texts: Are cryovials really better than regular tubes for cryopreservation?

texts:
What is the rationale for using cryovials instead of regular, sterile centrifuge tubes for the storage of mammalian cells?

With a good aseptic technique and without touching the cap directly, there should not be a significant risk of contamination in regular microcentrifuge tubes. Is the plastic quality fundamentally different (in terms of leaching chemicals etc)? Both kinds of tubes are usually made of polypropylene so it's not obvious how they would otherwise differ.

There may be a difference when storing things in direct contact with liquid nitrogen (as regular tubes may leak), but many cells can be stored for years in a -80°C freezer, a temperature at which most molecular biology tubes are perfectly stable.


texts: Which mammal has the largest change in size from birth to fully grown percentage wise?


texts: Why can we use mouse-produced antibodies on mice tissues?

texts:
I have seen biologists use mouse grown primary antibodies in mouse tissue, and they've told me that if the blood is perfused well then there is no problem with this method. How does the secondary antibody (anti mouse) not stick everywhere on all the mouse antigens in the tissue?

Clarification: I  understand that the secondary antibody is very specific to all mouse "class" primary antibodies. Can I ask then why using a secondary mouse antibody does not recognize background antibodies in the tissue, the ones that the mouse produced for itself naturally before I added any of my primary antibody? Are the existing primary antibody levels already present in the mouse much lower than the levels of the primary antibody I am adding?


texts: What restriction enzyme was used in cutting this DNA piece?

texts:
So, i was given this cut piece of dna and i was required to choose the restriction enzyme used to cut it. I had to pick either XhoI(CTCGAG) or TaqI(TCGA), where the sequence between parentheses is their palindrome sequence. Which one is it and why? I've picked XhoI since i know that the enzyme cuts in between the palindrome

GAGCT        C
C        TCGAG

DNA after the cut.


texts: Why does ant queen keep the eggs out of her hive?

texts:
I have captured an ant queen and now I'm trying to create an artificial ant nest.

I have noticed that though she has dug a hole to hide in, she keeps the eggs out of it unless she feels that they are in danger.

I have two theories explaining why she does that:

Ants naturally put eggs in sunlight to keep them warm. In her situation, they are not gonna be any warmer of course - the jar is whole about the same temperature.
She is digging a nest and she needs some space. If this is true, where is all the dirt?


texts: Is this a counter-example to Darwin's theory of evolution?

texts:
Somewhere I read following paragraphs giving one counter-example to Darwin's theory of evolution.

(By the way, I am a physicist and not a biologist, but I am interested in this field.)

Do these paragraphs point to the reality? What is the current status of "theory of evolution of species" ?

  "Darwin cited the giraffe as an outstanding example of natural
  selection.  Supposedly, as a result of extended droughts, the supply
  of green leaves could be obtained only at the top of the trees, and
  therefore the shorter necked giraffe died off.  The giraffes which
  grew longer necks survived.  However, there is no evidence whatever in
  the fossil record or elsewhere that giraffes with short necks have
  ever existed.  And what would have happened to young giraffes with
  relatively short necks?

  Darwin failed to realize that body characteristics in offsprings are
  determined and programmed by DNA factors of the Genes or the Genetic
  material of the parents, and not by the stretching of the neck or any
  other bodily exercise."


texts:
I ran an enrichment analysis with custom annotations using TopGO and surprisingly I obtained new GO terms inside the significant GO terms.

Is that  possible? The only reason I can imagine this is possible is because TopGO adds new GO terms based on the input GO terms, since GO ontology is structured hierarchically.

Please let me know if you need more details about the experiment.

Code:

https://drive.google.com/file/d/0B8-ZAuZe8jldbjNuTHhNeXRVX00/edit?usp=sharing

TopGO output:

https://drive.google.com/file/d/0B8-ZAuZe8jldZnlYUzlxZ3psMWc/edit?usp=sharing

Thanks, Bernardo


texts: Source of journals collecting titles of scientific publications regarding clinical trials with dogs fed medicinal herbs

texts:
After some time researching on the web, you can find a lot of websites telling you that some herbs may have or have specific properties(unfortunately most seem to be "advertised" as if they were wonder drugs), but none or few give references to specific titles of papers.

Another alternative is the pub med website but papers don't seem to pop up regardless of any search words.

Where is all that research information posted?


texts: Is DNA a single molecule or 46 separate pieces (out of 23 chromosome pairs)?

texts: It seems that biology books refer to DNA as 'a' molecule (implying that it is a single continuous uninterrupted double strand) ... but in those same books chromosomes are depicted as 23 separate objects (chromosome pairs) containing DNA. Are these illustrations misleading ? Are chromosomes somehow connected end-to-end or are they disjoint ? Is it a single noodle or is it 46 pieces ?


texts: Homeopathy is placebo, but isn't placebo good?

texts:
I never considered homeopathy as a serious and scientific medicine, and now we have plenty of evidence supporting this (http://www.theguardian.com/commentisfree/2015/mar/12/no-scientific-case-homeopathy-remedies-pharmacists-placebos).

But placebo effect is also a thing that works, strange as it may be. The placebo effect deals with the importance of the brain's role and perception in physical health. So, in my understanding, placebo is better than nothing.

But now I can't treat myself with homeopathy, because I don't believe on it. Other people believe, and are happy with it (benefiting from the placebo effect).

So, my question is, wouldn't be benefitial to illude someone (or yourself) in order to achieve the placebo effect?


texts: Determining how much energy a plant takes in?

texts:
I asked a question on WorldBuilding.SE, "Are diamond berries possible?".

This led to asking a question on Chemistry.SE about the amount of energy required to burn a 1 ct. diamond (−6.527kJ).

The helpful commenter on WB.SE said that a plant would roughly require three times this amount of energy to essentially reverse the process through some biological means to create the diamond berry.  And that I would need to know the "wattage input" of various plants to compare with my hypothetical plant.

Is there a way to arrive at how much energy various plants take in?

Also any other related information from a biological perspective would be helpful.


texts: Difference between rate of elimination and clearance?

texts:
I honesty don't get the difference. I need a simple explanation so that I can grasp it.
Rate of elimination is


texts: How do the chromosomes arrange themselves after fertilization in humans?

texts: In human reproduction the male produces sperm containing 23 chromosomes and the female has the oovum containing 23 chromosomes , so after fertilization the zygote contains 46 chromosomes. What I want to know is , how do the chromosomes identify each other and pair up,  fir example say ,how does chromosome '1' of the male pair up with chromosome '1' of the female to make set '1' of the zygote?


texts: What is the kind of this wasp killing spider from UK?

texts:
I heard a wasp buzzing rigorously and when I looked at it, it was caught in a spider web. The spider was on top of the wasp. After some time, they become silent. When I exhaled gently on them, spider moved but wasp did not. Later, the wasp was dead. The spider was obviously smaller than the wasp, yet it emerged victorious.

I attached a photo of the spider. While I am not sure whether this is the one killing the wasp, this certainly lives around the event site.

It should be around 1 cm in body length, excluding the legs. It is situated in UK.


texts:
I got curious about peanuts and when I found some photos on the internet, I could see they have flowers. However peanut fruit is underground.

How does pollination of peanut flowers affect the fruit underground? Or are there two kinds of fruit, one from flower and one from the underground?


texts: Is photosynthesis faster in aquatic plants rather than terrestrial plants?

texts: For example : In which of these two plants photosynthesis is faster and why? water hyacinth or sedge?


texts: From which ancestor species did humans inherit orgasm?

texts:
From what ancestors did humans inherit orgasm?

Do fish experience orgasm?

Are the male and female orgasm the homologues that can be traced to the time when there was no difference in sex between individuals (as in fish) or developed independently?


texts: I was in Germany recently, and I saw again a flower that I'd only ever encountered before at Meijer Gardens. It's interesting to me because I'd never seen a flower with color variation in only the 'interior' petals. Try as I might, however, I can't seem to find it anywhere! Can anyone tell me what this is? I'd like to be able to learn more about it.


texts:
I read this article in the following:

  ... Mice that have been reconstituted with geneX-transduced cells

Now, someone who is not familiar with animal sciences, what does this exactly mean? It is in the context of hematopoietic stem cells. I have two possible interpretations as a result:

An Hematapoetic stem cell with geneX was successfully transplanted into the mouse
The mouse cells (from the embryo) were engineered to contain geneX, and hence the mouse has been reconstituted with geneX transduced cells

Are any of these correct? If I am wrong please let me know!


texts: Will a less favorable allele's frequency go to 0?

texts: For example, a pond is dark in color. There are two alleles. The dark color allele is dominant over the light color one. Let's assume that the relative fitness of both the homozygous dominant and heterozygous is 1, and the relative fitness of the homozygous recessive is 0.5. When I ran the simulation, I changed no other values.  My data after 251 generations is this:  My question is that being homozygous recessive is clearly less favorable, and even though being homozygous dominant and heterozygous carry the same advantage instead of heterozygote advantage, why wouldn't the recessive allele disappear?


texts: I learned this at a lecture, but somehow I have trouble in understanding this. It is said that the bacteria such as E.coli need 20 minutes to divide, but its chromosome require 40 minutes to multiply. It is explained that the E. coli will have copied half of it, which will spend 20 minutes and after divided, it will continue another 20 minutes to complete the chromosome copy. However, it is said that each daughter cell will have one complete and half copy after they divide. I am confused that if the bacteria only spend 20 minutes to copy half of it, how  can each daughter cell could have one and a half?


texts: What differentiates bound antibodies from unbound ones?

texts:
When an antibody is bound to an antigen, it can then stimulate a FcR receptor on a phagocyte etc. to respond to the threat. What stops 'free' antibodies from spuriously activating an immune response?
Even if an unbound antibody won't elicit a response, it can still hog the FcRs of expressing cells or cluster around them and degrade the immune system efficiency.
This article seems to imply that being bound to an antigen causes some change in orientation: "their Fc regions point outwards, in direct reach of phagocytes" but I don't really see how its bound state causes that any more than random movement.
It also states

The low individual affinity prevents Fc receptors from binding antibodies in the absence of antigen, and therefore reduces the chance of immune cell activation in the absence of infection

but I fail to understand the logic in that; let there be low affinity, but as much as a bound ab is somehow able to activate the FcR so can an unbound one, unless the bound/unbound state itself affects the affinity, something the article does not explain.


texts: Cell cycle is as follows- g1,s,g2,m( mitosis). Does this m stands for mitosis only or does this "m" stands for meosis also


texts: How did sulfasalazine become a disease-modifying treatment for rheumatoid arthritis?

texts:
Sulfasalazine has been around for about fifty years, starting as an antibiotic. More recently it is used as a disease-modifying anti-rheumatic drug (DMARD, see also arthritis.org). While biologics (biopharmaceuticals) are becoming more widespread in early treatment of some types of RA, sulfasalazine has a known safety profile and is inexpensive. Sulfasalazine is on the World Health Organization's Model List of Essential Medicines. See section 17.3, Anti-inflammatory medicines.
Wikipedia says:

The mechanism of action is not clear, but it appears that sulfasalazine and its metabolites have immunosuppressive, antibacterial, and anti-inflammatory effects.[refs] It also appears to inhibit the cystine-glutamate antiporter.[ref]

Why was this "old antibiotic" tested as an anti-inflammatory medicine? Is the situation similar to Minoxidil where a "side-effect" turned out to have significant medical value? What is the evidence (if any) that sulfasalazine has a disease-modifying effect in the treatment of RA - that it actually slows down the progress of the disease rather than just temporarily reduce symptoms?


texts: Gene transfer between Gram positive and Gram negative bacteria?

texts: How does transfer of genetic material occur between Gram positive and Gram negative bacteria?


texts: Why do we go blind for a few seconds after switching off the light?

texts:
At night, when I switch off the lights, I always seem to go blind for a while. The room becomes pitch black and I am unable to see anything. After a while, however, my vision slowly recovers and I start to see things around me again. I always have to wait a while before my vision returns to that functional state.

I am interested in knowing the mechanism behind this phenomenon. What do we call it?


texts: Understanding food composition data from USDA for Vitamin A

texts:
When researching the nutritional value of carrots the Vitamin A comes in two  measurements as RAE and UI:

https://ndb.nal.usda.gov/ndb/foods/show/11124?n1=%7BQv%3D1%7D&fgcd=&man=&lfacet=&count=&max=25&sort=default&qlookup=Carrots%2C+raw&offset=&format=Abridged&new=&measureby=&ds=&Qv=1&qt=&qp=&qa=&qn=&q=&ing=

After reading the following article
https://ods.od.nih.gov/factsheets/VitaminA-HealthProfessional/

I understand that IU can be transferred to RAE, but I wonder if in case of USDA does two records represent the same value or they are supposed to be combined? :shy:

If you had previous experience working with this database I will be more then glad to hear you opinion about that :)


texts:
From Wikipedia

  The community begins with relatively few pioneering plants and animals and develops through increasing complexity until it becomes stable or self-perpetuating as a climax community.

From Wikipedia again,

  Self-perpetuation, the capability of something to cause itself to continue to exist, is one of the main characteristics of life.

What I  don't understand is every organism has the capability to perpetuate (except the sterile ones, which are not under consideration) even a seral community does then why is climax community specifically labeled self-perpetuating?


texts:
In this question, the OP uses giraffe necks as a supportive example of evolution. Is the mechanism described in this post accurate? At some point, I thought I remember hearing that giraffes did not evolve long necks to reach higher food resources, but instead longer, stronger necks gave some sort of mating advantage (male competition perhaps?).

Is there a consensus in the scientific community as to evolutionary mechanism(s) that contributed most to the evolution of long necks in giraffes?


texts: How to model social structure in SIR models

texts:
I refer to J.H. Jones' Notes on R0.

More details in this question at Mathematics SE: How does the reproduction number depend on characteristics of the physical contact graph of a population?

The basic SIR model - as described in Jones' Notes - considers three factors that make up the reproduction number:

$\tau$ = the transmissibility (i.e., probability of infection given contact between a susceptible and infected individual)
$\overline{c}$ = the average rate of contact between susceptible and infected individuals
$d$ = the duration of infectiousness

The (basic) reproduction number then is

$$R_0 = \tau \cdot \overline{c} \cdot d$$

I wonder how to model social structure in a SIR model, which might influence both transmissibilty $\tau$ and average rate of contact $\overline{c}$ and thus the reproduction number $R_0$, resp. the infection rate $\beta = \tau \cdot \overline{c} = R_0 / d$.

Specifically I wonder which "control parameters" appropriately describe the social structure of a population and may influence transmissibilty $\tau$ and average rate of contact $\overline{c}$ in a specific and comprehensible way.

Among these parameters may be:

typical (mean) numbers of household members and acquainted persons
typical ratio of shared acquaintances
typical numbers of strangers one meets (e.g. per month)
typical times of contact to household members, acquainted persons, and strangers
the amount of persons with outstanding many social contacts, better: the standard deviation of the contact rate
the accepted physical distance to family members, acquainted persons and strangers
(source)

I am looking for approaches that let go such parameters into the infection rate $\beta = \tau \cdot \overline{c}$ in a quantitative way.


texts: Pseudoautosomal regions of the X chromosome showing heterozgyosity

texts:
I've always had questions for myself about sex differentiation, mostly on account of an unusual history & puberty. I won't go into details, but needless to say it was unique.

My question is... I got results back from 23andme showing hetereozygosity at the beginning & ending of the X

I've been diagnosed as XY androgen insensitive & pseudohermaphrodite with mullerian structures intact.  Born with questionable stuff internally, only definitive thing is nothing male (no prostate, no seminal etc..)

They also did show a Y, but it was apparently missing half of it (though I've read thats not unusual for half of it to be --)

Can you have a hetereozygosity at the ends of the x and not have another x?

rs6644972   X   178624  AG
rs28475515  X   182276  CT
rs28463388  X   191998  TT
rs28669107  X   195014  CC
i6033542    X   200928  CC
rs6655397   X   201935  GG
rs7890186   X   202458  GG
i6033543    X   209741  CC
i6033544    X   215805  CC
rs28736870  X   220770  GG
i6033545    X   228250  GG
rs6603204   X   298440  GG
i6033547    X   301596  CC
rs2738344   X   310897  AA


texts: Is there a known mutation of an insertion type that prevents being infected by a virus?

texts:
Recently there was big news about the mutation CCR5 delta 32, that prevents HIV from infecting white blood cells, that was a deletion type of a mutation.

Do we know of an insertion type of mutation that have similar affect? i.e prevents being infected by specific/some virus(s)


texts: Hoechst red and blue spectra - what does the red emission tell us?

texts:
I understand that the blue spectrum is emitted when Hoechst 33342 binds to nuclear DNA. But what exactly is the red spectrum telling us?

I read that the red spectrum can be indicative of apoptosis, cellular complexity, or a proxy for cytoplasmic content.

What exactly is the red spectrum indicative of in terms of the cellular context?

edit**

Sorry for not getting back to this question sooner. I found the answer in this paper:
http://www.sciencedirect.com/science/article/pii/0022175995002146#

Apparently condensed chromatin during apoptosis causes hoechst to shift to a red spectrum.


texts: Why is hyper pigmentation the common aftermath of skin lesions and abrasions?

texts:
I'm aware that melanocytes produce melanin, giving color to the skin, but why are these cells recruited or overactive when healing skin abrasions, lesions and sores when T-cells and inflammatory cytokines of the immune response help with healing. I'm just wondering why the production of color is associated with the healing of the wound and if it proves beneficial, or if it just a side effect so to speak.

EDIT: In this study, it explains the recruitment of melanocytes after the initially response of innate immune cells and inflammatory cytokines, however, it does not delve into how this is beneficial to the cell.
[source]


texts: Why do kefir grains stop growing in soy milk?

texts:
Kefir is a fermented milk drink made with kefir grains. It usually is prepared by inoculating cow, goat or sheep milk with kefir grains.

I would like to prepare the drink with soy milk, which worked fine for some months. Then the kefir grain stagnated in its growth. I use bottled soy milk from the supermarket. I do not produce the soy milk by myself.

In "real" milk the kefir grains never stop growing (and dividing), but in soy milk they apparently do.

Why do the kefir grains stop growing in soy milk? Are they lacking a specific nutrient that is only contained in milk from animals?


texts: Why do males with baldness have  shiny skin on their head, whereas we don't experience such "shiny skin" in other parts of body without hair.


texts: How do chromosome count differences produce viable offspring during speciation in animals with sexual reproduction

texts:
So, many closely related animals  have different chromosome counts.

It would seem that most chromosome count differences lead to sterile offspring. Further, it would appear that gametes with irregular chromosome counts must be paired with other gametes with matching irregularities to pass on these differences, which feels like a unlikely scenario.

On the other hand, obviously, chromosome count differences happened. What are some explanations?


texts: Getting xyz co-ordinates from a .map file (CCP4 format) in VMD

texts:
I have a .map file which contains x-ray crystallography data of a bacteriophage. The format of the file is CCP4. I can open the file using VMD. However, I am unable to get the xyz co-ordinates. It shows the following error when I click on the option of saving data in xyz format:

`No timesteps selected; trajectory file will not be written.'

It is a big file of 64MB.

The file I am referring to may be downloaded at:
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1086/map/emd_1086.map.gz

Can't we save xyz co-ordinates for CCP4 files? Or is it possible to extract any other form of data?

I am new to VMD and these formats.
Any help would be appreciated.


texts: Manual Primer Design for a gene on the reverse strand

texts:
My question might sound very naive and stupid but I am hopeless now. I read so many websites and pages but could not figure out this PCR primer design thing completely.

Some genes are on the reverse strand of the DNA as we can see on the certain databases. Like this:

Source: http://www.wormbase.org/species/c_elegans/gene/WBGene00019616#0de1-9g4356caf-3

So when I click and get the sequence data of that gene, it also says it's on (-) strand. My most potentially silly question is: Do I just copy paste that sequence and try to find my primers manually or do I need to get a reverse complement of that sequence to make it (+) strand so I can design my primers? This minus, plus stand and reverse complement thing confuses me a lot! And I also do not get why do we get the reverse complement of the reverse primer sequence once we design it.

Thanks for the help in advance!


texts: Do some vascular tissue cells have chloroplast?

texts:
Vascular tissue includes xylem, phloem, parenchyma, and cambium cells. Does photosynthesis occur in some vascular tissue cells? Do some of them have chloroplast?
Vascular tissues are made up of xylem and phloem, each of which are complex tissues (having more than one cell type). So some of their parenchyma cells may have chloroplasts.
The bundle-sheath cells are the photosynthetic cells arranged into a tightly packed sheath around the vein of a leaf. It forms a protective covering on leaf vein, and consist of one or more cell layers, usually parenchyma.
I am not sure whether these two "parenchyma"s are the same or not.
Are the bundle sheath cells vascular tissue cells?


texts: Why is black and yellow such a nice camouflage?

texts: Many people can`t differenciate between cheetahs, leopards and jaguars, but there are serveral other animals with a similar pigmentation (servals, ocelots...), why is it so effective? It gets exciting when you realize that cheetahs and leopards are evolutionaray relatively far away, and therefore that their resemblance exsists due to evolutionary convergence.


texts: Why should benzalkonium chloride (an antifungal agent) be used during your laundry machine's "rinse" cycle, not its "wash" cycle?

texts:
I'll first provide lots of background information. My actual question is at the very end.

Background

The spread of athlete's foot

Athlete's foot is a fungal infection which is mildly contagious. The infection can be spread by skin particles left on towels. (Source.)

If one person in a family has a fungal infection (e.g. athlete's foot or jock itch), their laundry may also contain fungi. I suspect that towels and laundry machines might make it easier for these fungi to spread: e.g. from the patient's feet to their groin. See, for example, here.

Water at 140 °F

You can kill fungi using water at 140 °F (60 °C). Unfortunately, your water heater probably doesn't produce such hot water, because such hot water is dangerous and can kill unsuspecting individuals. (Sources.) Still, you can make such hot water in other ways. (Source.)

Antifungal rinses

Another option is to use a suitable antifungal rinse.

The most common cause of athlete's foot is T. rubrum. (Source.)

T. rubrum is a dermatophyte-type fungus. Dermatophytes spread through spores. These spores can sometimes live for up to 20 months. (Source.)

Canesten Laundry Hygiene Rinse is 7% benzalkonium chloride. (Source.) A competing product is Bluo Laundry Sanitiser, which is also 7% benzalkonium chloride. (Source.) These products are sold in Australia but not in North America. (How safe are they? I dunno; I'm not a toxicologist.)

The Canesten rinse label makes an impressive claim: "eliminates ... fungi from your washing". Still, it looks like these rinses' fungistatic effects are stronger than their fungicidal effects. In reality, they're not perfect at killing T. rubrum, but they're still better than nothing. An Australian lab found that, in 20 minutes, these types of rinses reduced T. rubrum by between 90% and 99%. (Source.)

(Each rinse is marketed as both antifungal and antibacterial, though there's limited evidence that people can catch bacterial infections from clothing. I'm not convinced that their antibacterial effects are really necessary.)

Use during the rinse cycle, not the wash cycle

Each manufacturer says that its benzalkonium chloride rinse should be added during your washing machine's final rinse cycle, not its initial wash cycle.

You can do this using your clothes washer's fabric-softener dispenser, if present. On a top-loader, this is usually a cup-like device on top of the machine's central agitator post. (Source.) Or you can buy a softener dispenser ball, though they're not always 100% reliable. Or you can add the rinse manually at the correct moment.

A sample washer program

Washing machines can vary. Here's a description of the normal program of certain inexpensive top-loading Whirlpool agitator-type washing machines:

Fill - agitate: 16 minutes.
Drain: 2 minutes.
Spin: 2 minutes.
Rinse, fill, & agitate: 4 minutes.
Drain: 2 minutes.
Spray & spin: 2 minutes.
Spin only: 4 minutes.

Total: 32 minutes.

(Based on: wiring diagram W10118358, rev. A.)

The wash cycle is longer than the rinse cycle.

My question

To summarize the above background information: Canesten laundry rinse (7% benzalkonium chloride) has both antifungal and antibacterial effects.

And so I wonder: Why does the manufacturer recommend that it be used during your laundry machine's rinse cycle instead of its (longer) wash cycle?

Any answers or guesses are welcome.


texts: So I have two substrates for one enzyme and I measured the product formation-> michaelis menten kinetics. The Vmax for both substrates is the same, the Km however is higher on substrate number 2.  What can I conclude from this in terms of enzyme-substrate interaction?


texts: Are there any predators without camouflage?

texts: Are there any predators that don't use camouflage?


texts: What is a Protein contact map, and how do I read one?

texts:
Protein contact maps are symmetrical and look great, but how does one read one?
I tried to underside the following source: 'Understanding contact patterns of protein structures from protein contact map and investigation of unique patterns in the globin‐like folded domains' Journal of Cellular Biochemistry (Pay-wall) .. but it has proven to be difficult to understand.
For illustrations, subfigure 1.A is an example of a 'Protein Contact Map':

Could someone explain or are there other useful texts I could use?


texts: What equipment is needed to perform simple plant electrophysiology?

texts: What is the minimum needed equipment to perform simple plant electrophysiology? I am looking for some simple experiments that I could run at home for learning. Ideally, I would transfer the skills to stud neuroscience later on (the skills could be related to operating a microscope, doing recordings with microelectrodes, signal processing, statistics, etc). How expensive this would be?


texts: How does the population fitness change after a change in mutation rate?

texts:
The mean population fitness as given by mutation load theory depends only on the genome-wide mutation rate ($U$). My question is: How many generations is needed to reach a new mutation load equilibrium after a change in $U$?

Following is an article were they perform the kind of calculations I am interested in:

Let $U$ be the genome-wide mutation rate, $\delta U$ a change (between two time steps) in the genome-wide mutation rate and $s$ the mutational effect (effect on fitness) of a given mutation. In Agrawal and Whitlock (2012), page 13 (or 127 in the journal), $3^{rd}$ paragraph, the authors say:

  [After a change in $U$,] it can take a long time to approach mutation-selection balance. For example, if the mutation rate is increased by $\delta U = 1$ deleterious mutation per genome per generation, then it would take ∼120 generations for fitness to decline 80% of its expected amount if s = 0.01. However, by obtaining a time series of data, one could infer the equilibrium load after tens or hundreds of generations even if equilibrium is not reached

How were these ~120 generations estimated/calculated?


texts: What's the feedback regulation of Thyroid diseases and body temperature?

texts:
While going through the feedback regulation, the control of blood glucose level by insulin and glucagon is quite discussed in multiple materials including the textbook. I also understand the basic fever and cold feedback regulation with regards to hypothalumus given in the below picture.

But I am not able to find either a digram or a material that explains the relationship between hypothalamus, pituitary gland and thyroid gland in controling temperature1, specially for those who are suffering from thyroid diseases. e.g. some people with thyroid issues feel too cold or too hot (fingers, hands, legs, skin is quickly cold or hot depending on the external change). Their body seem to fail in maintaining the set point of temperature.

What's the endocrine and feedback regulation behind this1 scenario? What's the hormone pathway? Also in terms of energy, heat and metabolism.


texts: Why are different lengths of nucleotides taken for structure prediction from an miRNA match area after BLAST analysis?

texts:
Generally in miRNA prediction most researchers do as Blast search with a set of miRNAs downloaded from miRBase with the parameters they require. Later on usually custom methods are utilized to get an area around the match area for structure prediction.

In one paper, I found that ~70 flanking nt of match area was taken as pre-miRNA for structural analysis while in this paper ~100 flanking nt of the match area was taken for pre-miRNA structure prediction. Any idea why so?


texts:
Bacteria can produce toxins like endotoxins and exotoxins. In diseases like cholera or tetanus they can harm infected people due to these toxins.
Now, although viruses are much smaller and are dependent on the host cell for their production, are there DNA sequences in viruses which can produce similar toxins, or are viruses made of something that is toxic?

If not, can viruses be seen as causing an allergic reaction because like common allergies they don't harm directly, only our immune system generates the problems?


texts: Goodness of fit: How to decide which ratio to deal with?

texts:
While solving problems of Goodness of fit, I'm faced with an issue, how to decide which ratio to consider to find the test statistic from given set of observations.

E.g. 1

  A supplied sample contains four types of seeds and the total number is 64. The types of seeds are large red 42, large white 8, small red 10 and small white 4. Calculate goodness of fit.

Problem: As df=3, Ratio= 9:3:3:1 / 1:1:1:1?

E.g.2

  You are supplied with two different varieties of plant samples;tall-76 and short-24. Determine the observed number, apply Chi square test to state whether it is in agreement with expected ratio.

Problem:  As df=1, Ratio= 3:1 /1:1?

I was vaguely told by my propessor that which ever ratio seems to apply(by logical guess) we should choose that one to determine the expected values and thus the statistic.

I couldn't find any good read in this regard, except those that are full of mistakes. I've been reading Statistics blogs to understand the concepts but they don't cover these typical biological problems and those that did had the ratios mentioned.

I've another question in mind, from experimental result it is also likely that we won't get one of the four types of seeds (given that mating is random and the progenies appeared by dihybrid crosses) so determining the actual ratio behind becomes more difficult as df = 2  =/= 3!


texts: Principle of 16 S rRNA technique for bacteria identification

texts: Why do we isolate DNA not RNA in 16 S rRNA technique for bacteria identification?


texts:
EURASIAN MAGPIE VS GORILLA

   VS

How could be the "Eurasian magpie" bird won the "Mirror Test" where Gorillas failed ?

  In 1982, mirror tests on two, zoo-reared gorillas failed to demonstrate self-recognition. The authors wrote "[These studies]...suggest that the gorilla may be the only great ape which lacks the conceptual ability necessary for self-recognition." In 1993, a report was published that although six gorillas had previously failed to exhibit self-recognition.

  The Eurasian magpie is the only bird to pass the mirror test. Researchers applied a small red, yellow or black sticker to the throat of five Eurasian magpies where they could be seen by the bird only by using a mirror. The birds were then given a mirror. The feel of the sticker on their throats did not seem to alarm the magpies, however, when the birds with colored stickers caught a glimpse of themselves in the mirror, they scratched at their throats - a clear indication that they recognized the image in the mirror as their own. Those that received a black sticker, invisible against the black neck feathers, did not react.

  Reference

Birds lacks neocortex, the area where self-recognition was thought to reside. Then which part of the brain do birds like Magpies uses to process these complex cognition ?
Why do Gorillas failed the mirror test ?


texts: Genes related to senses and their variation across animals

texts: Animals often have very different numbers of active genes related to any sense. For instance, most fish or even aquatic mammals have very few olfactory receptor genes, whereas this is higher in terrestrial animals. Even among them, there is huge variation; compare dogs and humans, for instance. But this comes at a cost; for instance, dogs are dichromatic, the blind mole is, well, blind. So there is a compensation across the senses which is not merely a plastic change. I was wondering if there is any way to reconcile this with some notion of conservation of the total proportion of active genes involved with sensation.


texts: What is the maximum altitude where humans can survive?

texts:
What is the highest altitude that a human can survive without being pressurized?  Let's assume that oxygen and heat/insulation are not the limiting factors?
Why I asked.


texts: how much can changing light enter the eye shap what you see?

texts: Does it change the shape and how objects are seen or does it just stop you from seeing certain things?


texts: How can dopamine modulate synaptic strength?

texts:
Does dopamine act on G protein coupled receptor, leading to more Ca2+ channels on the postsynaptic knob?

Also, how is the specificity of the location (of the brain) that dopamine acts on controlled? Or is it controlled at all? Is this chemical associated with addiction?


texts: Are mosquitoes attracted to blue lights in particular?

texts: I've been confronting the fact since childhood that mosquitoes are attracted to lights, especially blue lights. Now I know that all insects including mosquitoes are attracted to bright light but I never got it verified that if they are specially attracted to blue light or not. Is it true or just another urban myth?


texts: Using evolutionary algorithms in molecular biology?

texts: I am currently an MSc student studying molecular biology (on paper I'm a chemist) and soon I have to talk to my supervisor about my future, PhD research topic. Besides molecular biology I'm also interested in machine learning, mostly in evolutionary algorithms (evolutionary strategy alg.s, genetic alg.s) and Bayesian optimization, from both of which I have written multiple, working programs in C# at home. Due to the massive need for people trained in informatics I'd like to convince my supervisor to include this topic into my future research, especially as I have already acquired some basic skills in these areas. However I have only seen research examples that are purely computational and these didn't include any laboratory work. Can you provide me some insight into the use of these techniques in molecular biology and ways of connecting these with laboratory work?


texts: What would cause proteins to get stuck in the stacking layer of a SDS-Page gel

texts:
Typically when proteins aggregate, they will get stuck at the top of the well. However, we're seeing some protein aggregate in the stacking layer even when we're treating the loading volume with DTT.

One peculiar attribute of this experiment is that we're trying to carry out a Cu(I) catalyzed Azide-Alkyne Click rxn. Without the Cu(I), the proteins run normally. However, after Click rxn, we do see some of our expected clicked product, one of our proteins is disappearing into the top band. Hypothesis is that either the copper(I) is changing the migration or oxidative damage from the Cu(I)-> Cu(II) transition is altering the protein.

Returning to the original question, what would cause a protein to stop at the stacking layer vs. at the combs?

[edit]
According to my labmate who was having this problem, the protein was crosslinking with itself to create fairly sizeable polymers. We also saw ladders of the protein with ascending size. Spinning the clicked reaction removed the issue but also resulted at a lost of the protein. It sounds like he wasn't treating with a sufficient amount of DTT to break up the mixture.

This unfortunately still doesn't differentiate between proteins stuck at the combs vs stuck at the stacking layer.


texts: If oxygen is such a good energy source, why do plants release it?

texts: Why do plants release excess oxygen, rather than consuming it entirely given it is an excellent energy source?


texts: Are some virus loads introduced to human cell but never triggered?

texts:
Is there a term or any evidence of phage DNA integrating into chromosomes/ DNA but never being triggered?

For example, could a virus that affected Neanderthals still infect human cells today but is never expressed, triggered, or executed?

How often is latent viral DNA ignored by the host?


texts: Terminology of the sequences of promoters in relation to DNA strands

texts:
I'm studying molecular biology and I'm trying to understand an experiment which shows the importance of promoters in the relative transcription level (RT). The image below comes from Rolf Knippers' book "Molekulare Genetik" (8th edition).

The legend says (among other things):

  Die erste Zeile gibt die normale "Wildtyp"-Sequenz der 5'-flankierenden Region wieder.

Which, in english, means something like:

  The first line repeats the normal wild-type sequence of the 5' flanking region.

The column on the right gives the relative transcription (RT) level, 1.0 being the highest possible level of transcription. As we can see, the lines where some parts of the "5' region" have been deleted give quite low RT levels, since some regions of the promoter are missing.

My questions are the following:

1) According to this and this, I understand that RNA polymerase reads and uses both coding and non-coding strands in order to synthesize RNA. Therefore, how did they manage to use the sequences strands regions had been deleted to make a polymerase "read them" and perform transcription?

2) If the polymerase reads the template strand in the 3' -> 5' sense, shouldn't we talk of "ATAT box" or "TAAC box" instead of "TATA" or "CAAT" boxes? Does it mean that the "promoter" regions they are using on the graphic above are actually on the coding strand?

Thanks a lot for your help.


texts: Large spider identification, Kentucky USA

texts: What kind of spider is this I live in KY and it was found on my stairs.


texts:
I am wondering if animals do evolve even after birth and gain DNA changes that give them advantages and make them more suitable to the environment while they are alive, then pass these "enhancements" to their children

UPDATE

After all, cell do split and multiply when the animal is alive, and it could end up with a totally different cells than the one born with, so if a mutation happened during this period that led for it to be the dominant "property", what stops it from being passed on?
Is there a research on this?


texts: Provisional vaccine for fast spreeding new viruses?

texts:
Developing a standard vaccine for coronavirus will take at least a few months - what might be too late:

However, its sequence is already known, and is nearly identical - suggesting a recent single point of origin for human host, e.g.

  "The researchers also found that the eight complete 2019-nCoV genomes were more than 99.98 percent identical" https://www.genomeweb.com/genetic-research/coronavirus-genome-sequencing-finds-distinct-genetic-differences-2003-sars-virus

So the question is if/how there could be quickly started production of some provisional vaccine - not perfect but fast to introduce? Also exploiting the fact that these viruses are now nearly identical.

For example synthesizing its outside proteins and putting them on liposomes - would its introduction to blood have a chance to prepare immune system for the real virus?


texts: What is the mechanisms responsible for downregulation or loss of MHC-1 expression on the surface of cancer cells？

texts:
Downregulation or loss of MHC-1 expression on the surface of cancer cells generally have been thought to be involved in the mechanism of immune escape.
It seems to be very attractive but I don't know the mechanisms of downregulation or loss of MHC-1 at cancer cells. Would you tell me the molecular mechanism,


texts:
Over summer the ants invade our house, including our kitchen. In winter and the shoulder seasons they are not to be seen.

I can think of a number of possible reasons for this, including:

they are cold-blooded, and need heat from the outside atmosphere (similar to flies), making winter too cold to go outside for ants
ants need water, and tend to run short on it in summer when the temperature is higher, so travel further for water
the higher temperatures cause aromas from food crumbs to effervesce more strongly, and so ants are attracted to a stronger smell
ants natural natural nest cycle means they run their food supply low in summer and they need more

My question is: Why do ants raid the house in summer when it is hot, but in cooler months they don't come in?


texts: The question pretty much explains itself. How do the two methods compare? I've always used Assembly PCR but the method is prone to mistakes and I'm curious how it compares to Ligase Chain Reaction (LCR).


texts: We know something about the origin of the first cell. But what do we know about prions? How did they originate?


texts: Creating a phylogenetic tree from my selected publicly-available sequences (WGS) in NCBI

texts:
I'm currently writing a paper on the comparison of virulence genes for a group of bacteria. I got my data from publicly-available whole genome sequences in NCBI. Now, I want to create a phylogenetic tree for these species but since I'm working from home, I'm using my old laptop that makes it hard for me to process data. Can you recommend any software/ site/ tutorial/ paper that I can use to generate a phylogenetic tree easily? This is also the first time that I will create a phylogenetic tree and I'm not sure how to proceed without downloading and processing too much data that my current laptop can't handle.
Thank you!


texts: Current scientific theories for evolution of Cucurbita

texts:
I'm attempting to find research on scientific theories surrounding the evolution of certain plants, and am unable to find any footing with respect to a certain genus.

In this case, I am researching Cucurbita (ie: squash, pumpkins, etc), and can't find any basis for how it survives inherently without outside manual intervention. Unlike hot peppers (eg: Capsicum annuum), it is not easily ingested by birds, who do not suffer from the painful effects of capsaicin, and effectively transport the seeds, undigested, to new areas to spread the plant.

Also, unlike fruit growing on a tree, such as apples, it doesn't (seem) to provide a means to transport seeds any meaningful distance.

Finally, it seems most animals; ruminants, scavengers, and insects alike, would consume and digest the seeds.

Are there any generally-accepted (or at this point, plausible) theories with research to back it with respect to how such plants could survive long term without being manually grown and harvested by a species which eats them? While I understand (and acknowledge) the scientific theory of evolution, I'm not sure how the survival of such plants seems to be a special case.

Thanks!


texts: What are the methods to quantify the bacterial adhesion rate for the biofilms grown on coupons in CDC or annular bioreactor, non-invasively?

texts:
I'm interested to know that if I grow the biofilm on coupons in the CDC bioreactor at a particular shear stress, and after say 48 hours, I take out the coupon from the bioreactor to quantify the bacteria attached to it; what are the commonly preferred 'non-invasive' methods that I can use to do so? Can LIVE/DEAD staining be used in this case?
Additionally, if I want to know the bacterial adhesion rate (when the coupon is still inside the CDC bioreactor, and the baffle plate is rotating at say 80 rpm) at different time intervals (say after 1 hour, 4 hours, 8 hours), without disturbing the coupons, can I do that by using any Imaging technique?
Please let me know. Thank you for reading my question.
Regards,
Grishma


texts:
I've been tempted on cooking.stackexchange to answer a question, and I did, out of my mind.

(In retrospect, I shouldn't have done so, based on my lack of citable resources.)

I've heard that a water in oil emulsion can penetrate cell walls.

Is it true, and how does it work?


texts: Why is it that cats can jump so high for their size, compared with humans?

texts:
My cat is about 1' high at the shoulder, and I am a little over 6', but my cat can easily jump onto something as high as I am. That is 6x it's height. If a cat can do this, then Why can't I jump up onto my barn roof? That is a little less than 36' up. I have a hard time jumping onto even a 4' platform. Now if my cat had trouble jumping onto an 8" platform, I would think that pathetic. Do cats have muscles 20x stronger than humans, for their mass?
Is it just their skeleton providing leverage?


texts: In marine DNA viral diversity studies, what would "paradigm of rampant mosaicism" refer to?

texts:
The recent paper in Cell Marine DNA Viral Macro- and Microdiversity from Pole to Pole describes the (huge) new Global Ocean Viromes 2.0 (GOV 2.0) dataset.

In the Results and Discussion section, the subsection Validating Viral “Population” Boundaries begins with the paragraph:

  Defining species is controversial for eukaryotes and prokaryotes (Kunz, 2013, Cohan, 2002, Fraser et al., 2009) and even more so for viruses (Bobay and Ochman, 2018), largely because of the paradigm of rampant mosaicism stemming from rapidly evolving ssDNA and RNA viruses, whose evolutionary rates are much higher than dsDNA viruses (for review, see Duffy et al., 2008). The biological species concept, often referred to as the gold standard for defining species, defines species as interbreeding individuals that remain reproductively isolated from other such groups. To adapt this to prokaryotes and viruses, studies have explored patterns of gene flow to determine whether they might maintain discrete lineages as reproductive isolation does in eukaryotes. Indeed, gene flow and selection define clear boundaries between groups of bacteria, archaea, and viruses, although the required scale of data are only available for cyanophages and mycophages among viruses (Shapiro et al., 2012, Cadillo-Quiroz et al., 2012, Gregory et al., 2016, Bobay and Ochman, 2018).

I know what "rampant" means in the colloquial sense, and the colloquial form of "paradigm" is familliar as well. Mosaicism usually relates to genetic differences between groups of cells within an individual multicellular organism. I am not sure how it applies to virus populations.

Is it possible to explain the meaning of "paradigm of rampant mosaicism" in this particular context, and give it some background?


texts: Corrupted chromosome will be in any cell of body if zygote was corrupted?

texts: For example, zygote had abnormal number of chromosome (45, 47, 48 etc) or corrupted chromosome. And fetus was born. Then it means that in any cell of newborn's body there will be the same not normal or corrupted amount of chromosome?


texts: I want to get a list of FDA-approved drugs with unknown mechanism of action. I think that there should be a database where for each drug there is a short field "mechanism", but I haven't find one. Do you know any database where I can find such information? Another possible way is to use text-mining programs to analyze scientific libraries like PubMed and find the drugs which names often occur together with words "mechanism" and "unknown". Are there any good programs which can do it? Any other suggestions are welcome too, of course.


texts: Do mycorrhiza only form with angiosperm?


texts: Isolation of Intact Granules from Mast Cells

texts: How to isolate intact granules from mast cells without using sucrose and percoll?


texts: Does "Garbage Enzyme cleaner" contain cleaning enzymes?

texts:
There are many recipes which call for using fruit peel fermentation process to make a concentrated enzyme cleaner solution, some variations call to add bakers yeast. So the question arises that does this recipe really have those cleaning  enzymes and how are they generated?

This says that it may not have the cleaning enzymes, but maybe some other cleaning agents like vinegar or alcohol.

A discussion from two independent researchers on this topic give contrasting positions

Moreover if fruits  like Pineapple and papaya are used does it make the solution more potent?


texts: What is the main difference in chromatin fiber and chromonema?

texts: What I understand is both are coiled version of DNA along with histone but are termed different based on their degree of condensation. My question is when do we call it chromonema and when chromatin fiber? Do we consider 30nm fiber as chromatin and 10nm fiber as chromonema or something else?


texts:
Solunar theory, which states that animal activity in wild (fishes, deer) depends on position of sun and moon in sky.

Based on the solunar calender, hunters seek for optimal time for hunting fishes.

I am wondering that how solunar calender is developed from the sun's and moon's rise/set timing or from their positions in sky? For instance if I know the position of sun and moon in sky how would one forecast the animal activity timings of that day? OR the solunar calender is based on some statistical forecasting?

Thanking you.


texts: What is the difference between "Bisphosphate" and "Diphosphate" in biochemistry?

texts: I have often found bisphosphate compounds ( e.g. RuBP, RuBisCO, 2,3-BPGA etc.) and diphosphate compounds (e.g. ADP, GDP etc.) in biochemistry. They are commonly seen and are important compounds in both animals and plants but what is the basic difference between a bisphosphate and a diphosphate?


texts: Which enzyme curdles milk in human infants?

texts:
Following, this question -

Do humans produce rennin?
Rennin does not exist.
And
What inactivates pepsin in infants?

Rennin exist.

What do I know is-

Rennin is found in calves and acts on milk to curdle it.

Pepsin acts as rennin at pH of 6-6.5 and curdles milk.

Humans have pepsin, in infants as well as adults. Pepsin can perform both functions in humans.

So, in infants, is curdling of milk done by rennin or the rennin like activity of pepsin?


texts:
mutation-selection-drift equilibrium is one of the most important concept of population genetics. I could easily find the calculations for mutation-secltion equilibrium and for mutation-drift equilibrium but not for mutation-selection-drift equilibrium.

mutation-selection equilibrium

At mutation-selection equilibrium the expected frequency $p$ of a given allele is

$$p ≈ \frac{\mu}{s\cdot h}$$

, where $\mu$ is the mutation rate, $s$ is the selection coefficient and $h$ is the coefficient of dominance.

mutation-drift equilibrium

At mutation-drift equilibrium the expected frequency $p$ of a given allele is

$$p ≈ \frac{1}{4N\mu+1} $$

, where $N$ is the population size.

What is the allelic frequency at mutation-selection-drift equilibrium?


texts: Could the proteome of E. coli be fluorescently labelled?

texts: What proportion of the total number of proteins in E. coli could be fluorescently labelled for PALM/STORM imaging?


texts: In analysing amino acids content in a protein through gel electrophoresis, What's the purpose of the gel? Wouldn't putting the amino acid in the gel prohibit the amino acid from dissolving into the buffer solution (which its pH controls the protonation and de-protonation of the amino acid)?


texts:
Are researchers able to assemble viruses in vitro?

For example, I imagine that a phage display library may be generated by throwing in a test tube the capsid proteins (or what have you) along with relevant DNA that will self assemble. Has this been done? If so, is it a technique readily applicable to a broad range of viruses?


texts: Minor Allele Frequency (MAF) higher than 0.5?

texts:
I have a set of data in PLINK format (*.bed, *.bim and *.fam files).  There are around 2000 individuals in my dataset.

I used PLINK to calculate allele frequencies in the population:

p-link --bfile data --freq

However, in the produced results file, many SNPs have a MAF over 0.5 (up to 0.82).  Would that not then make that the major allele frequency, as the other allele would have a frequency of 0.18?


texts:
I'm currently learning about using PCR techniques to make fluorescently labelled DNA probes, and the textbook mentions "conjugated deoxyribonucleotides"

Can someone explain what these are? Nothing too in-depth and detailed. Just a decent description/explanation so I can get somewhat of an understanding.


texts: What is this plant that spontaneously sprouted in my balcony?

texts:
I have a big pot on my balcony that has inhabited many kinds of plants over the years. One spring I got to unexpected sprouts from seeds the size of an apple or orange seed. One survived and grew to what is depicted in the pictures here, but then unfortunately I got an infestation of spider mites that killed it.

I had previously rented out the apartment, and I suspect that this is the result of a couple of seeds that they intentionally or unintentionally put here. My best guess is that this is some kind of berry or something else edible that you buy in a grocery store.

You can also see some sun damage on some of the leaves in the picture. The plant in question is the most visible in the pictures, the others in the packground are passion fruit.

There were no thorns, and the leaves felt a little bit hairy, kind of like a common nettle but shorter and a fussier feeling. The height in the pictures is about 30-40 cm and it was growing fast until the spider mite attack.

What could it be?


texts: How did biologists find out that bacterial plasmids were circular?

texts: I was always curious how it was determined that bacterial plasmids were circular, since there isn't an obvious way to find this out. I heard somewhere that there was a difference when gel electrophoresis was conducted. Could anyone give an explanation?


texts: Does anyone know the details about which line they are using to sequence as the Drosophila melanogaster reference genome?


texts: What is the difference between scale vs cataphyll?

texts:
What is the difference between scale and cataphyll in botany - aren't these the same type of organ?
E.g. do cycad cones have scales or cataphylls? Pine cones have scales, I understand the compound nature of pine cones - does that make them scales?
On fern petioles/stipes there are often scale-like organs I've seen called scales (though they are not very scale-like).


texts: Which type of test tube should not be used for blood collection?

texts:
The following question is presented in my biology textbook:

You are required to draw blood from patient and keep it in a test tube for analysis of blood corpuscles and plasma. You are provided with the following four types of test tubes. Which one of them will you not use for the purpose?

Test tube containing calcium bicarbonate
Chilled test tube
Test tube containing heparin
Test tube containing sodium oxalate

In thinking through the question, I reasoned that since we are collecting blood from a patient for biochemical assay or hematocrit, we would want it to be in an anticoagulated stage. Sodium oxalate and heparin are both anticoagulants and therefore should serve my purpose well. I don't think a chilled test tube would have any effect directly, except the fact that low temperatures delay clotting. So, I had chosen the test tube containing calcium bicarbonate to be unsuitable, as $\ce{Ca++}$ is one of the factors required for clotting and hence would accelerate the clotting procedure.
The textbook disagrees with me, and gives (3) as the answer.
Is this an error in the textbook key, or a flaw in my reasoning? Which should be the correct answer, and why?


texts: How do scientists decide which version of a polymorphism is the main one?

texts:
This in fact has bugged me for years, but now I finally remembered to ask.

I suppose that if one variation is more frequent, it can be labeled as the default, but what about variations that are equally as common?
The example that I just saw, it seems that the frequency of both variants is the same, and yet somebody claims that G is the default and C is the polymorphism:
Polymorphism with genotypes CC, CG and GG occuring in 30, 40 and 30% of the control group, respectively http://hell.org.pl/~kamyk/stackexchange/Zorena1.jpg

Maybe it is possible to determine which one was first, but how? Is there ancient data about polymorphism frequencies?


texts: Arm at Heart Level when Measuring Blood Pressure

texts: How come that one's arm has to be at heart level so that the blood pressure can be measured accurately. I've tried researching this question, but most answers to it were just "if the arm is above the heart level the blood pressure is too high and vise versa," but I want to know why this is so.


texts: Are Night Parrots (Pezoporus occidentalis) really extinct?

texts: This incredibly rare animal has been reported to be extinct since 1990, however several cases has been raised that night parrot was spotted in the areas of Australia. What is the cause of their extinction, or in the first place, are they really extinct?


texts:
I read in Bruce Alberts Molecular Biology of The Cell :

  ....If,however,cells from one strain of mouse are introduced into a neonatal mouse of another strain , some of these cells survive for most of the recipient animal's life, and the recipient will now accept a graft from the original donor, even though it rejects "third party" grafts.

As far as I understand , in this experiment,they got these results because thymus hadn't yet learned what was "own" and what was "foreign".

Is  the reason for why maternal microchimerism does not invoke immune response related to the above experiment ? Can we apply the same logic here ?


texts: Why isn't life expectancy normally distributed?

texts:
Lots of phenomenon in nature can be plotted onto some sort of normal distribution, and that makes intuitive sense to me (such as human height). Why then, does global human life expectancy drop off so suddenly after ~85 years old? Is there some factor which suddenly increases mortality significantly? How come so few people (statistically speaking) age above 85 years old?

Inspried by this question


texts: Creation of healthy genetically modified crops

texts:
GM crops are huge at the moment, and the noticeable 'counter movement' is for people to continue to purchase organic foods (please note I am specifically talking of GM crops and not meats, etc).

The argument as fair as I am aware is that some of the GM crops actually contain poisons to the human digestive system that cannot be broken down, and we have yet to find out their effects on long term health.

However, my question is: What can be achieved, if anything at all, in terms of creating GM crops which do not incur health issues? Is there a specific way of going about this?
EG:

Could crops be made larger?
Could crops become more pest-resistant?
Could a 'uniform shape' be created?
Would this be done with genes from other plants? Or artificially?

Thank you for your time.


texts: What is the molecular basis of hangovers?

texts:
Well, most of us have experienced the wonderful feeling of the dreaded hangover. How does it work exactly? I imagine it has something to do with dehydration but what are the underlying mechanisms?

Extra points for explaining why mixing drinks makes it worse and why (or if) a hair of the dog (another drink) the next day can help. Someone once told me that hangovers are the first symptoms of withdrawal and if you drink (anecdotal evidence suggests that it should be the same drink as the night before, but I doubt this is true) a small amount of alcohol, the symptoms are alleviated. I don't really see how that can be true.


texts:
I am supposed to construct a plasmid that contains features from two other plasmids.
My strategy is to generate three fragments form the two other plasmids. I was encouraged to try Gibson assembly, so I went to NeBuilder entered my sequences and got I list of primers with overhangs and ordered them… But now I am I bit unsure about the linearization of the backbone and insert into that fragment.

In NeBuilder you can choose "by sequence position" in for the insert in the backbone the description reads “Entering the sequence positions of the bases immediately flanking the insert site. Primers for inverse PCR terminating at these endpoints will be calculated automatically”.

Does anyone have experience using NeBuilder? i am completely unfamiliar with inverse PCR ?
also my regular software package Geneious is unable to comprehend the two primers for the inverse PCR reaction


texts:
I know that in terms of post-translational modifications of genes, prokaryotes and eukaryotes differ highly because of the lack of introns in prokaryotic DNA.
With this said, do prokaryotic DNA sequences contain enhancer elements other than the UAS(upstream activating sequence)?

In addition, are enhancer elements like promoter-proximal elements and enhancer elements encoded directly within the DNA? Or are they proteins that attach themselves to the strand of DNA in order to enhance transcription?


texts: Which sequence characteristics influence the transcription efficiency of T7 polymerase?

texts:
The T7 polymerase doesn't transcribe all sequences equally well, the transciption efficiency can vary widely for different sequences. One well known requirement of the T7 polymerase is that the sequence should begin with 2-3 guanines for efficient transcription.

Is there any literature that quantified the effects of the sequence on the transcription efficiency? I'm mostly interested in the effect of the first few nucleotides, as changing other parts of the sequence is usually not possible.


texts:
Since I was young, I always understood that evolution taught that we descended from monkeys (or apes, not too sure a distinction was ever made). However, someone recently told me that this isn't correct, and that we actually share a common ancestor, but not a direct line of evolution.

Can anyone clarify which approach (if either) is correct?

Assuming the latter is correct, doesn't it raise problems of missing fossils? If we descended from monkeys, there is less of a gap to fill, but if we share a common ancestor, we would need to fill a much bigger gap, right the way back to the point where our family trees diverged.

As I said, I don't know much about this, and find most of the online material too technical to understand. If anyone could explain this in simple terms, I would be very grateful.


texts:
I know that sieve tubes do not have ribosomes, nuclei and cytoskeletal elements.
What other organelles does it not have? Does it have a cytoplasm?


texts: Are drones from one honey bee queen all clones?

texts:
The Honey Bee queen lays eggs that develop into worker bees (female) if she fertilizes the egg.  If she does not fertilize the egg, it will develop into a drone (male).

The drone only has the queen's DNA so are all drones exact copies of each other, ie clones, or is there some other mechanism that will make each brother slightly different?


texts: When infected with malaria, how many parasites are within a human host?

texts: When infected with malaria, how many P. falciparum cells are within a human host? And how does this compare with the average infection parasitemia of A. gambiae? I can't seem to find a reliable source to guide me on this question.


texts: Do metastatic cells still have their parent's identity?

texts:
If a liver cancer, for example, gives metastases. Will metastatic cells still have liver identity? I mean, if we mark liver cells, will we see the cancer cells too?

Thanks a lot!


texts: Why does the wavelength in curly hair differ?

texts:
Different people and animals have different wavelengths in the curls in their hair. I understand what purposes hair serves in protecting the skin from light and bugs. I am wondering about the eventual physiological consequences of curly vs straight hairs.

Do the curls help in cooling, blocking light or catching wind over flat hair? Does the wavelength in curly hair have intrinsic properties that physically would give an animal advantages in climates where straight hair would not?

I will be happy to accept another answer.


texts:
The following table is from Deonier's text Computational Gene Analysis at p. 152.
This is an exercise in global sequence alignment and scoring of alternative sequences.
The text proposed a solution (in parentheses). Setting aside the upper left hand portion of the table it seems there may be a better path.

It's more likely I  misunderstand the idea than that there is a typo.

$$\begin{array}{c | c | c | c | c | c | c |}- & -& T & G & G & T & G\\ \hline  - & (0 ) & -2 & -4 & -6  &-8  & -10 \\ \hline
A &(-2)  & -1 & -3 & -5 & -7 & -9 \\ \hline
T &-4 & (-1)  & -2 & -4 & -4 & -6  \\ \hline
C &-6 & -3  & (-2)  & -3 & -5 & -5  \\ \hline
G &-8 & -5 & -2 & (-1) & -3 & -4 \\ \hline
T &-10 & -7 & -4 &-3 & (0)  & (-2 )\\ \hline  \end{array}$$

Just looking at the upper left corner,

$$\begin{array}{c | c | c |} (0) & -2 & -4...\\ \hline -2 & (-1) & -3...\\ \hline  -4 & (-1) & -2...\\ \hline  -6 & -3 & (-2)...\\ \hline  \end{array}$$

which seems to give -7 versus -8 for the book's path. Below are the book's alignment and the one corresponding to my scoring, which may reveal my error.

$$\begin{array}{c | c | c | c | c | c | c |} A: & A & T & C & G & T & - \\ \hline
B: & - & T & G & G & T & G  \\ \hline
\end{array}$$

$$\begin{array}{c | c | c | c | c | c | c |}
A: & A & T & C & G & T & - \\ \hline
B: & T &  - & G & G & T & G  \\ \hline
 \end{array}$$

I had no trouble constructing the matrix just scoring it. it's a small point but I don't like to move on without understanding it.  Thanks for any assistance.

Edit: Both current answer seem clear on this but just for completeness: a match = 1; mismatch = -1; indel = -2.


texts: Is happiness or pleasure an evolutionary programming for survival?

texts:
I think that whenever we feel some kind of happiness or pleasure it is always related with improving our chances of survival, that might be temporarily or in long term, might be of only of an individual or his/her relatives or all human beings or all living beings as a whole.

I find that a sense happiness or pleasure is linked with the survival (might not be true as it's based on personal observation).
 We crave for things like attention & being cared, beauty & physical health, power (& money). Attaining them gives us a sense of pleasure, and these things improves the chances of our survival. People having power & money dont die out of scarcity. People having beauty & physical health get to pass their genes more often(keeping whole human history in mind). Dogs developed their behaviour around humans so as to get more attention & care thus improving their chances of survival. We also feel happy helping other people, we feel happy making more friends.
  But there is no simple answer to this one as we also have tendencies to hurt ourselves and some people derive pleasure in hurting others.

So is pleasure or happiness evolutionarily programmed into us to better our chances of survival?


texts:
Found on the shoreline of a tributary of the upper part of the Chesapeake bay in Maryland:
[![enter image description here][1]][1]
More pictures:
https://photos.app.goo.gl/Cg8t4Ttsde4oDDDg7
ichthyology??
[1]: https://i.stack.imgur.com/1dEfH.jpg![enter image description here](https://i.stack.imgur.com/Wjgvq.jpg)


texts: I am trying to identify an unusual cone or fruit found today on Tayside in Scotland. Here is an image. Can you help?


texts:
While moving large, old oak logs I'd stacked a year ago to form a terraced garden, I noticed it was very moist under the logs.

I saw 5 kingsnakes, a scarlet snake,  a couple of small brown earth snakes and an unidentified snake:

Thicker body than the King snakes, very skinny head, 3-4 feet long, and  almost all brown.

Can you identify the snake?

  Note: Picture taken from about 10 feet away. The debris on the snake pictured is sawdust and wood pieces.

We catch, picture and release kingsnakes, rat snakes and hog nosed snakes all the time, but this one escaped before capture or a good picture. Only one copperhead in 18 years.

Location: Gasconade County, MO (USA; 1 mile from Rosebud, MO).

We have a 1.5 acre pond about 80 yards from the picture site.


texts:
During a pit stop on the road from North Carolina to New York (somewhere in Delaware) I found the following (dead) insect in the car park:

As you can see from the quarter next to it (25 mm diameter) it is rather large - maybe six centimeters, including the "horns".

What was it?


texts: If mammals evolved to be nocturnal, then how did we get so staunchly diurnal in such short time?

texts:
Much of human health revolves around sleeping well through the night.  We know about circadian and body temperature rhythms which make us sleepy at night, peak melatonin production in the middle of the night, deep sleep phases, sleep disruption from light at night, and high cancer rates among people who work the night shift.

Clearly, we are built to sleep at night.  You would suppose, then, that we must have evolved to be diurnal long ago and descend from a long line of diurnal animals.

Yet, the evolutionary legacy of mammals is predominantly nocturnal.  Mammals started out as nocturnal (to avoid the reptiles) and most mammals today are still nocturnal.

How did we get so staunchly diurnal so quickly?


texts: Vitamins that could help "make us smarter"?

texts: I was at Sprouts health store and saw a lot of vitamins/herbs that claimed to be "Study Aids" etc, so if there is any basis to it, where exactly does it hold truth? And are these supplements safe?


texts: Should gene therapy safety protocol include isolation?

texts: In the case of a gene therapy trial where viral vectors are used to deliver genes into mammalian cells, including humans, should biosafety and ethical protocols include isolation of the patient as a precaution post administration that the viral vector may recover its ability to cause disease and harm the environment (more so the patient as the animals tested can be destroyed by incineration)? And how long should that isolation stay be to ensure safe disarmament of the viral vector?


texts: Reason behind selection of sites of administration of pituitary extracts?

texts:
There are two ways by which pituitary extracts are administered in a fish's body during induced breeding of fish.

Intramuscular injection is the most common practice in India and it is less risky in comparison with the other methods.The extract is injected into the muscle near the tail above the lateral line.
Intra-peritoneal injections are given through the soft regions of the body, generally at the base of the pelvic fin or sometimes at the base of the pectoral fin.

Why are these sites chosen? What physiological effects arise as a result of administration that these sites got chosen ?


texts: Physiological or molecular difference before and after sleep?

texts:
I know that the details of the process of sleep aren't entirely known, but have always wondered why I feel rested after sleep.

Biologically, what differences can be directly observed in the human body before and after a good night's sleep?


texts: I'm trying to figure out what the name of this flower is

texts: This is a flower that grows in my backyard. I really want to know the name so I can read about it and possibly get more.


texts: Simple experimental design of a chemostat without pumps

texts:
A chemostat is a device to maintain a cell culture in equilibrium, by continually pumping nutrients in and pumping excess cells and nutrients out.

What's the simplest design of a chemostat one can make? Has anyone tried to mount one without pumps?

A particularly sensitive issue here is sample taking, because you risk contamination of the culture.


texts: Are there any differences between qRT-PCR and GEO (microarray data from NCBI) regarding dealing with internal control genes?

texts: As we know, when we do qRT-PCR, the two most commonly used methods are absolute quantification and relative quantification, both the methods are involved in dealing with normalization of house-keeping genes or internal control genes (like GAPDH, Actin). In the microarray experiments, the similar normalization should also be adopted (I did not have any experimence with this kind of experiment). But I do know that someone obtained GEO file from NCBI, and simply did t-test analysis to find differenced expressed genes without any operation with the internal control genes. So I wander whether this is the right way, if not, what should we do with internal control genes to normalize data?


texts: My teacher told me that Chitin is a heteropolysaccharide but my book regards it as a homopolysaccharide.I am so confused


texts: Why are embryonic germ cells considered stem cells?

texts:
In a class that I'm taking we were presented 3 types of stem cells.

Adult stem cells which come from bone marrow
Embryonic stem cells which come from embryos
Embryonic germ cells which come from testes

I understand that adult stem cells are a bit more specialized than embryonic stem cells, but I'm confused why embryonic germ cells are considered stem cells. From Wikipedia, the definition of stem cells is:

  Undifferentiated biological cells that can differentiate into
  specialized cells and can divide (through mitosis) to produce more
  stem cells

But from my limited understanding of biology embryonic germ cells can't specialize into any other cells unless they fuse with another gamete, so why would they be considered stem cells? What am I missing here?


texts: What's the difference between tumor cells and host cells?

texts: When you talk about cancer, is there a difference between tumor cells and host cells ? What is the role of immune cells ? in a nutshell ?


texts: Species identification: what kind of fungus is this?

texts:
Found in a cave
Location: Israel

The white tentacles appear to be sticky. When they touch something, they stick to it and detach from the main body


texts: What kind of insect is this? (seen in Goma, Democratic Republic of the Congo)

texts:
We recently (in November) saw this insect in Goma, DRC.

I would appreciate help identifying it.


texts: What is this beetle? Found in heather in snowdonia

texts:
We were walking in the hills of snowdonia the other day and my girlfriend found this in the heather:

I've never seen anything like it. Can anyone identify it? It was the biggest beetle I've ever seen.


texts: Would some dinosaur egg be the most massive cell that ever existed? Are dinosaur egg relatively small compared to eggs of modern birds?

texts:
The egg of a large modern bird is a very large cell, not the largest possible biological cell since there are very long nerves in squid, but it's likely the most massive modern cell.

But, what about the cells of prehistory? Many dinosaurs were far larger than modern birds, but I had trouble finding information on just how large their eggs could be. I was also surprised that the eggs were not bigger than those of modern birds. It seems the ratio of egg size to dinosaur size was much smaller... or has that even been studied?

Maybe the large eggs were all destroyed?


texts: Human perception of time depending on age

texts:
From what I can tell and what thus far all people with whom I discussed this subject confirmed is that time appears to "accelerate" as we age.

Digging a little, most explanations I found basically reduced this to two reasons:

As we age physically, a time frame of constant length becomes ever smaller in contrast to the time we spent living
As we age socially, we are burdened with an increasing amount of responsibility and thus an increasing influx of information which impairs our perception of the present

To be honest, neither sounds entirely convincing to me because:

In my perception "local time" (short time frames that I don't even bother to measure on the scale of my lifetime) is also accelerating. Just as an example: When I wait for the bus, time goes by reasonably fast as opposed to my childhood tortures of having to wait an eternity for those five minutes to pass.
Even after making a great effort to cut myself off from society and consciously trying to focus on the moment, the perceived speed of time didn't really change. (Although I did have a great time :))

Which leads me to a simple question (and a few corollaries):

Am I just in denial of two perfectly plausible and sufficient explanations, or are there actual biological effects (e.g. changes in brain chemistry) in place, that cause (or at least significantly influence) this?
Is there a mechanism, that "stretches out" time for the young brain so that weight of an immense boredom forces it to benefit from its learning ability, while it "shrinks" time as the brain "matures" and must now act based on what it has learned, which often involves a lot of patience?
If there is such a mechanism, are there any available means to counter it? (not sure I'd really want to, but I'd like to know whether I could)


texts:
Can anyone tell me what kind of insect (if it is one) is this...!! Or is it the pupa of some insect?

Well I don't think that the whole big thing is the insect itself, it appears to be just a kind of protection or shelter which moves along with the tiny little thing that keeps on popping out and going it so as to move.
Location:  India


texts: How does PCR mutagenesis add restriction site near the gene of interest?

texts:
I have been learning about PCR mutagenesis to add restriction site right next to the gene of interest using a primer that's attached with single stranded restriction site (first image). I have drawn my own diagram (second image) to better understand how this works, but I am stuck at the last step in question mark. How does DNA Polymerase 'insert' the green sequence (restriction site) so I would end up with the gene shown in the bottom?
Thanks for anticipiated response.

[![enter image description here][3]][3]


texts: How to calculate information content of a DNA sequence

texts:
How does one calculate the information content of DNA sequence like ATCGGCT where mutation rate of G's is 10% and the most common mutation product binds with C and A with equal frequency.

I know that the individual information of a sequence is the dot product of the sequence and the weights matrix for each base. Essentially I = sum (base1xweight + base2xweight + ...)

What I can't figure out is how to determine the the weight of each base so as to incorporate the 10% probability of mutation of G's.. Can anyone help me figure that out

EDITED since wording may be confusing:
Original problem says:
" Spontaneous deamination of exocyclic amine is dG (deoxyguanosine) can occur occasionally in DNA strand. Given probability of this occurring  during the time it takes DNA polymerase to copy DNA is 20% per dG in a particular DNA. Given that most common deamination product pairs with dC and dA with equal frequency calculate information content during DNA replication in the given sequence. "
     As an example I choose ATCGGCT and changed it to 10% deamination of dG.

PROPOSED SOLUTION:
For sequence ATCGGCT,
I am only consider the initial strand bases A,T,C are 2 bits a base, given by I=-1/ln(2)ln(n_before/n_after) ,where n_before = 1, and n_after = 4
In the case of mutated G (Gm) ,
I say, I = -1/ln(2)ln(1/3)= 1.58 bits , n_after=3 since A,C are equivalent to Gm

Perfect copy would give us 7 bases x 2 bits each = 14 bits content of strand.
Since there are 2 G's, with 10% change of mutating --> 0.02 of G in strand will mutate.

Thus I content during replication,
    Information content I(ideal) - I(inc. mutation) = 14-0.03 = 13.97 bits during time of replication


texts:
In the evolution of sociality among animals, different degrees are acknowledged. Some species present overlapping generations, some division of labor, and the minority present reproductive division. Those that present the three traces above are called "eusocial" (e.g. some wasps, some bees, all ants and termites, and an african mole).

Maybe our own species could be eusocial? After all, homosexuality is present in virtually every culture studied by anthropologists. Some say it may bring an advantage to the group via group selection (not having kids of their own, they could study plants, medicine, weapons, and so on). What do you think? Are we an eusocial species?


texts: What is the human energy consumption by organ?

texts:
The human brain uses about 25% of the human body's metabolic energy. How are the other 75% spent, in terms of portioning to its various systems?

I thought this could be answered by a simple search, but I can't find the answer after searching very hard. I only got dieting advices.

I am envisioning the best answer to look like


texts:
I am working on large scale biodiversity simulations and have collected a lot of data on simulated phylogenies. I have a list of child-parent edgelist species in the form:

list = [1, 1, 2, 2]

      /-- 3
1 -- 2
      \-- 4

children = [1, 2, 3, 4]
parents = [1, 1, 2, 2]

Where the index is the child and the value is the parent. 1 is it's own parent (the root).

I have such a tree for a large dataset upwards of 1000 individuals. I can build the tree programmatically in igraph or networkx easily and visualise it. However, I cannot find a way to convert the tree into a format for phylogenetic analysis. There are function to convert dendropy and ete trees from igraph/networkx into their own formats but no way to re-import the igraph/networkx trees. There also appear to be no way to write the igraph/networkx trees into phylo formats (newick).

There also seems to be no support in dendropy or ete to programmatically build trees and it would be infeasible to manually build all the trees I have.

Is there a way to build the trees so I can analyse and visualise them as phylogenies?

Tried approach

library(ape)
p <- c(NA, 1, 1, 3, 3, 4, 4)
x<-data.frame(name=as.character(c(1:7)) , id=1:7,  parent = c(NA, 1,   1, 3, 3, 4, 4))
x1<-na.omit(x)[,3:2]
n <- c(c(1, 3, 4), c(2, 5, 6, 7))
edges <- matrix(c( x1$parent, x1$id), ncol=2)

tree<-list(edge=edges, Nnode = 3, tip.label = as.character(x$name[c(2, 5, 6, 7)]), node.label = as.character(x$name[c(1, 3, 4)]))

class(tree)<-"phylo"

#plot.phylo(tree, show.node.label=TRUE)

The plot command just causes R to crash and the tree object has an invalid structure.


texts:
I have a vector of GOIDs that are specific GO IDs outputted from an enrichment analysis. I want to cluster my GOIDs by their parent GOID term. I used GOstats to do my enrichment analysis, and I have noticed there is an inducedTermGraph, which outputs a graphNEL object of direct children and direction parents of the GOIDs you query. If you set parents=TRUE and children=FALSE, your graph includes only parent nodes which relate to your GOID query.

However, how can I extract the node names of these parent nodes??? See code below:

gene.ids <- c(51141, 84968, 140850, 388289, 406994, 677828, 693217, 100287428,
             100505685, 100506540, 101926966, 101927244, 101928659)
require(RnBeads)
uids <- rnb.get.annotation("genes")
uids <- sort(unique(as.numeric(na.omit(unlist(sapply(unlist(uids)$entrezID,
        function(i) strsplit(i, split=";")))))))
params <- new("GOHyperGParams", annotation = "org.Hs.eg.db", geneIds = gene.ids,
             universeGeneIds = uids, ontology = "BP", conditional = TRUE,
             testDirection = "over")

res <- tryCatch({
    hyper.genes <- hyperGTest(params)
  }, error = function(ee) {
    print("Errorfests.")
  })

go.ids <- summary(hyper.genes)[,"GOBPID"]
result <- inducedTermGraph(hyper.genes, id=go.ids, children=FALSE, parents=TRUE)
nAttrs <- list()
z <- attributes(result)$nodes
    names(z) <- nodes(result)
    nAttrs$label <- z
plot(result, nodeAttrs=nAttrs)


texts: I learned that mushrooms are normally classified as either decomposers or symbiotes. I would like to know the differences between the two types and whether they are detrimental or beneficial to their host, often a tree.


texts: How long do your eyes need to adapt to darkness and reach full contrast?

texts:
I heard you should wait some time until your eyes adapt to darkness and are able to see smallest luminosity differences, otherwise you might overlook faint objects in the ocular. Are there any rules of thumb here?

What about looking for 5 minutes on your bright laptop, do you have to wait again the same time or wear some sunglasses? ;)


texts: How much should one smoke in order to prevent Parkinson's?

texts:
There are studies who claim that nicotine has a neuroprotective effect against Parkinson's(such as this: http://www.ncbi.nlm.nih.gov/pubmed/11772120)

What would be the minimum amount of nicotine(cigarettes smoked) and frequency in order to prevent Parkinson's, at the same time not to damage his health by becoming an addicted smoker?


texts: I am a little confuse when I try to figure out the molecular weight of the marker on my gel. I used NuPage Novex 4-12% bis-tris gel and Mark12™ Unstained Standard as a marker. Could please someone help me to figure out the molecular weight of the marker on my gel? I find different images in internet and I am confuse.


texts:
A well known way to have a rest of mosquitoes during camping is to stand in the fire's smoke. Moreover, I learned recently that shepherds in certain regions of Africa use the same tactic for cattle. They make smoky fires and cattle gathers in smoke to get rid of mosquitoes.

Why humans and cattle can stand smoke, but mosquitoes can't? Does this technique work for other kinds of insects?


texts:
I have a plant in my USDA zone 5 garden that appears to be in the ribes genus.

Details:

The location is east of Toronto (Ontario, Canada).
The plant is currently flowering (today is May 18th, 2019).
It is approx 4 feet tall.
The plant flowers every year, but does not set fruit (not self-fruitful).

More photos here:

https://i.stack.imgur.com/coEp5.jpg
https://i.stack.imgur.com/wv0TA.jpg
https://i.stack.imgur.com/pFmtk.jpg
https://i.stack.imgur.com/KvjGe.jpg

What species is it?


texts: The spleen is considered a graveyard for red blood cells. So in case of Splenectomy (complete surgical removal of the spleen), what would be the fate of red blood cells? Would this cause Polycythemia?


texts: Energy transformations in chemiosmosis and ATP synthase

texts: In terms of energy, how does chemiosmosis drive ATP synthase? How does electrical energy turn into mechanical energy and then into chemical energy? Would the movement of $H^+$ be considered passive diffusion or secondary active transport?


texts: After a few days of raining, I found these larvae in a puddle. What animal are they from?


texts: Are "constraint trees" in phylogenetic analysis cheating? How can I correctly use them?

texts:
How do phylogenetic experts evaluate results which use constraint trees? Are there examples in the literature where phylogenetic experts detail how they use constraint trees?

Here is my problem. I have 500 samples. These are five different "categories" of species A, B, C, D, E, 100 samples each.

Category A: A1, A2, A3, ..., A100
Category B: B1, B2, B3, ..., B100
Category C: C1, C2, C3, ..., C100
Category D: D1, D2, D3, ..., D100
Category E: E1, E2, E3, ..., E100

There are two classes of which these "categories" fit in: Class 1: A and B, Class 2: C, D, and E.

For the purpose of this discussion, let's say A=whale, B=dolphin, C=mouse, D=gerbil, E=hamster

When I do the analysis, there are some problems. The output tree resolves the samples into two classes which meet my expectations; it splits the samples into two groups: ( A & B) and ( C & D & E ). That's great. However, it doesn't resolve the species into separate categories, e.g. it mixes together "whale" samples with "dolphin" samples, and mixes together all the individual C, D, E . I see

(A1, B3, A27, B23, B2, A2, A3, A4, ....), (C3, C5, D72, D3, E1, E2...).

This would mean whale1 is more evolutionarily "related" to dolphin3 than whale 27.

I try to use a constrain tree instead to constrain each of these groups, using the form

((A1, A2, ..., A100), (B1, B2, ..., B100), (C1, C2, ..., C100), (D1, D2, ..., D100), (E1, E2, ..., E100))

Sure enough, my tree now resolves each "category" A, B, C, D, E into a distinct category.

Question 1: Isn't this cheating? I feel like I stipulated "resolve the tree in this manner I expected" and RAxML output that.

Question 2: How do I evaluate whether this is correct?

Question 3: For experts, could direct me to published literature which used this approach? Which papers used RAxML constraint trees?

Thanks for any help. I'm happy to clarify things.


texts: Reference for the bite force for Nile Crocodile

texts:
The (maximal) bite force of the Nile Crocodile (Crocodylus niloticus) is estimated around 22,000 Newton (refer to YouTube interview with Ofer Kobi, a crocodile conservation ranger and croc farm owner, time 7:50-8:00, Hebrew , where he estimates the bite force as above 2 metric tons). However, I didn't find a proper reference for this. Dr. Gregory Erickson measured the bite forces of a 5.2 meters long Saltwater Crocodile (Crocodylus porosus) and obtained a value of about 16,000+ Newton and estimated a 6.7 meters long Saltwater Crocodile can exert a bite twice as strong (about 34,000 Newton). See Paper by Gregory Erickson et al. Interesting to note that Erickson measured small Nile Crocodile (total body length < 3 meters) so it does not represent the bite force of a full adult big crocodile.

Remarks on units of force:

1 Newton = 1 kg * 1 meter / sec^2

$1 \ \mathrm{Newton} = \frac{\mathrm{kg} \times \mathrm{meter}}{\mathrm{second}^2}$

1 Newton = 0.224808943 lbf = 0.225 lbf (pound-force)

10,000 Newton is approximately 1 tonne-force (1 tonne = 1 metric ton = 1000 kg)


texts:
I have a problem understanding a PCR exercise, it says to calculate the number of cycles to get 1µg of the DNA fragment, starting from 10ng and then from 500ng, I know about 2^n, and the exercise even gave the answers:

For 10ng, we need 29 cycles
and for 500ng, we need 24 cycles

But I don't know how they did it, I tried with 2^n and ended up with something totally different. I would be grateful if someone explained it to me. Thank you.


texts: Understanding what passes through and doesn't pass through the plasma membrane

texts:
I have difficulty in understanding the reason why certain molecules can pass through phospholipid bilayers.

Firstly, I understand that the outer layer of the lipid bilayer is hydrophilic - my understanding is that they "like water" and can interact better with water.

Bilayers can absorb hydrophobic substance like N₂ and O₂.

Does this mean - because the hydrophilic surface are capable of hydrogen bonding - that's why they are able to absorb hydrophobic substances like F , O and N ?

They can absorb non-polar molecules.
They can absorb small uncharged molecules like H₂O and CO₂.

I'm not sure of the reasons behind 2 and 3 ...

And of course , vice versa ... (what can't pass through the lipid bilayer easily).

Any help would be appreciated!


texts: How does rate of evolution/innovation scale with population size?

texts:
I understand that there will be many other factors that affect rate of evolution/innovation. However, other things being equal, how will the rate of evolution vary between two populations of different sizes? Does doubling the population size double the rate of introduction of new traits?

Is this answerable for evolving life in general, or do different forms of life have different scaling laws? For example, is it different for sexual and asexual life?


texts:
I've recently learned about ion leak channels in the context of membrane potential and action potentials. Neurons have ion pumps that require energy in order to maintain the resting membrane potential and concentrations of K+ and Na+, yet the K+ and Na+ leak channels seem to directly oppose this purpose. It seems like, if left unopposed, the ions would eventually diffuse across the membrane such that there would be equal concentrations on both sides and a membrane potential of 0.
If the ion pumps spend energy and store it in an electrochemical gradient, don't leak channels let that potential energy dissipate back across the membrane? Wouldn't it be more efficient to tightly seal ions into their respective sides until the energy is released during action potential?
Am I missing:

An important function of leak channels directly involved in maintaining membrane potential or causing action potentials?
Some broader evolutionary purpose of leak channels that help ensure a cell's health in other ways?

Additional clarification requested: Would it be correct to say that leak channels function in facilitating changes in membrane potential (and return to "baseline") until the threshold, at which point the voltage-gated ion channels allow for a much larger influx/efflux?


texts: Is there a web tool for species identification?

texts: I know this stack exchange provides the ability to post photographs of animals/plants for species identification, but is there a web resource that can automatically identify a plant/animal using image processing/correlation tools - so the user doesn't have to painstakingly work with keys?


texts: What physical evidence exists that shows motor proteins "walking" within a cell?

texts:
Various animations on the internet show the motor protein kinesin walking within a cell. Is this an approximation? How does this happen and (based upon what physical evidence) how do we know it "walks" like this?

https://www.youtube.com/watch?v=y-uuk4Pr2i8

http://imgur.com/gallery/WOTJdLp

https://www.youtube.com/watch?v=tMKlPDBRJ1E