texts: How is it that ionic diffusion is independent of other ions?

texts:
This question arises from the explanation of what the resting potential of a cell membrane is. In the Goldman formula, there is no interaction between different ion types.

If diffusion is caused by random movement of ions and collisions, then how is it that the K+ ions do not seem affected by the very high concentration of Na+ ions outside of the membrane? Shouldn't there be an effect due to the fact that outside, the ion concentration overall is higher than inside? How come they are all independent?


texts: Sexual Differentiation in Monoecious plants with unisexual flowers

texts:
In monoecious plants having unisexual flowers (eg Zea Mays, Ricinus Communis etc), there must be some mechanism as to produce two sexually distinct flowers from the same genotype. Since both the type of flowers are placed on the same plant, the genetic constitution of the cells of both the type of flowers will be similar. What is the mechanism by which the development of two sexually distinct flowers is carried out in such plants?

Is the mechanism similar to the mechanism for differential gene expression in case of embryonic development (Homeobox genes)? And moreover, is the genetic constitution of the pollen produced by the male flower similar to that of the egg produced by the female flower, with respect to the composition of autosomes and allosomes (if any)?


texts: What is the point of Meiosis II, considering Meiosis I already produced haploid cells?

texts:
Meiosis I is required so that the 2N cells become 1N, and so a 1N sperm and 1N egg can fuse to become 2N again.

But why is meiosis II required? Why does our body need to go from  2 1N cells to 4 1N cells? Can't it just use one of the 2N cells after Meiosis 1?

Source


texts: How can I change the payload of a bacteriophage used to transform E. coli?

texts:
I was looking at bacteriophages and how they're used to transform E.coli. While the whole process of how a bacteriophage works makes sense theoretically, I wanted to know how one goes about changing the default payload of a bacteriophage with the payload of interest (engineered plasmid) in practice?
Clarification:
payload - Genetic material that the phage inserts into the bacteria
default payload - Whatever genetic material the phage inserts into the bacteria naturally
payload of interest - Engineered plasmid that I want to insert into the bacteria


texts: Is NADH found in all type of cell in human body?

texts: Is NADH found in all kinds of cell in the human body? I am curious about microglia specifically.


texts:
My husband and I noticed a dog today that looked like a smaller version of a purebred Border Collie, although it didn't appear to be a puppy. It made us wonder if other animal species experience dwarfism.

Are dogs known to display a dwarfism gene?


texts: How to calculate relative fitness from absolute fitness with recapture data?

texts:
In Grant 1986, it says:

  For this analysis the absolute fitness of an individual id scored as 0 if it disappeared and 1 if it survived, and these scores are then converted to relative fitness values by dividing them by the mean absolute fitness.

Grant, P. R. 1986. Ecology and Evolution of Darwin's Finches

If we have this dataset (for example):

   id x1 x2 x3 x4 x5
1   1  0  1  0  0  0
2   2  0  0  1  1  0
3   3  1  0  1  1  0
4   4  1  0  1  1  1
5   5  1  0  1  0  0
6   6  0  0  0  0  1

Imagine that id is a column of individuals and the rest (x#) are the absolute fitness. Then, how would you calculate the relative fitness? For an example, what would be the relative fitness between x3 and x4?
X1 is the first event of capture. I.e. I went on the field and capture birds for examples and noted who was there (0). I went on the field on X2, X3, etc. and noted which bird was there.


texts: If one endures the same form pain over a long period of time, would the pain begin to lose intensity?

texts: Metaphorically thinking, if one endured the pain of constant burning for decades, would the pain slowly lose its strength?


texts:
Feynman writes, in his Lectures on Physics Vol. 1, Chapter 1:

  The most important hypothesis in all of biology, for example, is that everything that animals do, atoms do. In other words, * there is nothing that living things do that cannot be understood from the point of view that they are made of atoms acting according to the laws of physics.* This was not known from the beginning, it took some theorizing to suggest this hypothesis, but now it is accepted and it is the most useful theory for producing new ideas in the field of biology.

He would have written this around 1961-1963. Was he right then and/or is he right now? Is what he says applicable for the entirety of biology (say evolutionary theories) or only for a subset of biology?

Would Feynman have been referring to a few specific advances or to the general state of biology at the time?

Please note that this question comes from an (interested) amateur to both physics and biology, I hope the question is appropriate for this site.

Edit: Perhaps this will clarify the intentions behind my question:

I would be interested to know how much atomic theory actually helps biological research. For instance, it often happens that the specific low level details are not necessarily important for explaining the high level theory. A nice example is abstract algorithms vs implementation in programming languages vs hardware implementation. Is this the case with biology or do the details of atomic theory matter? For instance, have advances in physics led directly to new biological discoveries?


texts:
I've read a couple of articles that state that HIV is an enveloped Retrovirus that is so sensitive to the acidity of the environment and it cannot survive or will be inactivated at pH below 7. What exactly happens to the virus when exposed to an acidic environment. Does it denature the GP120 AND GP41 proteins on the virus envelope and make them ineffective? If not, how do hydrogen ions in the acid react with the virus?
Thanks for your attention.


texts:
Today morning I was surprised to see this flower as it has four normal pale orange coloured petals and one bright red one. This is a flower of Hibiscus and all the flowers of this plant have the normal pale orange coloured petals, while this one has a bright red one.

What can cause this?


texts: Different Effects of Detection Probability Between Presence and Count Data at the Same Location

texts:
I'm modeling habitat suitability for a large, mobile animal using occurrence data (presence only - I have no true absence data in this case) collected from camera traps (stations with automatic motion/heat sensing cameras). At each camera trap location I have 0 to several occurrences recorded.

Typically, when such data is modeled, they are modeled as count data, and detection probability is included in order to mitigate for covariates that affect detection, which otherwise may be identified as covariates that affect suitability. For example, an area where detection is less likely due to, say, dense vegetation, may be mistaken as less suitable due to that vegetation structure when in fact that may not be the case (or even the opposite may be true).

My question is, if the count variable were to instead be used as a detection/no-detection variable (so, a binary) would the probability of detection have less of an effect on the model (*when modeling relative suitability, not probability of occurrence)? i.e. if you didn't account detection probability, would using a binary response variable give you a less biased estimate of habitat suitability than if you were to use count data? And if so, why? It doesn't seem like probability of detection would change, or would be more homogeneous across the study area with this change, but it seems like the effects would be smaller in magnitude by not reinforcing differences in detection probability with multiple occurrences.

Also, I understand that it's not desirable to toss out all the other occurrences assuming you can calculate detection probability. I'm asking this in an attempt to better understand the possible differences in outcome between these two modeling approaches when using such data, as I've seen both methods in the literature, but have not seen this question specifically addressed. If you could reference any publications that may shed light on this, I'd be very appreciative.


texts: List authors (scientists) by various attribute

texts:
Is there an easy way to list authors of biology articles by

University
country
number of published articles
sum of citations of all articles he/she wrote
fields of study (population genetics)
...

For example, I want to know who are the 10 most popular/cited authors in population genetics in UK's universities. How can I achieve such search?

For example, do WebOfKnowledge provide such tools?

Please, let me know if this question should be asked on another SE website.


texts: Really confused. How many chromosomes pairs do humans have in their sex cells? How many single chromosomes do humans have in their sex cells?


texts: How does one measure the length of telomeres?

texts:
My questions are:

What techniques are available for doing so?
Are they destructive ?
What is their accuracy ?


texts: Hundreds of Red Spiders in Individual Webs

texts:
I live in the USA in south Louisiana. I woke up this morning to find my yard covered in hundreds of spider webs.

Each of those little white puffs is a spider web. Inside of each web is one little red spider.

The spiders are pretty small. Less than half an inch long.

Anyone know what they are?


texts: Is there any evolutionary reason why male traits appear in the heterogametic sex and female traits in the homogametic sex?

texts:
If you define male as the heterogametic sex, and female as the homogametic sex, then my question sounds like a tautology. But, what I'm trying to get at is why is it that the traits we associate with "males" (e.g. having an unlimited amount of possible offspring, greater average height, etc) appear in the heterogametic sex, and why traits that we associate with "females" (e.g. having a limited amount of possible offspring, shorter average height, etc) appear in the homogametic sex. Or, is it simply by chance that the homogametic sex became the female sex and the heterogametic sex the opposite?
As far as I understand it, heterogametic chromones allow for a greater chance of mutations being displayed, so I wonder whether there is something advantageous about this occurring in the male sex rather than the female sex. Perhaps it is because males are more "expendable" since they can have an unlimited number of offspring? Is this line of reasoning accurate, and are there any alternative explanations that go deeper than this?


texts: How to convert a test tube assay to microplate assay?

texts: I am trying to measure Ascorbic acid levels in tissue using Omaye et al protocol (Methods in Enzymology, Volume 62, 1979, Pages 3-11). This method is based on reduction of ferric chloride and subsequent detection by 2, 2'-dipyridyl. However, this assay is a test tube based assay. I want to convert this protocol into a plate based assay, however, I could not find any already published protocol for this. Is it possible to do it?


texts: Why don't surfactants destroy or incorporate into cell membranes?

texts:
How do surfactants remain on the surface of pneumocytes without  (1) acting as a detergent or (2) the phospholipids getting incorporated into the membranes of pneumocytes...

I'm guessing the answer has something to with the secretions of clara cells, but I'm curious for a more biophysics-y answer... for example how do the phospholipids that compose surfactant not form miceles or are the miceles simply larger that the individual component phospholipids (I'm basing this off the answer to "how do detergents get in hydrophobic membrane interior"), but even so why wouldn't the micelle simply fuse into the membrane


texts: How does the brain manifest and realize the intention to resist sleep?

texts:
The question title says it all. What happens in my brain when I resist sleep? I would appreciate explanations on neurotransmitter changes, what areas of the brain activate to resist sleep, what can an EEG tell us about that condition, are there any phases to that condition..

Switching to sleep mode is very complex and automatic process and it takes over and changes the functions of the whole brain (and the whole body also), so..

What actually does the brain do to not fall asleep?


texts:
(1). Why does having cold hands create a painful sensation?
Is it a physical effect, maybe a protection mechanism from evolution?
(2). Why, if one's hands are cold, does it feel as if they are more susceptible to pain?
Note: I have (2) as a separate question because the painful sensation in (1) refers to that from the coldness, whereas in (2), I mean that certain 'ordinary tasks' would feel painful, for example, holding a shopping bag.


texts: How do B memory cells provide immunological memory? Do they differentiate into plasma cells?

texts:
My text book doesn't say anything about how B memory cells actually ensure a faster response the second time the antigen is encountered. My guess is that they differentiate into plasma cells which produce antibodies, and release cytokines to cause clonal expansion of the correct T killer cells, but I'm not sure...

Thanks in advance for any responses ^_^


texts: Is it possible to accurately measure micronutrient levels with the blood volume from a Dermal / Capillary puncture?

texts:
I have not been able to find much information beyond what tests are normally done with Capillary puncture sampling, as opposed to what tests are possible.

Could we test for a single micronutrient, or maybe some subset of nutrients with the blood drawn in this way? Is the issue purely volume, or are there other factors?

Thanks!


texts: Can cerebrospinal fluid deliver nutrients/drugs to neurons during sleep?

texts:
I'm looking at this article on the possible mechanism of detoxifying brain during sleep using cerebrospinal fluid. It states that at night, the space between neurons may allow better (up to 20x) circulation of cerebrospinal fluid within the brain to clean out metabolic by products of daytime activity.

My question is if this may also work in reverse and allow to deliver drugs within the fluid to the brain.  If a person ingests a drug or nutrient before sleep, would the increase in circulation of cerebrospinal fluid deliver the drug to deep regions of the brain? Or does the blood-brain barrier prevent drugs from entering cerebrospinal fluid?


texts:
In _Robbins Basic Pathology 9th ed., edema is defined as

  [E]dema is an accumulation of interstitial fluid within tissues. Extravascular fluid can also
  collect in body cavities such as the pleural cavity (hydrothorax), the pericardial cavity (hydropericardium), or the peritoneal cavity (hydroperitoneum, or ascites).

Though hydrothorax is mentioned here in relation to edema, it is not mentioned explicitly whether it is actually a subtype of edema or not. I also looked into multiple sources for edema definition; “accumulation of fluid in the interstitum”; interstitium refers to the tiny spaces between cells which is not the case for hydrothorax since pleural cavity is not interstitium (right?). So is hydrothorax considered as a subtype of edema?


texts: What is the standard deviation of adult human heights for males and females?

texts:
The wikipedia article on human height reports mean height for many different countries by sex but it does not report standard deviations.

What is the standard deviation of adult human heights within sexes?

Obviously the size of the standard deviation would vary across countries and by other factors.  That said, I think good data on a few representative countries would be sufficient to get a reasonable sense of what it typically is and the extent to which the standard deviation varies.


texts: Do all bacterial cells have a double membrane?

texts:
I’m reading that gram positive and negative bacteria have an inner plasma membrane surrounding the cytoplasm, then a periplasmic space, then an outer membrane.
How does this compare to my general knowledge of bacterial cells having one plasma membrane surrounded by a cell wall?!


texts: Can Nanodiscs be used to study membrane energetics?

texts:
Nanodiscs have changed they way we can study the structures, insertion, and functions of transmembrane proteins. Below is an image of a nanodisc bilayer.

The key difference, as far as I can tell, over traditional liposome studies are that one can alter the lipid composition more easily.

Have any studies been achieved on quantifying energetics in these nanodiscs ie energy transfer upon insertion, or stability of the protein in the nanodisc etc?


texts: Is there a practical upper limit to amount of nucleotides or genes in a transformed plasmid?

texts:
I'm currently working on a synthetic biology project which involves working with lots of different parts. I would ultimately like to integrate these genes by transforming a single plasmid. I've heard (casually) that 9-10 foreign genes on a transformed plasmid is often the practical upper limit for these types of experiments, without a real explanation other than "beyond that, it just doesn't work".

Is there a practical upper limit to size of amount of genes in a transformed plasmid, assuming all need to be expressible? What causes this upper limit?


texts: Any food crops that could grow in a desert provided that they get fertilizer and water

texts:
I am working on an idea to provide nearly unlimited amounts of water in desert regions. To make this commercially viable. I would use the water to irrigate desert sand and grow crops. Given my extremely limited understanding of biology, I cannot find an answer to the following question:
Are there any food crops (preferably high valuable/low maintenance ones), that can grow in a desert, given that I can just provide the seed, water and fertilizer and stop sandstorms.
My motivation for investigating this is the following map showing regions that are either already deserts or at risk of becoming deserts:

Source: http://en.wikipedia.org/wiki/Desertification


texts: Is there any way bicondylar/bigonial, bizygomatic or bitemporal breadth can change in adults?

texts:
Without cosmetic surgery or etc., are there any cases/example wherein a human adult has had a change in significance regarding these regions of the face? I have seen many anecdotes where people have asserted that certain things (not surgery) like diets, drugs, or etc. has affected these regions.

Is this possible and what are any such means in which these regions of the face can change?

This isn't a personal medical question as this is widely applicable and generic to any human adult.


texts: Clostridium tetani (C. tetani) is a bacterium commonly found in soil and is excreted in the faeces of many animals (both mammals and birds) and serves, by means of the exotoxin, tetanospasmin, causes the life-threatening condition tetanus.


texts: Why doesn't peritoneal dialysate leak through the fallopian tubes?

texts: It is my understanding that the female peritoneum does not form a closed (potential) space due to its puncture by the uterine tubes. If that is indeed the case, why is peritoneal dialysis in women not typically complicated by vaginal leakage of dialysate? Similarly, why do we not expect surgical insufflation (e.g. in laparoscopy) to suffer from CO2 leakage via the same route? Does this have to do with muscle tone in the fallopian tubes, or a duckbill valve effect where intraperitoneal pressure effectively seals them off? There seem to be only a handful of case reports of PD dialysate leakage, but more suggesting flow in the other direction where sexual activity, for example, resulted in unintended pneumoperitoneum.


texts: How do some deep sea creatures lower their metabolism to stay alive for a long time?

texts:
I was watching some bio related videos and saw in one that some deep sea creatures  and other organisms purposefully limit their movement to decrease metabolism rates. Do they live longer?

If we apply this same theory to humans, doesn't it mean that exercising less and regulation of diet may help decrease metabolic rates? I know exercise is extremely good for the body but this just got me thinking...


texts: I'm taking a 3-week Bio I summer course, and my textbook says the cell is the smallest/basic unit of life. I asked my professor why organelles aren't a living unit, and her reply was that they aren't self-sufficient. But it seems that cells in multi-cellular organisms need other cells with different specializations in order to survive. You can't just (or can't always) pluck a cell out of a larger organism and leave it to fend for itself outside of it. Same with an organelle. She said only the entire cell fits all the requirements for life, referring me to the textbook, but I couldn't find an actual description of these requirements. So, what is the relevant difference between an organelle and a cell such that only the entire cell is considered alive?


texts: How does Natural Selection shape Genetic Variation?

texts:
Background

Importance of the additive genetic variance

As stated here, the fundamental theorem of Natural Selection (NS) by Fisher says:

  The rate of increase in the mean fitness of any organism at any time ascribable to NS acting through changes in gene frequencies is exactly equal to its genetic variance in fitness at that time.

NS reduces the additive genetic variance

On the other hand, NS reduces additive genetic variance (discussion about the origin of this knowledge can be found here). The genetic variance of a population for multiple traits is best described by the G-matrix (here is a post on the subject).

What is a G-matrix

A G-matrix is a matrix where additive genetic variance of trait $i$ can be found at position $m_{ii}$. In other words, the diagonal contains the additive genetic variance for all traits. The other positions $m_{ij}$, where $i≠j$ contains the additive genetic covariance between the traits $i$ and $j$.

Question

How can one model how the G-matrix changes over time because of selection (assuming no mutation)?


texts: Why are belly buttons on the stomach (why does the umbilical cord end up attached to the stomach)?

texts:
Belly buttons are at the site where the umbilical cord was attached to us as we developed inside our mothers. The same is true for all placental mammals.

Why are belly buttons on the stomach? Why didn't the placement end up somewhere else like the chest, the back, the head, etc.? Is it optimal for the umbilical cord to be near the intestines?


texts: Is there a specific word for bacterial death?

texts: What do you call it when a bacterium dies? Cellular death is apoptosis, necrosis, and bacterial is ...? I don't simply want to write in a paper that it - well dies!


texts:
I was reading about fossils and thought of this question: what was the purpose of the shells of heteromorph ammonites (for example, ammonites of the genus Nipponites)?
Wouldn’t the odd shapes of these shells cause more drag? So why did their shells evolve to be that way?


texts:
Someone gives you a short DNA sequence that comes from the middle of a gene.

5'- TCTAACTGATTAGC -3'
3'- AGATTGACTAATCG -5'

From this sequence, determine the following:

Is the promoter located to the left or right as the sequence is written?
Is the sense strand the top or bottom strand?
What amino acids are encoded by this gene fragment?

The only thing I have been able to come up with, is that since this is from the middle of a DNA sequence I need to choose a frame with no stop codons.


texts: Do some genes follow Rock-Paper-Scissors model of dominance?

texts:
Assuming there are at least 3 alleles of the gene $G$ in total - $G_R$, $G_S$ and $G_P$ - is there any gene for which the following is true?

$G_R$ is more dominant than $G_S$.
$G_S$ is more dominant than $G_P$.
$G_P$ is more dominant than $G_R$.


texts: How are Maggots Sterilized (Disinfected)?

texts: For maggot therapy, how are maggots disinfected? I'd imagine there's a limited scope of measurements that can be taken to sterilize the maggots - i.e. we don't want to sterilize them and kill them too.


texts: Can one eye affect the other eye's low-light adaption?

texts:
This previous question addresses how long eyes need to adapt to darkness and reach full contrast. My question is how does one eye affect the "transition" and/or efficacy of this "night vision" of the other eye? Specifically:

Are the eyes' adaptation to darkness linked or is it possible for one eye to transition to "night vision" while the other does not?
Would exposure to bright light in one eye slow the other eye's progression toward being adapted to low light?
If one eye had transitioned to low-light vision, can light exposure to the other eye reduce the ability for the first eye to see effectively in low light?

I understand that the dark-adaptation of eyes seems to occur primarily at the rod and cone level, but I'm wondering if perhaps over-stimulation from bright light in one eye would have a saturating effect on the signal being sent to the primary visual cortex (and thus impact the dark adaptation)?


texts:
I am trying to mathematically model the dynamics of a particular cell in circulation and its binding to another nanoparticle that is intravenously injected. The concentration of this cell is very low (about 5 cells per mL of blood). I want to see how many nanoparticles are needed to bind to as many of these rare cells as possible.

So first, I am trying to model the cell dynamics in the blood flow. I am not sure how to start. I wanted to model the cell movement through the entire cardiovascular system, but I would have to simplify it. I am thinking of modeling the blood flow through some of the major organ systems, and estimating the absorption through the capillaries. I am thinking something like the physiologically-based pharmacokinetic model (PBPK). However, there would be some parameters that I wouldn't know about that I would need for the model (at least that is what I think, I am new to pharmacokinetics) Also for the actual fluid dynamics, I'm not sure how to model this, because the blood isn't just a fluid, and has many other cells, so I don't know if there are some other effects.

So, my question is, in what direction should I go to model the dynamics of this cell in circulation? I want to model the circulation in the entire cardiovascular system, because I need to also model the other nanoparticle dynamics, and how likely it is to find and bind to some of the receptors on the cell. Is there an example of a similar model that has been done?


texts: How can I download histological slide from Cancer Digital Slide Archive

texts:
Could you tell me if it possible and how to download images data from http://cancer.digitalslidearchive.net ?

Thank you.


texts: What elements are a possible basis for life?

texts:
I've been told that life on earth is carbon-based, Then I got curious about one thing: What are the possible bases for life and under which circumstances could lifr based on other elements exist?

If the existence of a silicon-based life is possible and if it is, under what temperature, pressure, etc?


texts: Cambrian explosion and evolutionary arms race

texts:
I've seen many times mentioned in textbooks and popular articles that a reason of the Cambrian explosion is an 'evolutionary arms race' between predators and prey. But this isn't really a sufficient reason, since that happens all the time, but evolution seems to happen only at brief intervals separated with long intervals of stasis, which is described extensively in the Punctuated equilibrium hypothesis.

So, my question is, what made the evolutionary arms race of the Cambrian possible?


texts: How HIV Affects and Its Treatment using Combination Therapy

texts:
Can someone please help me with the following questions. I've written my specific questions right after the text question.

Human immunodeficiency virus (HIV) is a retrovirus. Its genome is a single (+) stranded RNA that is packaged with the reverse transcriptase enzyme within a protein capsid. This is further packaged into an envelope that is derived from the plasma membrane of the host cell in which the virus had replicated. The surface of the envelope is covered with the envelope glycoprotein, called gp120 & gp41.

a) HIV specifically infects the T-helper (TH) cells of the human immune system. If the HIV enters the host cell by means of host receptor recognizing a viral protein, what would be the most likely ligand and its corresponding receptor during HIV infection?

b) Some individuals are resistant to HIV infection even after repeated exposure. Assuming that these individuals express a normal level of the functional receptor that you have recognized above, how can you explain their resistance to HIV?

c) In recent years, therapies have been developed to fight AIDS using nucleotide analogs. The drug used to combat AIDS is Azidothymine (AZT). The structure of AZT is very similar to thymidine except that in AZT, the 3’-OH group on the deoxyribose sugar is replaced by an azido (N3) group. Which process of the life cycle of HIV do you think is inhibited by AZT?

d) Combination therapy is the new treatment strategy for treating HIV patients.

i. Why is combination therapy more successful in preventing the emergence of the disease resistant clones?

ii. If the combination therapy involves a drug that prevents…

1) HIV binding to the target cell, what protein does this target?

2) Integration of HIV genome into host cell genome, what protein does this target?

3) The cleaving of viral polypeptide into individual proteins, what protein does this target?

e) If the AIDS patient were given combination therapy, would the patient still be able to transmit the HIV virus to his/ her partner (Yes/ No)? Explain your choice.

**

a) No idea.

b) Maybe their T-helper cells have some sort of mutation that makes it impossible for HIV to bind to them?

c) I'm thinking "formation of HIV RNA" because in the absence of 3' -OH bonds, phosphodiester bonds cannot form.

d)
    i. It kind of makes sense because a virus being resistant to multiple drugs would be very unlikely but maybe there's some definite reason why?

ii. No clue. Is this talking about proteins of the virus or of the host? Also, enzymes are also proteins, right?


texts: How do DNA viruses keep themselves in the nucleus without inserting themselves into genome?

texts:
If I'm not mistaken only RNA viruses insert themselves into the host genome. As an example of DNA viruses, herpes viruses for example do not insert themselves in the host genome.

Then how do DNA viruses keep themselves inside the nucleus? Do they just float around without their capsid? And if the cell duplicates, would the DNA of a DNA virus also be duplicated even though it isn't inserted in the host's genome?


texts: Chickpeas as feed for house sparrows , ringneck parrots?

texts:
I've put up a bird feeder outside my house, and so far I have been feeding uncooked
 white rice , and the birds seem to enjoy them.

However, since I read somewhere  that a variety should be maintained in the diet, lest the birds start suffering malnutrition, I want to know whether I can use chickpeas as a substitute for a while. Is it safe for house sparrows, ringneck parrots ? These are the only type of birds that have been visiting my feeders for a while now.

Thanks !


texts: What is meant by "Expression" of Non-Coding RNA?

texts:
I was having a look at lncRNAdb and its help says:

  The ENCODE project gene annotation list, GENCODE, has predicted that the human genome contains 14,470 lncRNAs whereas only a small proportion of these have been shown to have function.

  We have examined thousands of publications in order to find and
  manually annotate lncRNAs that have been shown to be functional by
  overexpression or knockdown experiments.

What is meant by Overexpression of a Non-coding RNA here? Even if you have a look at any lncRNA in the DB, its entry has a column for "Expression":


texts: Does anyone know if there is a term to describe the following process?

texts:
I'm actually currently studying physics but this came up in my textbook (taken from Giancoli 7th edition section 16-10):

The random (thermal) velocities of molecules in a cell affect cloning. When a bacterial cell divides, the two new bacteria have nearly identical DNA. Even if the DNA were perfectly identical, the two new bacteria would not end up behaving in exactly the same way. Long protein, DNA, and RNA molecules get bumped into different shapes, and even the expression of genes can thus be different. Loosely held parts of large molecules such as a methyl group can also be knocked off by a strong collision with another molecule. Hence, cloned organisms are not identical, even if their DNA were identical. Indeed, there can not really be genetic determinism.

I'm aware of different biological processes that can affect gene expression but this is random kinetic motion! Would you call this one of the epigenetic mechanisms that can affect gene expression? If so it would underlie ALL epigenetic mechanisms because all molecules have random kinetic motion.


texts:
Why do solutions of purified protein condense into droplet phases?

I'm trying to understand the protein phase transitions.

Here is the article http://www.cell.com/cell/fulltext/S0092-8674(12)00634-4#

It's on Intracellular Granules as Liquid Droplets


texts: Sample suggestions for phase contrast microscopy

texts:
I am a non-bio student working on an academic paper recently and would like to have some sample preparation for phase contrast microscope.

For it to work, I imagine the sample to be:

Transparent;
Easy to obtain from daily stuffs;
Easy to slice and prepare (i.e. approachable to people untrained in bio).
Best dimension around 10 micros, and is well seen under x100.
Preferable to be seen dynamics at room temperature.

My current thoughts are:

Human: oral cheek cells, red blood smear, sperm.
Plants: onion surface cells.
Others: yeast, pond water.

Any further suggestions (especially dynamic ones)? Thanks!


texts: At what levels of muscle energy intake does catabolism start?

texts:
From my own reading, there are three ways used by the body to produce energy:

Alactic anaerobic (direct degradation of ATP and creatine phosphate for regeneration of ATP)
Lactic anaerobic (breakdown of muscle glycogen with lactic acid production)
Aerobic (breakdown of carbohydrates and fats primarily and secondarily of proteins)

My questions are:

1) Knowing that the anaerobic mechanisms (alactic and lactic) are triggered when the effort is intense and / or greater than body oxygenation capacity, it seems logical, at rest, the body uses mainly aerobic way for producing energy. Am I right?

2) If 1) is true, what are the conditions (trigger elements, trigger events) which lead to muscle catabolism (so protein degradation) in order to produce energy? ? Is it well the last resort used by the body to produce energy that is to say after degradation of total carbohydrates and lipids?


texts: Why aren't more prostate glands just removed?

texts: Some 80-90% of men have some problem with their prostate gland as they get older. Beyond about age 60 it is unlikely that men will need the prostate to contribute to seminal fluid, so there seems little point in keeping this troublesome organ - yet a huge proportion of older men end up with either benign prostate hyperplasia and/or prostate cancer. So why isn't the standard treatment just to remove the prostate altogether?


texts:
I read in Tortora and Derrickson Anatomy and Physiology that :

  Another type, called brown adipose tissue obtains its darker color
  from a very rich blood supply , along with numerous pigmented
  mitochondria that participate in aerobic cellular respiration.

From Wikipedia :

  ...brown adipocytes contain numerous smaller droplets and a much
  higher number of (iron-containing) mitochondria, which make it brown.

The conclusion seems to be that there should be some iron containing pigment in the mitochondria of  BAT which (along with a rich blood supply) gives brown colour to the BAT.

What is the brown pigment present in the mitochondria of BAT ? Is it the uncoupler protein - thermogenin ?


texts: Why is the cough reflex triggered when we hear others cough?

texts: Very often, I see a "chain reaction" in people coughing in an exam hall. One person coughs and many follow. It's not necessarily the person closest to him who coughs, it can be someone sitting far away. This doesn't just occur in this setting but also in other situations, such as in public spaces. I was wondering if this is a reflex which has evolved over time as a means of protecting our body from pathogens and harmful chemicals in the air.


texts: Hepatitis Lab diagnosis based on serology

texts: HBcAg which can't be detected in serum can be detected in hepatocytes , why is it so that they become detectable in hepatocytes?


texts: Is it considered feasible to genetically improve plants for better Carbon dioxide breakdown?

texts:
I have found several somewhat related questions and answers here and elsewhere, but I couldn't find, if any  scientist groups are researching genetical improvement possibilities of existing plants' photosynthesis processes to produce plants, which would be net oxygen producers and/or significantly increase their CO2 removal abilities.

For the most part, it seems people are preoccupied with getting energy out of plants, but if we allowed that potential energy to be used for photosynthesis, wouldn't such plants be useful even if we can't harvest energy from them?


texts: How does high-fidelity of DNA replication depend on the formation of hydrogen bonds?

texts:
Replication has an error rate of less than 1 in 100 million. DNA polymerase forms H-bond with the H-bond acceptor atoms in the minor groove. <-- enhance fidelity here?

Binding of the triphosphate group to the active site of DNA polymerase triggers a conformational change. Changing a conserved Tyr residue increases the error rate by 40 fold.

I don't quite understand the above two statements. Can anyone explain in detail to me? Thanks!


texts: What is meant with “the chest wall and lungs are coupled together”?

texts:
Since the lung and chest are elastic, we can represent them with springs. Under normal conditions, they are coupled together: the “lung” springs are stretched and the “chest” springs are compressed. During a pneumothorax, the lungs and chest are independent and the springs representing them go to their relaxed positions, causing the lung to collapse and the chest wall to enlarge.

This analogy is honestly completely flying over my head. How are the lung and chest wall “coupled”? Heck, earlier in this book it’s mentioned that one of the two forces keeping the lungs from collapsing is “the surface tension between the lungs and the chest wall” (the other being the intrapulmonary pressure).

This and the said analogy make it sound like there is a physical-contact adhesion force between the lungs and the chest wall, which, from what I’ve looked into (and several other analogical figures the book has provided), seems to not be the case.

I believe this analogy of “coupling” is probably related to pressure relations, but I don’t understand how those are exactly set up either, and why during a pneumothorax they just cease as the two become “uncoupled”.

For those interested, the book is Medical Physics by John R. Cameron.


texts: Visual Quality Indicators for Soil and Plants

texts:
I would like to know what are the visual indicators that can be used to determining the quality of the soil and plants by looking at the in-situ photos?
Can the following quality indicators be determined by visual check such that a decision making can be done?

Approximate Soil Salinity
Soil pH
Soil Moisture
Soil Content (red indicates presence of iron etc)

For Plants

Presence of weeds
Presence of bug infestation (perhaps different visual patterns to
identify kind of infestation)
Plant Health (rigid looking vs hanging etc)

The above is whats there in the top of my head, can this list be expanded and upto what degree the quality indicators can be relied upon?

Note: Soil salinity might not be easily determined if the excess salt doesn't precipitate (visible white layer on the soil can help determine the excess of salt hence its not a good visual quality indicator for most of the time.


texts: Why are (most) right hand dominant people also right foot dominant? And the same for left handed/footed people

texts:
Just as the title states -- Why do people who are right hand dominant also tend to be right foot dominant? And, the same question for left handed/footed people.

Does the brain actually designate an entire side of the body to use by default, when only one hand/arm/leg/foot/eye/ear is needed, or available?


texts: How does natural selection favour large body mass and size (or so it seems)

texts:
I was walking through a park this afternoon and observed a few birds having fun flying around and it got me thinking why would natural selection favour birds with flesh at all if it hinders their flight.

We started first with single-cell and micro-organisms flourishing the ponds and then they evolved into massive dinosaurs. It therefore seems, there are some unique reasons for growing to such a large size.

However, I thought it's counter intuitive because the large body slows down locomotion, requires lots of food and energy upkeep, is a big flesh target for predators, makes hiding ineffective.

Although it is obvious that the flesh protects the internal organs, but it seems like a chicken and egg problem because without a massive body, perhaps then there is no need for the internal organs.

On a different perspective, perhaps those animals that evolved without flesh are called plants.

That sums up my naive train of thoughts.

So, any expert can shed some light?


texts:
Hey I hope this question supposed to be in this forum.

I'm not from the biology community, I'm from the data security community so im not familiar with the words you might use for answers

I need to use an algorithm that very similar to the de novo assembly algorithm.
I'll try to explain myself better I've some sequences of '1' and '0' all of them are pieces of one big sequence.

I've seen some applications that work with this algorithm such as SPAdes tadpole and Geneious but i couldn't make any of them to work for me except the Geneious because it was the simplest.

Geneious is not good for me because i need something that i can use by command line in the terminal
what application do you recommand me to use that i give input the sequences and the output will be the big sequence.

BTW, in the Geneious I've used a FASTA file for my sequence where my '0' and '1' translated to 'C' and 'D'

Thank you very much wait for your answers :))


texts: What does T and the numbers mean in T coliphages?

texts:
I have searched a number of websites and articles relating to nomenclatures or phages but never found anything explaining what T in T-4,5,6.. Phages mean in the Coliphages. Also, what does the number mean? I have seen that many times, the T - even are grouped as one, why is it so?
Thank you.


texts: What species is this aromatic plant found in a mountainous region of Greece?

texts:
This plant was found in the Taygetos mountains, Greece, and had a lemony smell.

Small plant about a foot high.

The shiny recurved leaves are reminiscent of rosemary, and the dry seed-heads seem rather distinctive.

Any ideas of Genus or species most welcome!


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


texts: Why is Hydra classified under Hydrozoa when it has neither a planula larva, nor a medusoid form?

texts: If the general basis of classification of cnidarians is with respect to the body form - medusoid or polypoid, or in the incidence of metagenesis (as is common in hydrozoa), both, then, on what basis is Hydra placed in class Hydrozoa?


texts:
This is one of seven ant queens I just collected yesterday morning (2015-09-21 9AM) around home.

I live in Hong Kong, at a hillside facing south. The weather was as follows (Hong Kong Observatory Daily Weather Summary, Hong Kong Observatory Daily Extract):

Mean Pressure (hPa): 1008.6
Max temp in my district: 24.2C
Min temp in my district: 28.0C
Mean dew point: 23.8C
Relative humidity: 66% - 95%
Rainfall: 16.9mm

Judging by the ridged head and the large mandibles, I'm guessing this is one of the Tetramoriums (Wikipedia, AntWeb).

The colour is dark brown. The total length from the tip of the mandibles to the tip of the abdomen is about 17mm. The length of the large wing is also 17mm. I don't know what habitat it lives in and I also don't know how the workers or soldiers look like, as I have never seen where these ant queens emerge from.

If anybody is fairly confident in identifying this species, I would also appreciate some tips about keeping it and starting a colony. I have a make-shift ant farm made out of two plastic bottles, one nested inside the other like a Russian doll. Out of the seven queens that I collected, three are already dying. A fourth one already show signs that she won't make it either.

More info

When I picked them up, they were not exactly "outdoors". The short but heavy rain was mostly over and these queens were "taking shelter" in the stairwell of my building, which is usually dim, slightly damper and cooler than outside.

Here are more pictures; these should be better because I just took these in natural daylight:

Somebody at The Ant Farm and Myrmecology Forum suggests that this is in the genus Carebara (previously Pheidologeton). After some more Google search of my own, and image comparing, I believe that this is indeed a Carebara affinis, which has previously been spotted in Hong Kong. Could somebody confirm?


texts: observed luminescence in a piece of plaice

texts:
A plaice fish bought for human feed has been cleaned and cooked.
Some parts of the raw body have been left out of the fridge at about 22°C for about 15 hours.
During the following night a luminescence phenomenon has been observed on the meat of the fish.

The second shot has been taken in a dark environment with a professional camera using a high sensitivity and long-time exposure.

What could it be?


texts: How do the variable portions of antibody genes look in cells which don't produce antibodies?

texts:
There are several families of antibodies found in mammals.  They may have two or more antibody domains which contain heavy and light chains.  The variable regions of the light and heavy chains genes in the chromosome are spliced in antibody producing cells so that each cell produces a different antibody, with a unique sequence of amino acids in the variable regions.

Here's a cartoon:

The variable regions are disproportionately large here, but it gives some idea...

What I'm having trouble finding is how the DNA regions of these genes look in cells which don't produce antibodies.  Are they the same as that in the germline?  Do they undergo recombination but are not expressed?

Any help would be appreciated.


texts: I need a site which has online courses for anatomy of limb and head and neck and also embryology, so far I have used www.coursera.org and it was really organized and helpful but unfortunately it does not have courses about these subjects, does anyone know a site like that which contains some organized videos in English language, I have searched a lot but it was not successful!


texts: Are there constraints on where intron/exon boundaries occur with respect to the triplet codons of the reading frame?

texts:
I did a quick search (here and elsewhere) and couldn't find anything on this subject.
If all introns in a given primary transcript were spliced out in the same way, then this wouldn't matter.  But lots of eukaryotic transcripts have alternate splicing patterns so that one version of the mRNA will contain coding regions that are absent in other alternate forms.

The problem relates to maintaining an open reading frame, avoiding a frame shift and the attendant (and unpredictable) consequences. If a splice donor site occurs within the 3-base codon, it might require that the two (or more) alternate acceptor sites would be in the same relative position in a related codon.

The simplest solution to this problem in my view is to make sure that all splice donor and acceptor sites would be at a codon/word boundary.

Is there any evidence that this is true?


texts: What are the evolutionary benefits for herbs having beneficial health effects on humans?

texts:
There are many types of plants which produce chemicals which can be beneficial in treating human illnesses, or at least alleviate painful symptoms.

Why would they do that?

Is it just random chance, like some plants being poisonous, some having no effect, and some having beneficial effects? However, for poison there are evolutionary benefits, as it might reduce the chance of animals eating the plant.

Many plant species produce tasty fruits for the purpose of having animals eat them and disperse the seeds. However, for most plants used for medicinal purposes, the leaves, roots or flowers are used, the cultivation of which doesn't seem to be useful for the plant itself.


texts:
So I know plants store pigment in chloroplasts, chromoplasts, etc., but what do animal cells store pigment in? For example, is there like a chromoplast for melanin in the human body?

I tried Googling my question and didn't find anything, but maybe I was looking at the wrong sources.


texts: How does ultraviolet light influence the decay process of wood?

texts: Given a piece of wood, how does putting it in the sun or not influence the rate of decay due to rot (assuming that it's in an otherwise humid environment)?


texts: I've been trying to find complete sequences of mouse (Mus musculus) MHC H2 locus haplotypes for quite some time now with limited success. The EBI IMGT database has a table of mouse H2 haplotypes, yet IMGT only provides haplotype sequences for human HLA genes via an FTP sever. I've found similar data for several other species at EBI's IPD-MHC, but Mus musculus is not on the list. The MGI database provides access to H2 SNPs, but I haven't found a mapping from SNP combinations to reconstruct happlotype sequences given reference genes.


texts:
In parasitology, while examining the stool sample, one important thing you do is test whether the eggs float on water or sink. We never did that since our coursework limits itself to microscopic examination, but we still are expected to remember examples of eggs under each
category.

So my question is, what makes flotation such an important criterion? And how is it done? How do you know if the eggs are floating or not? Does it depend on from where you take the sample (as in, add the stool sample to water and then either take from top or bottom)?

Another interesting thing we are expected to remember is that the fertilized eggs of Ascaris float while unfertilized ones sink. What's the basic funda behind all this? What's in fertilization that changes the buoyancy?


texts: Why do mosquitoes appear to be repelled by magnets?

texts:
A few days ago, I was playing with magnets and thought of placing one near a live mosquito (I had it held between my two fingers so it had no chance of escaping). When near the magnet, it twitched and flew away! I tried the same with semi-alive mosquitoes, but nothing really happened.
I googled about this and learnt that mosquitoes have got to do something with magnets, but I'm still confused. Could anyone tell me why mosquitoes get repelled by magnetic fields?
PS. I'm no biology student, so please go easy on me, thank you ahead of time!
Source (PDF)
EDIT: Strickman et. al. (2000) says:

we found that some specimens had a significant magnetic remanence
Could this possibly be the reason why mosquitoes may get repelled by magnetic fields?

That paper also states:

the mosquitoes were able to detect the magnetic fields but sensed a magnetic pattern that was impossible in nature.

Reference:
Strickman, D., Timberlake, B., Estrada-Franco, J., Weissman, M., Fenimore, P. W., & Novak, R. J. (2000). Effects of magnetic fields on mosquitoes. Journal of the American Mosquito Control Association-Mosquito News, 16(2), 131-137.


texts: What is the most readily usable form of nutrients/energy source for heterotrophic microorganism in general?

texts: Consider a nutritious mixture containing abundant soluble sugars, soluble lipids and soluble protein etc. Would heterotrophic microbes preferentially use sugars first > lipids > proteins > insoluble polymer such as cellulose (please propose your own order if this is wrong)? If appropriate, you can further differentiate these compounds into e.g. sugars into monosaccharides and oligosaccharides. Is there a general trend or is it highly variable depending on the particular microbe concerned?


texts:
For my project I have to find an inexpensive, quick and simple-to-use method to extract DNA from horse hair. The sample does not have to be purified because the sample will be used for LAMP and not PCR.

I will do my internship at a university so most kinds of equipment and materials are available to me. I also have a budget for my project. I searched online for DNA extraction kits but didn't have much luck because many kits were for human hair and horse hair is a little bit thicker.

Does anyone have experience with a method that would work for my case as well and can advise me?


texts: What effects does being cryogenically frozen have on a person's body?

texts:
I'm wondering what effects are known to happen to a person's cells when a person is cryogenically frozen, especially those that need to be overcome in order to "bring them back to life."

From a cellular and maybe even molecular level, is the person exactly the same as before?


texts: How to do desalt reaction by passage through a Micro Bio-spin 6 column?

texts:
I want to perform the bisulfite sequencing on rRNA to detect the 5-mC. I followed this protocol

•    DNA-free™ DNA Removal Kit (Invitrogen)
•    Purified RNA, Treat RNA according to manufacturer's instructions.

Adjust DNAse-treated RNA to a volume of 10 μl.

2.Sodium Bisulfite Treatment of RNA EpiTect Kit (Qiagen)

•   DNAse-treated RNA preparation
•   PCR thermal cycler
•   Micro Bio-spin 6 columns (BioRad)
•   GlycoBlue coprecipitant (LifeTechnologies)
•   Cooled microcentrifuge

3.Transfer DNAseI-treated RNA solution into a PCR tube.

Add 42.5 μl freshly made bisulfite solution (EpiTect kit) and mix thoroughly by pipetting.
Add 17.5 μl DNA stabilization solution (EpiTect kit) and mix thoroughly by pipetting.
Place samples in a thermal cycler and run the following program to deaminate RNAs:

•   70 °C: 5 min
•   60 °C: 60 min
•   Repeat steps (i) and (ii) two to six times (depending on target RNA abundance and predicted secondary structures)
•   25 °C—hold

7.Desalt reaction by passage through a Micro Bio-spin 6 column according to manufacturer's instructions.

Add 1 volume (70 μl) of 1 M Tris–HCl (pH 9.0) and incubate at 37 °C—30 min for desulfonation.

9.Precipitate RNA by adding sodium acetate (pH 5.2) to 0.3 M, 15 μg GlycoBlue coprecipitant and 3 volumes of 100% ethanol and incubate at − 80 °C for ≥ 1 h.

10.Pellet RNA by centrifugation at 4 °C for ≥ 30 min at top speed.

11.Wash RNA pellet with 75% ethanol.

12.Air-dry ≤ 5 min at room temperature.

Store deaminated RNA pellet until further use at − 80 °C.

In the step-7 I got stuck. i do not know whether do I have to use flowthrough or do i have to elute from the column.

Ref. https://www.sciencedirect.com/science/article/pii/S0076687915002335?via%3Dihub


texts: When performing PCRs, usually in every protocol enzyme amount is specified as 1.25 U as optimal per 50 uL reaction. Then, when running 25 uL PCR reaction should i use 1/2 he amount the enzyme or should i respect the value on Units thus using the same volume as in 50 uL reaction?


texts: Aside from cockroaches and other insects, which species (of all kinds) are 'immune' to ionizing radiation?

texts:
I have just been reading this excellent question and answer about cockroaches ability to withstand ionizing radiation.  My question is an extension of that question: aside from insects, which other animals (if any) have an increased defence against ionizing radiation?

Are there species of plants, fungi, and bacteria also "immune"?


texts: Identification of a small to mid-sized, yellow moth species found in India at monsoon season

texts:
I am from India and it's monsoon here. What is the name of this insect?

Description:

Length: ~4cm
Width: ~2.5cm
Color: yellow, almost uniform across the wings. Slightly darker, dandelion yellow across the body.
Small black dot in the middle of each large wing.
White, speckled iridescence on wings.
Short antennae.
Longer than average hair for moths.


texts: Are there examples of Apis mellifera of different colors?

texts: Re: my previous species-identification question,  What species is this gray bee? I'm still curious: Are there any recorded/reported cases of either albino Apis mellifera, or at least with substantially different pigmentation/color? Is it possible that only part of a colony gets this trait?


texts:
It seems to be a flying insect about 2-3mm in length. It also doesn't seem like it's very good at flying. They seem to crawl around my desk until I try to hit them, which is when they'll start flying.

Location: Denver, Colorado, USA

They seem to come out more at night.


texts: How does a virus take control over the host cell?

texts: When the virus integrates its DNA with the hosts and enters the lytic pathway, do the viral proteins that produced destroy the cells DNA? Do they deactivate it? Also does the cell function in the same way as before?


texts: I recently saw this tree in Texas, with many bees on it. I think it attracts   bees. However it didn't have any specific smell, so I don't know why there were so many bees (they were bee for sure). I tried to identify the leaves but couldn't. Dear experts: could you please identify this tree?


texts: Do people with colorblindness have less cones or no cones of a certain type?

texts:
https://en.wikipedia.org/wiki/Color_blindness#Red.E2.80.93green_color_blindness

  Protanopia (1% of males): Lacking the long-wavelength sensitive retinal cones,

  Deuteranopia (1% of males): Lacking the medium-wavelength cones,

Do they lack all those cones, or are they just (severely) short?


texts:
Are plasmid genes always expressed? If so, then isn't a bacterium wasting it's resources in expressing genes (like antibiotic resistance) which are not required in "normal" conditions?

If not, then what triggers bacteria to express genes of recombinant plasmids? Can a bacterium survive in "normal" conditions if it is deprived of all the plasmids?


texts:
For an application I need to find a cheap antigen and cheap correspondent antibody. The antigen can be literally any molecule that is cheap and potentially easy to produce and with a correspondent antibody that is cheap and easy to produce as well. I imagine this antigen will need to be a molecule that triggers very easily an immune response to result in a easy to produce antibody.
I have never worked in immunology so I don't know what system antigen-antibody to choose. I know pregnancy test are common so probably the antibody for Human chorionic gonadotropin (hCG) is easy and cheap to produce but I don't think hCG is.
 Are bigger molecules better than smaller ones as antigens? Any suggestion is helpful.


texts: I know this may be silly, but I am confused to what a membrane potential actually is. I understand that at resting membrane potential is -70- -80 mV. But what does that exactly mean and how does this all tie into diffusion potentials and equilibrium potentials.


texts: Are the antibodies developed by differing vaccines still the same?

texts:
If one person gets an mRNA vaccine that teaches their body to deal with a specific virus, and another person gets a similar but different mRNA vaccine, and another person gets a more "classic" vaccine with modified/weakened/dead virus cells, will there be any real difference in the antibodies developed by the three different people?
My gut instinct says that the antibodies/proteins developed by all of the people will be mostly identical, but I'm not a biologist.
I'm having difficulty finding articles/research on this. Full disclosure: this somewhat pertains to the SARS-CoV-2 and the varying vaccines, but it is also a more general question. I was hoping to find research on this, but it is proving difficult to google for such a verbose subject.


texts:
In muscle cells most of the ATP's phosphate is with creatinine phosphate.

So why is the displacement of the phosphate group done ? Is it because creatinine phosphate would give it's phosphate more easily ? Is it done so that the negative feedback by ATP on mitochondria is not there and more and more ATP can be generated ?


texts: Cause of short sightedness/ far sightedness

texts:
I recently had gone for an eye test. The doctor told that short sightedness/ far sightedness is caused due to shrinking or expanding of the eye.
One thing i forgot o ask him was what causes that shrinking/expanding.
Can anyone explain it to me?


texts:
I have two questions regarding this experiment.

Online instructions say to use 5g washing up liquid, 2g salt and 100ml tap water mixed together with a mashed up kiwi. Do I use a full kiwi ?

Instructions say to use coffee filter paper or a fine sieve. Would laboratory filter paper work or would it be too fine ?

Also, how can I improve on this method to get maximum yield etc ? All advice and suggestions welcome.


texts: How does heat generated by metabolism differ compared with heat generated through exercise?

texts:
I am from a mathematical background so I don't have much knowledge on biology. I'm building a mathematical model to predict heat generation with parameters of metabolic heat generation and exercise heat generation.

Metabolic heat generation as far as I understand is the heat produced through body's chemical processes, digestion of food, and elimination of waste.

In this article here, the value for metabolic heat generation is given as 33800$W/m^3$. But the exercise intensities as given here only has values of around $582 W/m^2$.

I think we produce more heat when we exercise than through metabolic activities alone. Is this correct?

If so, why does this huge difference in values of 33800 and 582? Why would the heat generated via exercise be such a low value? (Of course they are not measured in same units.)

Is there any other unit other than $W/m^2$ that measures the heat generated through exercises so that it gives a resonably at least closer value to metabolic heat generation?


texts:
I have observed many times that ants are able to reach the box where sweet items are kept even if the box is kept in secret.
How do they identify it??


texts:
An eyespot is a marking to mimic the eyes. Many examples of eyespots can be found in fish, reptiles (including birds), and insects. Recently Radford 2020 has shown that artificial eyespots can reduce predations in cattle. However, apart from cats (tigers and servals), mammals, especially herbivores, rarely have this trait.
Why does mammals rarely have eyespots?


texts: How can facultative anaerobes exist without catalase?

texts:
Catalase-negative bacteria may be anaerobes, or they may be facultative anaerobes that only ferment and do not respire using oxygen as a terminal electron acceptor

  A facultative anaerobe is an organism that makes ATP by aerobic respiration if oxygen is present, but is capable of switching to fermentation or anaerobic respiration if oxygen is absent

But if facultative anaerobes can be present in oxygen rich environments, don't they have to have catalase in order not to die?


texts: I found a singular mushroom in my back yard,  It is jet black, seems to have gills and looks somewhat like a flower do to it's upturned-ness. Sorry for not having spore colors, but I didn't want to disturb it. I will post a picture soon. I found this mushroom at 4/11/15 and it disappeared the next day. I'm just south of San Antonio.


texts: How to grow fibroblast colonies from single cells?

texts: I need to establish a cell line starting from single cells seeded on a 96 wells plate by a FACS sorter. The cells I am using are human fibroblasts RPE-1 cultured in F12 medium supplemented with 10% FBS and antibiotics. After having seeded 5x96 cells (one cell per well in 5 plates) I have obtained only 4 colonies. Does anyone know any good (preferably personally tested) protocol to efficiently grow fibroblast colonies from single cells?


texts: What biological specimen is this? Seed? Excrement? Fungal form?

texts: Hundreds of these 1-3 mm "seeds" have been found a couple of times this summer on my deck shaded by a large oak tree. But, they are not seeds with typical seed parts.  Too small to be pollen or spores.  I am baffled. They each have one or more deep crevices or slits longitudinally. Structurally, they appear to be composed of tiny (almost microscopic) wood chips. (Though I am sure this is just the appearance they have.) The first time I found them was after a rain and they had absorbed water and swelled to twice or three times their size and had become gooey and almost gelatinous to the touch. Almost looked like hundreds of little piles of brown poop on our deck. This time the weather was dry and they look as pictured in the photo.  I swept up hundreds in a four-foot diameter area.  Another area of the deck had a similar amount.  None on the rest of our deck or any noticed in other areas under the oak tree. My biologist friend was also baffled.  Please help identify


texts: What are the differences between HPRD and BIOGRID databases?

texts:
What are the differences between HPRD and BIOGRID protein-protein interactions databases?

What are their purposes? Why do we need two different databases?
How is data collected into each one?
How different are they in the interactions they contain?
Is one considered more reliable than the other?
Which one is more commonly used when benchmarking models?
Are there any other commonly used PPI databases?


texts: How to anaesthetise mosquitoes during a mass-trapping field study?

texts:
Do any of you have experience in anaesthetising mosquitoes during a mass-trapping field study?

Normally, mosquito traps have a little net in which you catch the mosquitoes. The nets can, after collection, be placed in a freezer to knock out the mosquitoes. However, the trap used for my study doesn't have a net, so mosquitoes will fly around inside the trap.

I thought about using Ethyl Acetate to knock out the mosquitoes, however, the trap needs to stay clean of odours, so that's not an option. I think using CO2 would be most convenient, but I will not be able to drag a big CO2 cylinder to all my trapping locations.

Is it maybe possible to use CO2 tablets which can be dissolved in water? I could then use a plastic bottle where the cap is connected to a tube, which I can place in the trap. Would this be efficient? What do you think?

Thanks a lot!


texts: Why does the formula for blood velocity hold true?

texts:
v = Q/A
where
v = velocity (cm/s)
Q = blood flow (ml/s)
A = cross sectional area (cm2)
So the greater the cros sectional area, the lower the velocity, assuming that the cardiac output is a constant for a individual.
But i dont understand the formula content wise, why do you get the velocity by dividing Q by A? I do understand that the units are correct, and you get cm/s as final unit.
Can anyone explain this, perhaps graphically?

In the capillaries the A must be extremely low, yet why is the velocity so small? My book says that you have to add all capillaries up, but you cant do that, since you would get the velocity of an extremely big pipe, which isnt that of a capillary?
Thanks in advance for answering.


texts: Why are truncations in Receptor Tyrosine Kinases so sommon in transformations?

texts: Receptor Tyrosine Kinases (RTKs) present themselves on the surface of a cell as monomers until a ligand (such as a mitogen) binds and causes the formation of the active dimer. However I do not understand why truncations are so commonly seen in retrovirally delivered oncogenes or in oncogenic mutations. My confusion here is that if mitogen binding of RTKs facilitates the close proximity of two monomers, then simple overexpression should allow for increased transphosphorylation of monomers, and therefore be mitogenic (which it does). But then what advantage would a truncation that removes the extracellular portion of an RTK have in increasing transphosphorylation of monomer units?


texts: Are there land animals that use gill-like organs instead of lungs?

texts:
Among aquatic, water-breathing animals, gills and other continuous-flow breathing methods dominate over lungs and other storage-based breathing methods as in land animals. Notably, axolotls have gill-like structures around their heads which use a high surface-area structure heavily vascularized with capillaries to breathe water.

However, it seems all air-breathing organisms use storage-based breathing, air-breathing fish included, as lungfish use their swim bladders as lungs, a clear example of storage-based breathing.

Are there any land organisms that use continuous-flow breathing methods over lungs?


texts: How does a virus stick to a non-biological surface?

texts:
Recent events has triggered an renewed interest in understanding how a virus is able to stay on a surface.

For sake of argument, let's assume we are dealing with a Corona-type virus. One can then speculate that a virus sticks to a (non organic) surface due to a London-force (a Van der Waals force) interaction between the surface and the virus Spike S protein. But I really have no idea and it's just a wild guess.

I'm looking for research and experiments on this topic but I can't find any, most likely because I am not asking Google the right question or using the correct biology language.

How does a virus stay attached to a non-biological surface?
(Are there any "stickiness" measures for this?)

PS. When I say non-biological, I mean glass, metal and plastic.


texts: Can upper motor neuron lesions cause hypotonia?

texts: I have been taught that hypotonia is always caused by lower motor neuron lesions while hypertonia is by upper motor neuron lesions. However, I recently learned of an entity called central hypotonia, which means hypotonia caused by a central nervous system lesion. This makes it so confusing.


texts: How does a garlic clove thrive inside a closed refrigerator?

texts:
A garlic clove has been growing very well inside a closed refrigerator.

It has developed beautiful green stalks, which I think are the equivalent of leafs.  Since they are green, I assume they contain chlorophyll.

Without any source of sunlight (for photosynthesis) or soil (for nutrients), how can such a plant thrive so well?

Is it simply growing off the internal stored energy of the clove itself?

Will it continue to grow without sunlight and soil?


texts: Reference request - A complete step-by-step explanation of meiosis, inheritance in humans and epigenetics

texts:
I am a medical student and as such had contact with lots of superficial and bad biology/biochemistry literature. I have searched the internet for introductory articles, searched youtube for video lectures, they all fail at various stages!
What I want: I want a readable, logically-coherent and precise description/explanation of meiosis and a description of human inheritance, preferably in book-form and in one book. I want definitional precision, lots of my textbooks cannot even distinguish coherently between chromosomes and chromatides. Because of that, it took me quite some time to understand that "same" in "the same genes on homologous chromosomes" refers to sameness on a type-level not token-level. I have heard that Bruce Albert's book would be the right choice, but the price is hefty and I have grown skeptical of student literature.
Why I do not trust wikipedia but ask here? This supposed example of epigenetics:

"In a groundbreaking 2003 report, Caspi and colleagues demonstrated that in a robust cohort of over one-thousand subjects assessed multiple times from preschool to adulthood, subjects who carried one or two copies of the short allele of the serotonin transporter promoter polymorphism exhibited higher rates of adult depression and suicidality when exposed to childhood maltreatment when compared to long allele homozygotes with equal ELS exposure."

Call me stupid, but that sounds more like an example for a disposition to develope depression rather than an example of epigenetic inheritance. And for this reason I do not trust wikipedia on that matter.
Questions I want to have answered (by the book/requested reference):

In diploid organisms, if both alleles are different but neither is dominant over the other, what determines at what rate each protein is produced? What if the two alleles are co-dominant? Is it always fifty-fifty?

How do dominant genes repress the gene products of the same, recessive gene of the homologous chromosome?

A precise description of epigenetics!  What it is and what it isn't! Listening to my lecturers (physicians,medical school!) I get the feeling that with epigenetics "anything is possible" which I don't buy. How does

How does genomic imprinting work? By that I mean not so much the underlying molecular mechanism but its consequences on phenotypes of future generation. From my lectures one could conclude that Lamarckism is back, and I doubt that! I read somewhere (Jerry Coyne's blog) that genomic imprinting only lasts a few generations, otherwise it would seriously undermine natural selection as a mechanism of evolution and I can see that.

(A question I would like to have answered in this thread): According to my superficial lectures and German wikipedia, genomic imprinting can be understood as parent-specific expression of genes. Furthermore, there are certain alleles that under genomic imprinting can be either recessive, if inherited from the mother, or dominant, if coming from the father. Now, what if such an allele is located on the father's y-chromosome? Under the assumption that the father has a healthy son and that son has a son and that son has a son, and so on, it seems to me that there is no end to this kind of inheritance and genomic imprinting, contra Jery Coyne, can last indefinitely. Where am I wrong?

I hope you can guide a frustrated med student to some sort of understanding!
All the best!


texts: When running a gel, what could cause a standard to run "faster" than usual?

texts:
We are running a gel on the products of a restriction digest to determine the size of an insert. We know the vector backbone size should be ~2.9kb; however, the standard appears to be running too quickly (or our samples too slowly), causing the backbone size to be about 4kb (which distorts our results for the insert size).

What could possibly cause this? Thank you.


texts: Anybody know which traits of bird plumage are accurate indicators of a birds health? For example feather coloration, feather brightness, amount of feather wear, number of feathers, moult timing, moult duration etc.


texts: What is the necessary criterion for the maintenance of signaling honesty?

texts:
Zahavi's (1975, Journal of Theoretical Biology) handicap principle held that the cost associated with a signal is integral to ensuring that signal is accurate, since dishonest signals would be too costly to bear.  Grafen (1990, Journal of Theoretical Biology) held that in order for signal honesty to be maintained, the signal must be differentially costly, such that it is more expensive for lower-quality individuals.  Getty (2006, Trends in Ecology and Evolution) disputed this:  "Here, I show that (Grafen's) most well known and
influential result (‘the marginal cost of advertising.
should be greater for worse males’) [6], which is widely
interpreted as a proof of the handicap principle, is based
on a simplifying assumption that does not generalize to
signalling in sexual selection. I show that the general
criterion for reliable signalling can be interpreted to mean
that higher quality signallers must be more efficient at
converting signals into fitness and that, in sexually
selected signalling, higher quality signallers can be more
efficient in spite of higher marginal costs."

Nevertheless, Biernaskie, Grafen & Perry (2014, Proceedings of the Royal Society) wrote, "It has long been a challenge to test for the relevant costs of
animal signals [2,17,18,25,42]. This is because, as stressed
above, the modern view of costly signalling theory does not
necessarily imply that observed signals will be costly;
instead, the key prediction is that a given signal size will be
differentially costly for low-quality individuals [2,13,17,31]."  The criterion of differential costliness continues to be invoked despite Getty's critique of it.  So, my question is, what is the criterion necessary for the maintenance of signal honesty?

Note:  This question asks about the maintenance of costly signals that could theoretically be faked, not so-called index signals that cannot be faked.


texts:
This question is from a genetics session in my university:

The test cross between a plant with smooth and yellow seeds and a plant with wrinkled and green seeds gives the following results: 140 plants with smooth and green seeds, and 142 plants with wrinkled and yellow seeds.
These results are consistent with which case of the following?

Linked genes
Epistatic genes
Genes with intermediate dominance
Genes with complete dominance and independent assortment

In my answer key the correct choice is linked genes.

What I know is that in the case of linked genes, the outcomes are: either all parental (complete linkage) or the majority of offspring have parental traits and we have few recombinants(partial linkage).

But here it seems like all offspring are recombinants?! How can this be? Is there a mistake in the question, in the answer, or in my information?

Any help is appreciated. Thank you.


texts: What impacts penetrance of Huntington's disease?

texts:
From Principles of Life by H. Craig Heller, David E. Sadava, Mary V. Price:

From what I understand, Huntington's disease exhibits varying degrees of penetrance depending on how many times the mutation is found in the person's genome. Penetrance is nearly complete if the incorrect base pair sequence is found over a certain number of times.

My question is what affects penetrance? Is it exclusively environmental?


texts: Why does caffeine consumption cause one to urinate more?

texts: What is the physiological mechanism behind the diuretic effect of caffeine?


texts: Can one derive COVID-19 risk from a cheap consumer genetic test like 23andme?

texts:
Studies have found genes associated with a significantly higher risk of severe COVID-19, some of them claiming it to be 1.6 times the general risk.
They mention genes at markers such as rs35044562, rs1129183, rs679599192 to be significant.
Can people use the raw data from a consumer-grade genetic test like 23andMe to assess their risk, at least theoretically? The raw data has many gaps and the markers and their positions may not be included in the data. Can one then look at markers at positions close by, or at other markers? Does a more rare genotype imply higher risk?
Articles

https://www.nature.com/articles/s41586-020-2818-3
https://www.biorxiv.org/content/10.1101/2020.11.02.365551v1.full.pdf


texts: Using decoy proteins to treat viral illness

texts:
As a non-biologist, my understanding is SARS-CoV-2 uses it spike protein to latch on to the ACE2 receptor on cells in order to inject its genetic material into the cell.

Questions:

What would happen if you flooded a person with exogenous ACE2 proteins?
Would the virus attach to these decoy proteins and thereby save cells from being infected?
Would the injected proteins cause unwanted side effects?
Has this approach to treating viral infections been tried before?

Reference:
https://f1000research.com/articles/9-72


texts: What is a phospho-protein binding domain?

texts: Is this just a domain that binds proteins that have been phosphorylated? And it mediates signalling between an activated/phosphorylated protein? How is this significant with BRCA1?


texts: Difference between vacuolar and symplast pathway

texts: what is the difference between Vacuolar  Pathway and Symplast Pathway ? Is the symplast pathway does not take into account the vacuole to vacuole movement?


texts: What test to apply to detect genomic signatures of selection?

texts:
I would like to ask you for your sugestions for selecting a test to detect signatures of selection in the following mouse model:

We have three groups: animals exhibiting trait A, trait B and controls. These animals were selected over the last 4 decades (controls were mated randomly and do not show any of the traits). That is total 170 generations (~4 generations per year).

We want to detect the genomic signatures of selection for trait A and B.

I am new in population genomics, but according to this paper (http://www.ncbi.nlm.nih.gov/pubmed/21218185), showing a desition tree (fig 1). I should apply a the Fst and a Linckage 'Desequilibrium test, given that the time scale would be short (40 years, 170 generations) and there are multiple populations.

Could you corroborate if this is the correct approach?

Thanks


texts: Is the tip of the temporal lobe the "top" of the brain neural tube?

texts: The neural tube that forms the central nervous system forms around a cavity that becomes the ventricular system. Is the end of the lateral ventricles in the temporal lobe the top of this original neural tube?


texts: What is this insect in Southern Colorado?

texts:
We have found this insect in a bit of a swarm on a concrete pad and on some insulation next to and around our greenhouse in which we have tomato plants.

The insect is about 2mm wide at its widest, and 4mm long at its longest.

What is it?


texts:
According to several sources, Coronavirus is a helical virus, i.e. it should have a helical capsid. Although most sources did not labelled or pointed any kind of capsid. It was mysterious to watch diagrams of spherical envelops with no underneath capsids.

Cutaway view of coronavirus from Wikipedia

David Goodsell painting on PDB

No mention of capsid.

Initially I guessed the proteins around the RNA fibre formed the capsid, not labelled otherwise. Alternatively I was speculating whether coronavirus is lacking the capsid.

However a researchgate paper picture (heavily diagrammatic) shows a polygonal capsid, the picture is captioned as coronavirus.

It makes me think of whether the capsid is like a hollow spherical or polygonal thing spirally wrapped.

Now my questions are .

What is the actual/ realistic shape of coronavirus capsid?
Does it really contain a capsid?
(Just speculating) Is it SARS-CoV2 lacking a capsid, and thus special exception from g eneral description of coronavirus?


texts: BLAST 16s rDNA: Everything alligns to Bacillus sp

texts:
I'm trying to identify and isolate Pseudomonas and Bradyrhizobium strains from rhizosphere and endophytic compartments of a tree. I plated the strains on selective media (King's B. for Pseudomonas and YEM for Bradyrhizobium) and purified the colonies grown by picking them and let them grow on separate plates. There is a lot of variety in morphologies.

When I had grown colonies of bacteria and was able to pick up single colonies I did a 16s rDNA pcr reaction on the colonies. After sequencing the 16s rDNA sequence I did a quick BLAST search to annotate the sequences and thus the bacteria to a species. But from all colonies till now (already 25 reactions sequenced) I only found that they allign best to Bacillus. I think this is strange because there should be a lot of variety according to their morphology.

Does anyone has a solution for this? Is it, for example possible to exclude the Bacillus group from the BLAST search? Or does this mean my colonies are still contaminated?

This is probably not enough information to answer my question but maybe you have experience with doing this and have some ideas.

Thanks!


texts: Clustal Omega - convert from distance into # of substitutions

texts:
I have a set of nucleotide sequences for which I have aligned using Clustal Omega. In particular, I performed a full alignment, and obtained a full distance matrix.

The distance matrix scores range between 0 and 1. I am looking to use this score to back-compute the number of different positions present in the alignment. Is this possible? If possible, I'm looking to avoid using code (my own or otherwise) to re-compute the number of positions differing between each pair of segments, and instead compute it directly from the distance score.

Here is a toy example of what I am receiving from ClustalOmega:

Sequence    1    2    3    4
1           0    0.1  0.06 0.1
2                0    0.4  0.23
3                     0    0.05
4                          0

The numbers are the "distances" as calculated by ClustalOmega. According to the README file, they are computed by the k-tuple measure. I tried parsing the original paper (published in 1983 in PNAS), but I could not figure out how k-tuple distances are computed, and I could not figure out how the distance metric (as reported like above) is computed from k-tuple distances.

I would like to convert those numbers into the number of positions that differ between each pair of sequences when the two are aligned. This includes substitutions, insertions, deletions. I am currently doing this for 520 sets of virus sequences. Is this possible?


texts:
I am fascinated by the fact that an amputee can control their robotic arm by thinking of the actions they would normally execute when the limb was present.
The mind sends signals to the nerve endings of the amputated limb, which gets picked up by the robotic sensor to perform actuation. Can we send similar signal if we assume we have additional limb (Say a third hand)?
E.g. A phantom hand attached to certain part of our body or is it bit of a stretch. Can we train our mind to control a Phantom hand we never had?


texts: Why were wisdom teeth not eliminated by evolution?

texts: Supposedly evolution was very efficient and evolved many human proteins over a few thousand generations. Yet obvious detrimental traits like wisdom teeth remained. Why?


texts: Infectious deadly disease among free animals?

texts:
Sorry for the presumably naive question, I'm not a biologist and searched for that but didn't find a clear answer to this question.
What I would like to know if deadly infectious diseases are common also among free animals (I mean living free in nature, not in captivity)? Therefore I'm NOT referring to the transmission from animals to humans like covid, bird or swine flu, rather infections that have caused several deaths among animals living in a natural environment without affecting humans? Is that something quite normal in the animal kingdom too? Presumably also before the appearance of humans? Or does it not happen? Or is it rare but exists? Eventually a link to some article or paper on this would be welcome.


texts: Why am I getting low transformation efficiency with DB3.1 E.coli cells?

texts:
I am making competent cells using DB3.1 E. coli cells. Even after following the exact protocol (Inoue method for ultracompetent cells) given in 'Sambrook and Russel', I am not getting transformation efficiency of more than 104. I am using a 5.1kb plasmid for checking transformation efficiency.

I will be thankful if any of you can share your experience in this experiment.


texts: Experimental Analysis: What are possible reasons for this increase in N₂O production?

texts:
My professor wanted us to each conduct an experiment for class on something we thought would interesting. My experiment was very simple, but I'm not sure how to interpret my results. (Please note that this is not for homework – I'm just genuinely confused and trying to understand the data.)

Basic method:

Take soil samples, add varying concentrations of Roundup and water equalling a total of 50ml, seal in airtight jars, incubate for 7 days, run through a Gas Chromatograph, and record the rates of production for CO2, CH4, and N2O. Overall, there was the Control and then three treatments, for a total 8 jars because each had a duplicate:

Control (Roundup: 0, H2O: 50ml),
T1 (Roundup: 10ml, H2O: 40ml),
T2 (Roundup: 25ml, H2O: 25ml),
T3 (Roundup: 50ml, H2O: 0).

I expected the Control to have the highest levels of production, followed with a decrease in production for T1, followed by T2, and then T3, with T3 being the lowest because all microbial activity was inhibited by the massive dose of Roundup.

However, the results were a bit surprising.

In general:

The Control rates were the highest, as expected.
T1 showed a decrease in production, as expected
T2, again, showed a decrease in production, as expected.
And then T3 showed a significant increase in production.

Here are some graphs to illustrate this in more detail:

This is a new field of science for me, so forgive me if I'm missing something obvious, but my natural intuition is certainly not helping me out on this one. What are some possible causes for this increase – in particular for the N2O/denitrification? Or at the minimum, are there any particular resources I can take a look at to better understand why this happened?

Edit

This is my brain on paper, so forgive me again for any ridiculous things I say. But, could it have something to do with the denitrification process such that more gas is given off as N2O because the microbes responsible for processing the N2O into N2 have died. So in the previous Treatments 1 and 2, the N2O was lower because the N2O was being converted into N2 (but we never recorded the N2), but in the final treatment, no conversion occurred, so the N2O appears to go up, even through the microbes are functioning even less.

Thoughts?


texts: How do some plants grow in salt water, while others die?

texts: My question is basically out of curiosity and comes from observing how certain plants (such as mangroves or salt cedar) can grow in seawater. If this gives the plant an advantage, why haven't all plants that grow in coastal areas developed a salt tolerance? How can the plants keep from intaking salt, while absorbing other soluble nutrients through the roots?


texts: What advantage would the initial 'donor' in horizontal gene transfer by conjugation have received?

texts:
I am struggling to think why horizontal gene transfer between bacteria would have persisted during the course of evolution as surely it puts the 'donor' at a disadvantage?

For example, consider a hypothetical situation where only one species of bacteria has a gene to resist a new (almost) omnipotent antibiotic.  When growing on this medium, this species of bacteria has nil inter-specific competition for the resources it needs.  Yet if it passes on the plasmid containing the resistance gene via conjugation to individuals of a different bacterial species, they then too are able to grow on the medium and potentially out-compete the first species - thus the conjugation could possibly be extremely detrimental to the survival of the original population.

I'm obviously missing something as the feature has persisted, so what is the advantage to the donor species of conjugation?


texts: At what rate does C-BSE occur spontaneously?

texts:
BSE is back in the news here in the UK thanks to a new detection in Scotland. I haven't looked into transmissible spongiform encephalopathies much for a decade or so, but as I understand it the general model for TSEs is that an initial spontaneous misfolding of the protein PrP catalyses the misfolding of other PrP proteins until (over a fairly long incubation period) spongiform structural changes, amyloid plaque formation and other pathological changes cause CNS disease typically manifesting as behavioural changes. Ingesting a dose of misfolded protein can infect new hosts of the same species, and thus farming practices which include feeding animal byproducts to the same species can inadvertently amplify transmission, which resulted in the BSE epidemic in the UK back in the 1990s. Rarely, this transmission process can cross the species barrier.

I can find references to spontaneous scrapie in sheep and spontaneous CJD in humans, but very little on classical BSE in cattle. I do remember that there was a theory that BSE orginated when cattle were fed meat-and-bone-meal (MBM) from scrapie-afflicted sheep. I have found one peer-reviewed article suggesting that at least one type of atypical BSE (H-BSE) can occur spontaneously. I have also found one popular-science article that sounds like it describes spontaneous BSE, but it's unclear whether this is C-BSE or the H-BSE finding above (it's behind a paywall) and it's over ten years old, so I don't know what further developments there have been in this area.

Can classical BSE (C-BSE) arise spontaneously in cattle populations, and if so at what rate?


texts: Can one conduct “novel” research without an advanced laboratory? Has it been done by school pupils?

texts: I want to conduct an experiment but as a secondary school pupil I will be using my school’s laboratory and to make novel or interesting discoveries, wouldn’t one need advanced equipment, a prospect which is not feasible for one of my station in life? I want to know if anybody has done a simple experiment and discovered anything new? Thanks.


texts: How can eyeglasses improve vision beyond 100%?

texts: The result of a vision test by my oculist yielded a result of more than 100% while wearing prescription glasses. I wonder, how can a person see better using eyeglasses?


texts: Do plants with non-green leaves have chlorophyll and photosynthesis?

texts: Is it even possible that plants with non-green leaves have chlorophyll, and do such non-green leaved plants carry out photosynthesis?


texts:
I came across this washed up fish in Panama City, Florida in November 2015. I'm guessing it's a puffer fish but I can't find anything like it online.

Thanks.


texts: Scientific name of a lizard's reproductive system

texts:
I need to find the scientific (latin) names of the reproductive organs of female and male lizards. So far the only result I've got is that male lizards have hemipenes inverso, but nothing on the female part.

Thanks for the help!


texts:
I have a very tricky question....all the veg and fruit

cells contain cell wall and it is made of cellulose when we eat how our body digest though we

don't have the enzymes to breakdown 1-4 beta glucose sugar?


texts: Non competitive inhibitors and Uncompetitive

texts:
Non competitive inhibitors affects the function of enzymes and slows the rate of reaction. Can I say the same for uncompetitive inhibitors ? Because Vmax decreases and it takes longer to form products .

However when I plot the graph both gradients needs to be the same ? So I'm a little confuse here to whether for uncompetitive inhibitors, it does affect the function of enzymes and slow down the rate of reaction .


texts: Why do animal cells "mistake" rubidium ions for potassium ions?

texts:
So, I was browsing the Wikipedia article for rubidium, and came across this interesting tidbit:

Rubidium is not a known nutrient for any living organisms. However, rubidium ions have the same charge as potassium ions and are actively taken up and treated by animal cells in similar ways.

This immediately struck me as interesting, and a completely wrong explanation, as all singly-ionized ions have the same net charge.
Now, from my basic understanding of chemistry, elements of the same group have the same valence electron structure, which accounts for much of the element's chemical effects. And if you look at the periodic table, sure enough, rubidium falls below potassium, in the Group 1 alkali metals.

But, from my old memories of basic biology, even saying "these elements are vertically adjacent on the periodic table" is an incomplete explanation, because, for example, the body has no problem "telling apart" sodium from potassium, or plenty of other vertically adjacent elements.
A survey of other potentially relevant features reveals the calculated radius of rubidium (265 pm) is relatively close to the radius of potassium (243 pm), and the first ionization energy of rubidium (403.0 kJ/mol) is also pretty close to that of potassium (418.8 kJ/mol). So they do seem fairly similar, but question still remains, how "similar" does an element need to be to become a biological proxy?
This leads to me to the following questions:

Why does rubidium act as a biological proxy for potassium? Also:

Why is cesium also a decent, but less good, biological proxy for potassium?
Why is potassium not a biological proxy for sodium?

If rubidium acts as a biological proxy, why is it still not a "nutrient" and not considered to play a biological "role"?
Which other sets of elements can act as biological proxies for each other? (I presume expanding this question to molecules yields too many answers to be useful.)
Is this rubidium-potassium proxy effect specific to animals or to all life?

Some good references I've found, skimming the literature (I started by looking at some references in this article):

Relman AS. The physiological behavior of rubidium and cesium in relation to that of potassium. Yale J Biol Med. 1956;29(3):248–62.

Relman notes that this phenomenon was first noted by Sydney Ringer in experiments begun 1882, published in the Journal of Physiology in the year 1884 (or so).

Fieve RR, Meltzer H, Dunner DL, Levitt M, Mendlewicz J, Thomas A. Rubidium: biochemical, behavioral, and metabolic studies in humans. Am J Psychiatry. 1973;130(1):55–61.

But I'd rather someone present an intuitive explanation for this before or after I attempt to dive in.