to be tightly regulated for the benefit of the multicellular organism.


Genetic coding question, amino acid to base relationship I'm studying for a test and I am confused by these problems/statements.

How many amino acids will 18  bases code for? Answer: 6. I got this right.
If a certain complete protein has 33 amino acids that compose it, then exactly how many bases will it take to code the entire thing?

The answer to 2. is 105, but I'm confused on how we arrived at this answer. If possible or if necessary, please explain the related concepts to me!

I don't think that's right.  I think 102 would make sense, because you want 99 nucleotides to code for 33 amino acids and more more triplet to code for stop.  Maybe the question writer didn't quite realize that the starting methionine counts as one of the 33 amino acids.


Why honey bees built hive in perfect hexagonal shape instead of irregular shape? Why honey bees built hive in perfect hexagonal shape ?

Due to Hexagonal shape, I can go near without any anxious or fear.( Apart from Honey bee's stings)

From this Question, Most creatures look like or tries to look like irregular to fear the other creatures to attack.

Why honey bees built hive in perfect hexagonal shape ?

Honeycomb cells (not the hive or the honeycomb itself) are hexagonal, in some species of bees but not all.  The regularity of this shape has puzzled people for a long time, and Darwin (and others before him) addressed the reasons for it.  Darwin did a series of experiments with bees, and summarized his results in Origin of Species.  You can search for "hexagon" in the linked text for his long explanation, or read the (still long) summary 'Evolution of Honeycomb on the Darwin Correspondence Project, but the short explanation is that it's the most efficient way to pack cells without wasting wax, and Darwin identified a bunch of intermediate (less efficient) cell structures in various bee species that supported his hypothetized mode of evolution.

  Thus, as I believe, the most wonderful of all known instincts, that of the hive-bee, can be explained by natural selection having taken advantage of numerous, successive, slight modifications of simpler instincts; natural selection having, by slow degrees, more and more perfectly led the bees to sweep equal spheres at a given distance from each other in a double layer, and to build up and excavate the wax along the planes of intersection. The bees, of course, no more knowing that they swept their spheres at one particular distance from each other, than they know what are the several angles of the hexagonal prisms and of the basal rhombic plates; the motive power of the process of natural selection having been the construction of cells of due strength and of the proper size and shape for the larvae, this being effected with the greatest possible economy of labour and wax; that individual swarm which thus made the best cells with least labour, and least waste of honey in the secretion of wax, having succeeded best, and having transmitted their newly-acquired economical instincts to new swarms, which in their turn will have had the best chance of succeeding in the struggle for existence.


GEN file format, SNPs and alleles I have a few questions I can't seem to get a straight answer to, regarding the .gen file format and also biology in general.

The .gen file format specifies SNPs for individuals.

Since each SNP has associated allele A and allele B, I assume that the file only contains Causative SNPs, and not Linked SNPs, since the former reside in the gene, and the later don't. Since each SNP in the file has an associated gene (actually genotype, some combination of allele A and B). Correct?

SNP indicate a single position in genome, so why can allele be identified with a sequence larger then one? Or does it indicate just a starting point, where each allele can be of different length, which can be greater than 1?

Allele should be a particular variant of a specific gene, but in other places I saw the definition "Alleles are alternative forms of a particular sequence.". The later seems more logical, if looking at the .gen file, but it's contradictory to the first statement. So, what's the correct definition?

EDIT:

After further research I came up with findings, demonstrated in an example row for .gen file:

--- rs200405949 10023   CCAA    C   0.249   0.745   0.007   0.005   0.84    0.155 ...

--- - chromosome number, which is missing because it can be inferred from the filename, belonging to each chromosome

rs200405949 - ID of the SNP - a single nucleotide which can vary between samples/people; there are usually only two possible variations, but in rare cases there is a third or even fourth - which are ignored in .gen?

10023 - allele pair (base pair) coordinate/position inside the said chromosome. Either both major and minor allele are made of a single nucleotide (in which case the SNP coordinate/position inside the said chromosome might coincide with this position), or one of the alleles will have more than one nucleotide and the other allele will be the same as the first nucleotide of the former allele - because we need only one distinct sequence, and all other combinations of same nucleotide length are automatically the other allele?

CCAA - (usually?) major allele - the most common allele (specifically in this context, a single nucleotide or a sequence of nucleotides) for a given SNP (or near it, i.e. somehow connected to it) IN the cohort in question, i.e. the cohort being all the samples/people in the experiment/.gen file (hence, the number of samples equals the number of triplet columns after the 5-th column onwards). It occurs in more than 50% of the times COMPARED to minor allele. Compared to minor allele, they both start with C - shouldn't they differ at this SNP position by definition? Also, more than one nucleotide is specified here - why? SNP always has one nucleotide...

C - (usually?) minor allele - the second most frequent allele (specifically in this context, a single nucleotide). The SNP site can be bi-allelic (mostly picked/studied), in which case the major and minor alleles are the only possible alleles, but some sites are tri- or quad-allelic - in which case we don't have the info for the third (and fourth) allele variants, but we know they are even less common then the major and minor alleles?

0.249  0.745   0.007
0.005   0.84    0.155
... - each subsequent triplet of values then indicate likelihoods of homozygote CCAA/CCAA, heterozygote CCAA/C, and homozygote C/C genotypes (allele pairs) at this SNP, respectively, for one sample/person (each allele is present on one of the two copies of the said chromosome, either maternal or paternal). If one of the three values has a value 1 and the other two have 0, I guess this actual SNP was (somehow) tested for, hence we can be 100% sure which allele pair it is, and if not, then the probabilities were somehow deduced (e.g. from other, somehow related SNPs perhaps). What if they add up to less than one? Or even what if all of the three values are 0?

Are my conclusions correct? And what about the open question?

From what I could find the .gen file format for SNPs was developed for the IMPUTE2 program and is generally meant to be a flexible file format for SNP data. The description of the file format is supposed to documented here (multiple pages pointing to that link), sadly that link is broken / the site is removed.
However, I found some other descriptions of the format:

  In the GEN format each SNP is represented as a set of three
  probabilities which correspond to the allele pairs AA,AB,BB.

from here

  The genfile contains predictor values, one row per predictor.
  --gen-skip indicates how many header rows (typically 0 or 1);
  --gen-headers indicates how many header columns (typically 0 to 5).
  --gen-probs should be 0, 1, 2, 3 or 4:
   0 - haplotypes - predictor values should be "0 0", "0 1", "1 0" or "1 1"
   1 - dosages - predictors provide the (expected) number of A alleles
   2 - two probs - providing probability of being AA or AB
   3 - three probs - providing probabilities of being AA, AB or BB
   4 - four probs - providing probabilties of being AA, AB, BB or NA, where A and B are the A1 and A2 alleles

from here

Like finswimmer already wrote in his answer, it is very important to be clear about what is considered an allele in the context of SNPs. For the .gen file format this is the identity of the base at a given (SNP) position and since humans have a diploid genome, the allele of a specific individual can be one of three versions (usually called AA, AB & BB).

Regarding your specific points:

  Since each SNP has associated allele A and allele B, I assume that the file only contains Causative SNPs, and not Linked SNPs, since the former reside in the gene, and the later don't. Since each SNP in the file has an associated gene (actually genotype, some combination of allele A and B). Correct?

The alleles in the .gen file refer to the respective SNPs not genes.
There is no reason to assume that an given .gen file only contains certain SNPs; if it does this is not due to the data format.
The SNPs in a .gen file do not generally have to be linked to a gene.


Why does tetracycline have such a broad spectrum of activity? What are the structural and chemical characteristics that make tetracycline uniquely broad spectrum? I understand it acts on the A-site of the prokaryotic ribosome, but there exist many ribosome-targeted drugs that are relatively narrow spectrum. I assume it has something to do with its permeability in several different classes of bacterial cell walls and/or membranes - but I can't find any literature that links some characteristic part of its structure to this permeability.

This is a tricky question. First of all, I wouldn't call tetracyclines "uniquely" broad spectrum. They are broad spectrum, but there are other drugs with equally broad coverage absent acquired resistance (e.g., imipenem and chloramphenicol), and current clinical use of tetracyclines is limited somewhat by the spread of resistance.  They don't have any major class limitations, though. Again, absent acquired resistance, tetracyclines are effective against gram positive aerobes and anaerobes, and gram negative organisms, as you seem to be aware.

Tetracylines access their target on the 30S subunit of the bacterial ribosome (blocking the A site, as you said) by passive diffusion through porins of the outer membrane of gram negative bacteria, and active transport across the cytoplasmic membrane of gram negative and gram positive bacteria, but the mechanism for that active transport is still unknown. This is quite a good review despite being quite old. Now, some 30 years later, we have still not identified the exact mechanism, as you can read in Goodman & Gillman's most recent edition (13th), Ch. 59, crossing the cytoplasmic membrane requires metabolic energy, but the process is not well understood. Because of this, we can't point to a specific structural or chemical characteristic. For chloramphenicol, it would be the ability to diffuse across the cytoplasmic membrane; for tetracycline, we don't know. I suspect part of the reason for this is that people are now more interested in pumps removing tetracyclines from the cell than those that accumulate it, so it's more of a question about research priorities than some transport mechanism that is particularly difficult to detect.


iodine: how did they manage without it in old ages? (People who were living far from the sea) Knowing that today iodine comes either from fish products or (artificially) enriched table salt, how did people who lived far from the sea survive before (especially during the the Middle Ages)?

Edit 1: nowadays we could find some iodine in cow milk, cheese and eggs but those sources are artificial

  (Increased iodine content in food due to greater use in: food
  processing, animal rations, antimicrobial agents...)

source

Edit 2

  A small amount of iodine enters the atmosphere and, through rain,
  enters ground water and soil near the sea

source

Summarized of the comments: thanks to  ddiez this question has been partially answered. But as vsz pointed out the the mystery remains:

  areas with iodine deficiency didn't get completely depopulated during the Middle Ages
  seems to suggest that it does not affect all people that severely.

So the question remains: could humans survive and reproduce without any iodine source?

Edit 3:

  “If all women in the UK took iodine supplements while pregnant, IQ
  would rise by 1.2 points per child” but some says "Some observational studies suggest supplements could even lower IQ, perhaps because excess iodine might harm the thyroid gland." (Newscientist, August 2015)

Iodine is naturally found in sea water and soil but it is not evenly distributed, with many areas in the world with low levels of iodine. Iodine accumulates naturally in fish, and plants growing in iodine-rich soil. Mammals that eat these plants get iodine from them, which then accumulates in the milk, making dairy and its products (e.g. cheese) another natural source of iodine. Table 1 from the Iodine deficiency section at the American Thyroid Association web page contains a brief list of iodine-rich food.
Quoting the web site:

What are the sources of iodine?
Iodine is present naturally in soil and seawater. The availability of iodine in foods differs in various regions of the world. Individuals in the United States can maintain adequate iodine in their diet by using iodized table salt (unless they have to restrict the amount of salt in their diet), by eating foods high in iodine, particularly dairy products, seafood, meat, some breads, and eggs, and by taking a multivitamin containing iodine (see below). However, the amount of iodine in foods is not listed on food packaging in the U.S., and it can be difficult to identify sources of iodine in foods.

As mentioned, the amount of iodine in some food depends on how much iodine is present in the water or soil. For example, in the International Council for the Control of Iodine Deficiency Disorders (ICCIDD) there is some mention about the natural sources of iodine and its limitations:

Most of the iodine we consume comes from what we eat and drink. Seafood is usually a good source because the ocean contains considerable iodine. Freshwater fish reflect the iodine content of the water where they swim, which may be deficient. Other foods vary tremendously in iodine content, depending on their source and what may have been added. Plants grown in iodine-deficient soil do not have much iodine, nor do meat or other products from animals fed on iodine-deficient plants. Because the breast concentrates iodine, dairy products are usually a good source, but only if the cows get enough iodine.

Iodine deficiency causes important health problems. Iodine is necessary to produce thyroid hormones. Lack of thyroid hormones causes hypothyroidism, cretinism and goiter. However, iodine deficiency is not mortal per se.
Conclusion
As a consequence, in the Middle Ages iodine deficiency was not an issue in places where water and/or soil was rich in iodine. In other places they would suffer of iodine deficiency, leading to a higher impact of the related diseases.
Nowadays, iodine is added artificially to food in order to prevent iodine deficiency. This practice has diminished the impact of iodine deficiency-related diseases. However, iodine deficiency is still an important issue today, as reported by the World Health Organization in its map describing the Degree of Public Health Significance of Iodine Nutrition. As shown in the map, in many places in the world there is still risk of severe iodine deficiency.

Sources:

Iodine deficiency - Wikipedia
American Thyroid Association
World Health Organization
International Council for the Control of Iodine Deficiency Disorders (ICCIDD)


Where do the four ADPs come from in the second stage of glycolysis? In the first stage of glycolysis, the two molecules of ATP are broken down into 2 ADPs + 2 Pi through hydrolysis, then in the second stage of glycolysis they are phosphorilazed to obtain 2 ATPs. How can this process happen twice to yield 4 molecules of ATP if we only have 2 ADPs to begin with?

Note: I'm not asking why the process happens twice, since it's easy to see that the Fructose-1,6-biphosphate is being broken down into two Glyceraldehyde phosphate molecules. I'm asking how can the process of producing two ATPs happen twice if we only broke down two ATP molecules into ADP.

I think I understand your question, and stumbled upon it because i was wondering the same thing while studying for my Microbio test. I know its a year late, but someday someone else might need this info...so here it is.

To put it simply: there is a second pair of phosphates added to the two 3-carbon molecules cleaved from the preparatory stage before the 4 ATP are finally formed. These get added by an enzyme while reducing the NAD+ molecules.

In depth: The first pair of phosphates the cell uses to synthesize ATP come from the initial 2 ATP invested during the prep stage, but an additional 2 phosphates are added when the cell oxidizes the two Glyceraldehyde, 3 Phosphate (G3P) molecules to form NADH. In this step, two electrons are taken away from the G3Ps and an available inorganic phosphate is added to the "1" position, forming "1,3 Biphosphoglyceric Acid " (1,3BPG). Afterwards, the molecules each have 2 phosphates for a total of 4 phosphates available to get oxidized and used to synthesize 4 ATPs.

This step, (the addition of an inorganic phosphate as an intermediary step) is SO overlooked by regular textbooks that its not even funny. mine doesnt even list the enzyme; I had to look it up.
but yeah, that's the source of the additional phosphates available for forming the 4 ATP molecules of glycolysis, and possibly why you didnt see it from the diagram in your textbook (you're not alone!).

Hope that helps!

Sources, as of 4/18/17:

https://www.khanacademy.org/science/biology/cellular-respiration-and-fermentation/glycolysis/a/glycolysis
https://en.wikipedia.org/wiki/1,3-Bisphosphoglyceric_acid


Is "exhaustion" of the Hodgkin-Huxley membrane at constant stimulation a real phenomenon? I was playing around with a simulation of the Hodgkin-Huxley model using their original parameters for the squid giant axon.

By applying a constant stimulation current to the model in resting state, an infinite train of action potentials is triggered, which seems reasonable. However, if the current exceeds a threshold, these APs die off very quickly as both the membrane potential and the ion conductances reach a steady state.

What is this phenomenon called? Is it a real phenomenon, or just an artefact of the Hodgkin-Huxley model?

This phenomenon is called depolarization block and it occurs in real membranes in current-clamp experiments.

The key mechanism is that the membrane has not been allowed to repolarize sufficiently to relieve the inactivation of sodium channels. The Hodgkin-Huxley model reflects this in the "inverted" voltage-dependence of the h gate (sodium inactivation gate)--inactivation is greater at higher voltages. This means that sodium channels cannot open again, or trigger another action potential, until the membrane is repolarized. Canonically, the need to relieve inactivation of sodium channels is the reason for the afterhyperpolarization phase of an action potential where the AP downstroke becomes transiently more negative than the resting potential.

The relevance of depolarization block in in vivo physiological conditions is not well studied. It is not likely that depolarization block occurs in well-behaved neurons under physiological conditions. However, it's possible that it does occur during pathological states.


Constitutive mutation in operator gene If a constitutive mutation happens in the operator of an inducible operon, does that mean that repressors won't be able to bind them ? Or does it mean that even if repressors are bound, they will not have any effect on the gene ?

I am specifically talking about lac operon.

For the lac operon there are two possibilities for constitutive expression mutations:

The operator is never closed.

Reason: Mutation of the repressor, so its not present, doesn't bind or binds only with very low affinity for the operon.

The repressor can not bind.

Reason: The binding site for the repressor is mutated.

See this Website or this Website for more information.


What modern insects are not (flying OR descended from flying ancestors)? What modern insects are not flying or descended from flying ancestors?

(I read somewhere that 99% are, so of course I instantly became curious which aren't. xD )

EDIT:  Sorry, I should have been clearer: I meant examples of modern insects with no flying ancestors.

Silverfish, also known as Lepisma (order Zygentoma), does not fly and does not descend from flying ancestors.

It's close to Archeognatha, which don't fly either nor descend from flying ancestor.


Questions on mid-2019 Covid-19 Spread in Spain I recently read in the news from Reuters that Covid-19 was already present in the Europe in March 2019 as reported by the study by Chavarria-Miró et al (2020). According to  Chavarria-Miró et al they found traces of SARS-CoV-2 in March 12, 2019 sewage samples from Barcelona.
I am interested in this news because I do research on effects of covid-19 pandemic and government responses to covid-19 on macreconomic indicators. In macroeconomcis we are unable to run randomized control trials but sometimes nature can create natural experiments or situations that allow for use of quasi-experimental statistical techniques, and I think I can use the situation above in such way.
Consequently, I have the following questions:

How conclusive is that  Chavarria-Miró et al study? Are there any red flags that would indicate the conclusion drawn from the study should not be taken at face value? Essentially, I am interested in knowing if the study is reliable or if there are possibly other corroborating studies.

Is the SARS-CoV-2 found in march 12 the same SARS-CoV-2 that was circulating in 2020? Or we can't tell? Or to what degree it is similar if it is possible to know (in terms of infectiveness and mortality/morbidity)? If it is not possible to answer this empirically, is it at least possible to answer it theoretically based on how similar viruses mutate? (Here I would also appreciate some references to literature/data if possible).

The reason why I ask this second question is that given how dangerous and infectious is Covid-19 considered, I am surprised that there weren't spikes in deaths in Spain. In fact, according to statistics provided by Statista the number of deaths in 2019 was highest in January and even declined after March. When the number of death is totaled across whole year 2019, and compared to years prior years in data from Statista here, again the number of deaths was comparable to 2018. I realize that just looking at a crude naïve statistics like this is not rigorous but I would expect at least some visible effect if Covid-19 was already spreading in March 2019.

To judge about this assay, it is important to see how they worked. They used different sets of primers to analyze for SARS-CoV-2. Namely targets IP2 und IP4 from Institute Pasteur in Paris (see reference 1) and to validate results also primers targeting the "E" sequence (reference 2) and two against the nucleoproteins N1 and N2 (reference 3).
Then they tested frozen samples taken between January 2018 and December 19. Of those, only the sample from March 2019 come back positive for 2 out of 5 primer pairs, none of the samples before and after tested positive, despite mentioning that samples where already positive as early as January 2020 again.
If you look at the published amplification curve you see a very late Ct value for the sample (I would eyeball it somewhere between 39 and 40), which is basically in the area of non-specific amplification. Running the PCR another 10 cycles until 50 is highly unusual in my experience.

Conclusion: I see this result as a PCR artefact and I doubt, this will be published (at least I hope it will not). The reasons for it are:

only two of five sets of primers is positive. Since these are highly specific, I would expect all five of them positive.
the Ct value is very high, around the usual endpoint of qPCR. If you let PCR run long enough, it will eventually amplify something. The also show no melting curve to prove the have a good PCR product.
it is highly unlikely that the virus appears in March 2018 in the wastewater of Barcelona and then disappears again without leaving any trace. This is clearly not the experience we have been making throughout 2020.

References:

Protocol:Real-time RT-PCRassays forthe detection
ofSARS-CoV-2InstitutPasteur, Paris
Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR
CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic
Panel


Pseudomonas aeruginosa biofilms grows stronger after 95 % ethanol treatment I used 95 % ethanol to disinfect Pseudomonas aeruginosa biofilms from titanium discs and compared it to disinfection with water and hydrogen peroxide. The strange thing was that when examining in SEM, roughly ten times more bacteria was present in the ethanol treated samples than the water treated samples hydrogen peroxide treated samples showed no bacteria. Metabolic activity assay showed however more bacterial activity from the water treated samples than the ethanol treated, hydrogen peroxide showed least. Anyone have any theory why ethanol seamed to increase the bacterial biofilm compared to water? Ethanol are regarded as an effective disinfectant on bacteria.

@Chris is right. ~70% ethanol is the way to go.

From a discussion here :

  The effectivity of ethanol as e.g. desinfectant or antiseptic agent depends on the concentration of ethanol-water-mixture: An ethanol percentage of 50-80% destroys the cell wall/membrane of bacteria by denaturing their proteins and dissolving their lipids (effective against most bacteria, fungi and some viruses; ineffective against bacterial spores). Therefore, the ethanol has to pass the bacterial membrane/wall to get into the bacteria - if you use 100% ethanol instead, the bacteria get 'sealed' and they will survive... An other mechanism is the high osmotic pressure of ethanol/water-mixtures; and the 70% has the highest one.

By using a high ethanol concentration, you're effectively creating a layer of coagulated protein on the surface of the biofilm, "sealing" the bacteria in below that top layer.

As to why water seemed more effective than alcohol, I would venture a guess that some of the bacteria from the biofilm was flushed off. Maybe check the water for bacterial count to verify? :)


Are ribosomes assembled in rough ER and Golgi body, or in the nucleolus? I mean all the components, such as ribosomal RNA (rRNA) are synthesized in the nucleolus, but is the whole ribosome structure assembled in the nucleolus or is it also done in the rough endoplasmic reticulum and Golgi apparatus?

Ribosome assembly starts in the nucleolus (of eukaryotes) and finishes in the cytoplasm. However, in the cytoplasm the Golgi apparatus is certainly not involved, and, as some cells have little rough endoplasmic reticulum, assembly does not require that. Thus, the abstract of a review by Fromont-Racine et al. in Gene (2003) vol 313  pp. 17–42 starts with the statement:

  Ribosome synthesis is a highly complex and coordinated process that occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.

In the 26 pages of this review there is not a single mention of the words ‘endoplasmic reticulum’ or ‘Golgi’.

A more recent (and freely available) review by Thomson et al. in Journal of Cell Science (2013) vol 126  pp. 4815-4820 is in accord with this. It has a pretty poster insert which presents the assembly as a succession of events, starting in the nucleolus, proceeding to the nucleoplasm, and with some final polishing in the cytoplasm.


What is the name of this bird? Does anyone know the name of the bird in the pictures? It was found in the south of Spain in the month of June. (it is certainly neither a house sparrow nor a swallow nor a robin). Thanks for the help!

Thats a difficult one but my gut feeling is a 'bunting' and maybe a Rock Bunting juv ? - the bill is definitely bunting-like and there does seem to be a black and white eye stripe going on . There arent that many buntings in the south of Spain especially with a very warm brown colouring


What's the meaning of 'plasma' in 'plasma membrane'? I wonder why is it called plasma membrane - what's the biological meaning of the word 'plasma'?

I thought it was a no-brainer, apparently it's more of a historical journey into the origins of Botany. But I have a hypothesis: During the debate of whether the cell or the fluid within it was the origin of life, that fluid was called 'protoplasm' - first formed, i.e. it's the origin of life. The plasma membrane, then, is simply that which surrounds the 'plasma' - the protoplasm.


Homework : Sodium Potassium pump Why does sodium-potassium pump consume about 2/3 energy of a cell ?

A.maintains appropriate membrane potential

B.helps in co-transport

I think it should be A.

I can't yet comment, so here's a (sort of) answer:

I've only ever heard the "2/3 of cellular expenditure" rule applied to neurons, and frankly, it wouldn't make much sense in any cell other than a neuron.  The Guyton and Hall Textbook of Medical Physiology says, "For some cells, such as electrically active nerve cells, 60 to 70 percent of the cells' energy requirement may be devoted to pumping Na+ out of the cell and K+ into the cell."  A cardiac muscle cell, for example, would probably use more of its energy for contraction than pumping ions.

In a neuron, the bulk of energy expenditures are for electrical signalling done via allowing sodium and potassium ions to temporarily run DOWN their respective gradients.  As such, the "purpose" of a neuron is to pump ions across a membrane and then let them run back when needed.  Since a neuron doesn't really DO much else, it makes sense that the bulk of the energy produced will go towards pumping ions.  A practical example is the use of barbiturate comas to reduce metabolic activity in the brain.  Flat-lining the EEG drops metabolic requirements by ~50% (Source: Medscape).

Please keep in mind that this answer is specific to neurons...other cells perform other functions, and those other functions will take up significant fractions of energy produced.  Further, other cells probably aren't devoting large fractions of their energy towards signalling, and so the fraction of energy devoted to pumping ions will be markedly less.  They'll still be pumping ions to maintain a gradient to perform tasks like membrane transport and osmotic control, but those tasks are ancillary to the "purpose" of those cells.  I can't find any solid numbers for Na/K ATPase energy expenditures in non-neuronal tissue at the moment, but if I do, I'll update appropriately.

UPDATE:
With regards to the question itself, which I apparently forgot to answer:

Can a cell function without an appropriate membrane potential? Can co-transport run without a membrane potential?


What makes something food? From my (limited) understanding, animals get energy from food by breaking chemical bonds between molecules.

There's a lot of water here [citation needed], so it seems like natural selection would favor any organism that could live off it. Why, in the history of life on earth, hasn't an organism appeared that eats water?

Same applies to dirt, rocks -- (although maybe lichen eat rocks? I'm fuzzy on lichen.)

Or air?

Why are humans and other animals like us only equipped to eat certain types of molecules, when others are so much more plentiful?

You don't get energy from breaking chemical bonds, you only get energy from making chemical bonds, while breaking chemical bonds requires the input of energy.  However, in practice chemical bonds are always broken as others are formed, and the net number of bonds is generally constant.  Otherwise you would end up with free radicals, which are highly reactive and looking to form a chemical bond with the next thing it touches.

For example, the burning of glucose in respiration involves the breaking of C-C, C-H, C-O and O-H bonds in glucose and O=O bonds in oxygen, with the simultaneous formation of C=O bonds in CO2 and O-H bonds in water.  But the C=O bonds in CO2 and O-H bonds in water contain much less energy than the bonds we break within in glucose.  So the key is that the bonds formed contain less energy than the bonds broken, and energy is released overall.

And actually it's a bit more complicated than that, because you also have to consider entropy, which is how disordered the system is.  Generally the more molecules in a system, the more entropy, so breaking a few big molecules down into lots of small molecules tends to release energy by increasing entropy.

So to answer your question, "food" is what we can draw useful energy from in the process of turning it into something else as we make and break chemical bonds.  We can't do this with water, or indeed with rocks, because their chemical bonds would require more energy to break than the energy we'd get back out by forming alternative bonds with anything else.


Parthenogenesis Induction I have read about Parthenogenesis induction in a paper : "Hagimori T, Abe Y, Date S, Miura K (2006) The first finding of a Rickettsia bacterium associated
with parthenogenesis induction among insects. Curr Microbiol 52: 97–101 "

I was curious to know what is the evolutionary advantage of parthenogenesis induction for the parasite (in this case Rickettsia bacterium ) ?

This issue is addressed in this review by Cordaux et al, 2011, along with other, similar strategies.

The simple answer is that these types of bacteria are efficiently spread from females of the species they infect to their offspring; by inducing unfertilized eggs to develop into females, they increase their transmission efficacy.


dNTP concentration for reverse transcription from RNA to cDNA Does it affect the results if I use the half of dNTP amount in a reaction that it says in my protocol?
I usually use 4 microlitres per reaction and this time I did a mistake and I used 2.

The final cDNA will be used for qPCR relative cuantification,so I am not sure if that will affect my results.

You will probably be fine. Lower dNTP levels might reduce the amount of product you obtained since it is usually the primers or the dNTPs that run out near the end of the reaction. The only other effect I am aware of is that the reaction might be slightly less specific as dNTPs sequester magnesium which is a big factor in determining the stringency of the reaction.

You say how many microliters you used but it would be more useful if you mentioned the concentrations of the dNTPs and the desired final concentration.


Were there any marine/aquatic dinosaurs? Most dinosaurs were terrestrial, but there were a couple of groups of arboreal and flying dinosaurs (microraptors, birds etc).

I have read that the theory that Brachiosaurids were aquatic has been largely discredited1, but that Spinosaurids were probably semi-aquatic2.

Excluding modern marine birds (e.g. penguins etc.), were there any other marine/aquatic dinosaurs?

Note: I am aware that the marine reptiles mesosaurs, phytosaurs, mosasaurs, dolichosaurs, Icthyosaurs, thalattosaurs, Sauropterygia (placodonts, nososaurs, plesiosaurs etc), Choristodera were not part of Dinosauria.

1.

 • Three new sauropod dinosaurs from the Upper Jurassic of Colorado, Great Basin Naturalist.
 • The Physiology of Dinosaurs: Circulatory and Respiratory Function in the Largest Animals Ever to Walk the Earth, Respiratory Care
 • A note on the habits of sauropods, Annals and Magazine of Natural History
 • Tipsy punters: sauropod dinosaur pneumaticity, buoyancy and aquatic habits, Proceedings of the Royal Society of London

2.

 • Oxygen isotope evidence for semi-aquatic habits among spinosaurid theropods, Geology
 • Semiaquatic adaptations in a giant predatory dinosaur, Science
 • Convergent evolution of jaws between spinosaurid dinosaurs and pike conger eels, Acta Palaeontologica Polonica
 • Functional Morphology of Spinosaur ‘crocodile-Mimic’ Dinosaurs, Journal of Vertebrate Paleontology

There are a couple of specimens of a dinosaur species named Liaoningosaurus paradoxus that have been found with fish in their stomachs and skeletal features suggesting it was at least semi-aquatic.  It is a member of the ankylosaurian dinosaurs from the early Cretaceous period of China.

From Fish Hunting Ankylosaurs( Dinosauria,Ornithischia) from the Cretaceous of China:

  With elongate and fork-like denticles of cheek tooth crowns,L.
  paradoxus has a dentition capable of penetrating into animals like
  small fishes. The carnivorous adaptation of the dinosaur is also
  supported by the ungual modification to a sharp claw in both the
  fore-and hind-limbs. The evolution of a shield-like ventral armor
  plate and the loose sacrum-pelvic connection suggest that L. paradoxus
  may have adopted an aquatic way of life,using the ventral armor plate
  to protect the body from underwater attacks; as such,the open suture
  between the neural arch and centrum of the vertebrae cannot be used to
  indicate the juvenile nature of the type specimen. L. paradoxus is the
  first carnivorous ornithischian dinosaur since dinosaur was first
  known in the 18th century and represents not only the first aquatic or
  semi aquatic example of armored dinosaurs but also the smallest
  species of ornithischian dinosaur so far known.

Image Source: [Paleontology • 2016] Liaoningosaurus paradoxus • Fish Hunting Ankylosaurs (Dinosauria, Ornithischia) from the Cretaceous of China


What color was the most recent common ancestor of all swans? Was the most recent common ancestor of all swans black, or white, or some other color? How do we know, and how certain can we be?

According to the known phylogeny of Anserinae in this paper,

Cygnus atratus (the black swan) is most closely related to Cygnus melanocoryphus (the black-necked swan). All of the other swans in the genus Cygnus are white, or close to white.

Therefore, it is reasonable to assume via maximum parsimony and maximum likelihood that the two genera evolved their blackness from a white ancestor, and not that all of the swans independently turned white from a black ancestor.


rapidly growing mold on flat surface For an experiment I'm conducting, I need to grow mold on a 2 foot square piece of white fiberglass. I'm in Florida, with high heat and humility, so mold already grows easily. I've seen elsewhere that mold needs organic matter to feed on, to grow rapidly. Ironically, I've seen mold grow on the side of fiberglass motor-homes and showers with no present organic matter. Any suggestions on how to grow mold rapidly on my piece of fiberglass? I thought of locating fiberglass outside, in sun. I could mist it every hour or 2 to create more moisture. Maybe there is something I could rub/spray on the fiberglass sheet to encourage rapid growth? Any other suggestions about applying moisture, light, etc?

Mold is a general name for many species of Fungi, which are heterotroph so they need organic material to feed on. You can see them grow on fiberglass because many organic material can accumulate near or on fiberglass (skin cells, plants root hairs, microbes, oils) and become substrate for the mold.
If you want to grow a specific mold you should first identify it to find the best substrate for that species and not for other. If you simply want mold you can use some kind of starch on the fiberglass and keep it moist (not wet, wetness will give you also oomycetes and bacteria). No need to spray it every 2hrs. You can close the fiberglass with a box, dark box is better (bacteria grow best with light).
You can take (with mask and gloves) some mold and put it on your fiberglass to promote the growing of that mold.
Describing your mold or posting a picture can help to identify. If you see two different colors report both of them and location (center, periphery)


Peptides neither produced by the ribosome or the non-ribosomal peptide synthase complexes I read in Wikipedia:

  While there exist a wide range of peptides that are not synthesized by
  ribosomes, the term nonribosomal peptide typically refers to a very
  specific set of these as discussed in this article.

I was wondering what peptides are being referred to. I can only think of synthetically produced peptides. I can not find any source for other peptides not produced either by the ribosome or by the non-ribosomal peptide synthases described.

One peptide that comes to mind is the metabolically important reducing tripeptide glutathione — γ-L-Glutamyl-L-cysteinylglycine:

This is synthesized from cysteine, glutamate and glycine by reactions catalysed by glutamate cysteine ligase and glutathione synthase:

Synthesis of glutathione (GSH) — two subunits of glutamate cysteine ligase (GCL) are shown

Other examples may involve amino acids not specified by the genetic code which have particular roles in metabolism. For example, taurine, which has a sulphonic — rather than a carboxylic — acid group, can be metabolized to the dipeptide γ-Glutamyltaurine which may have a role in the brain.

These two examples relate to L-amino acids, albeit with a peptide bond between the side-chain glutamyl carboxyl group rather than the α-carboxyl group. However a D-amino acid dipeptide, D-alanyl-D-alanine, synthesized in the reaction catalysed by D-alanine-D-alanine ligase, is a precursor of bacterial peptidoglycan synthesis.

All the examples given have in common the fact that the peptides are very short (di- or tri-peptides) and can be synthesized in reactions requiring one or two specialized enzymes. Bacterial antibiotics synthesized by the non-ribosomal peptide complex tend to be appreciably larger, requiring repeated formation of peptide bonds.


Is the eyes' movement discrete? When tired and it was dark, I noticed that if I focused on a dim light source and moved my eyes fairly rapidly sideways, the resulting images that lingered for a short while were not smoothly blurred together, but were discrete.

I assume this is not due to the brain's inability to process the data fast enough or the retinas not repairing fast enough when light breaks part of them down, so I am lead to the conclusion that eyes (if not generally, sometimes) move in very small sudden jolts rather than smoothly.

Is this correct? What is the reason for this (is it due to the eye muscles being unable to sustain motion for a long time, or something to do with the mechanics of the eye)? Was this result anomalous?

There are two types of eye movement: smooth pursuit and saccadic. As the name suggests the latter movement involves quick and discontinuous movements of the eyes. Saccadic movement is used most of the time as the eyes move around analysing the current scene.

According to Wikipedia, these saccades are the fastest movements produced by the human body: peak angular speed of 900 degrees of rotation per second (this would be 2.5 full rotations of the eyeball per second, were such a thing possible).

The processing of information by the eye-brain system during a saccade is complex, and may be responsible for the effect that you report: it causes the phenomenon of saccadic masking explained in this quote from Wikipedia:

  A person may observe the saccadic masking effect by standing in front of a mirror and looking from one eye to the next (and vice versa). The subject will not experience any movement of the eyes nor any evidence that the optic nerve has momentarily ceased transmitting. Due to saccadic masking, the eye/brain system not only hides the eye movements from the individual but also hides the evidence that anything has been hidden. Of course, a second observer watching the experiment will see the subject's eyes moving back and forth. The function's main purpose is to prevent smearing of the image.


Why do humans have eyebrows? Why do humans have eyebrows? It seems that it isn't necessary but only humans have them, correct? So what is the use of them for humans? I hear that they protect our eyes. However, isn't that what eyelashes do? What other functions do eyelashes have?

Eyebrows function to protect the eyes from perspiration and provide shade.
Eyelids function to protect the eyes from foreign objects and sunlight.
Eyelashes function to protect the eyes from foreign objects, produce sebum (a lubriant that the eyelids) and acts as protection for the eyes from tears [1].

The above seems to be backed up by health how stuff works and the anatomy of the eye from emedicinehealth.
However, note that biologist dont have any concrete reasons for the eyebrow. This is just what many of them agree on I suppose. Here is another resource from sciencefocus.


Dimethyltryptamine and Sigma 1-type opioid receptor interaction Where exactly do dimethyltryptamine and sigma 1-type opioid receptor interact? I read in this When the Endogenous Hallucinogenic Trace Amine N,N-Dimethyltryptamine Meets the Sigma-1 Receptor but it does not say where exactly they interact only that they do.

From your article:

  Sig-1Rs localize at the interface between the endoplasmic reticulum (ER) and mitochondrion, which is known as the mitochondria-associated ER membrane (MAM).

Consequently, they are found in a variety of areas within the central nervous system as well as in other types of cells throughout the body (notably cardiac cells).

  An important biological activity of sigma receptor activation is the inhibition of ion channels, which operates through protein-protein interactions without mediation by G proteins and protein kinases. In addition to modulating various types of voltage-activated K+ channels, the sigma-1 receptor associates with the Kv1.4 K+ channel in posterior pituitary nerve terminals, as well as in Xenopus oocytes. Sigma receptor ligands also modulate N-, L-, P/Q-, and R-type Ca2+ channels in rat sympathetic and parasympathetic neurons. Sigmareceptor ligands modulate cardiac voltage-gated Na+ channels (hNav1.5) in human embryonic kidney 293 (HEK293) cells, COS-7 cells, and neonatal mouse cardiac myocytes. To evaluate the capacity of DMT to induce physiological responses by binding to sigma receptors, we examined the action of DMT on voltage-activated Na+ current.

From:

  Fontanilla D, Johannessen M, Hajipour AR, Cozzi NV, Jackson MB, Ruoho AE. The hallucinogen N,N-dimethyltryptamine (DMT) is an endogenous sigma-1 receptor regulator. Science. 2009;323:934–937.  [DOI]
  (reference 24 in the article that you cite)


IBD-value in pedigree with inbreeding I have a question about IBD. Please see the figure below. How many pairs of alleles are IBD for X and Y, or what is the IBD value for X and Y. Is it four (4)? I have seen it to be maximally 2, but then we assume that no inbreeding occurs, right?

An Identical-By-Descent (IBD) value is the number of alleles which are the same because of descent from a common ancestor.  Since each (diploid) individual has two alleles for a given (autosomal) gene, the number of them that are IBD with another individual can only be 0, 1, or 2.

In your example, X and Y inherit each of their alleles from A2, so their IBD value is 2.  Inbreeding is just an extreme form of descent from a common ancestor; it causes on average greater probability of high IBD values than when comparing less-inbred individuals. See the passage here for more detail.


Why doesn't nitrogen diffuse into blood? In school, I have learnt that the deoxygenated blood brought in to the Alveoli by Pulmonary Arteries contains Carbon Dioxide. And that Carbon Dioxide present in the blood diffuses into the Alveoli and squeezed out with the help of Diaphragm.

Then, why doesn't the Nitrogen present in the Alveoli gets diffused to the blood? My guess was that the blood vessels don't allow anything other than CO2 and O2 to pass through.

But I recently saw a video on KhanAcademy where Sal said that some amount of Nitrogen does get mixed with blood. Is Sal right? If yes, then why doesn't the whole Nitrogen present in the Alveoli gets diffused from there (where it is present in high concentration) to blood (where it is present in low concentration)?

To summarize,

Why doesn't the inhaled-Nitrogen present in the Alveoli diffuses into the blood present in Pulmonary Veins, similar to how CO2 present in blood gets diffused out to the Alveoli?

I like it that nitrogen came to your mind ;)

I guess in school they didn't tell you about the nitrogen at all, for the matter of simplification, because it is of no function in the body and the $O_{2}$ and $CO_{2}$ are the important gasses for biological function of breathing.

However, all of these small gas molecules are very small and generally the biological membrane is very permeable to them. That's why the cell cannot decide to let $O_{2}$ and $CO_{2}$ in and $N_{2}$ not as you suggest.

(However, the cell is able to control the permeability of these gases to some content, based on the level of cholesterol in its membrane$^1$)

The process of gas exchange is generally passive. In alveolar membrane the gas flows from the site of its higher concentration (in case of gases we talk rather about partial pressure) to the site of lower concentration. The speed of this process depends mostly on the difference in partial pressures and if you let the blood "interact" with the air in alveoles for long enough, partial pressure of all small gas molecules would come almost to equilibrium. (This happens under physiological conditions for all of the three mentioned gases)

Khan academy is right too actually. This is because as $N_{2}$ isn't either produced or consumed in the body, its partial pressure in the venous blood is similar to that in the alveolar air, and there is no force to cause its movement between these two compartments in general.

In the table you can see, that the partial pressure of nitrogen in the blood is the same as in the alveolar gas.

Picture source


Identification of a caterpillar from NY I recently camped at Harriman State Park in Southern New York, in early October.  Upon returning home, I noticed that I had a passenger with me.

The caterpillar in question is an almost translucent, pale green color with a single reddish stripe running down the center of the back.  It is approximately 1.5 inches long, with a reddish face as well.

I tried using a caterpillar identification book, but the closest one I could find also had a split tail, which this one does not.

Based on this picture, I'd say it's a Macrurocampa marthesia. I realize your specimen lacks the split tail, but I note that the "tails" of the larva of this species are longer in earlier instars. I wonder if this one is just an older caterpillar, getting ready to pupate? The image is a very good match otherwise, and this species does occur in the appropriate range.