texts: What are the most important factors influencing a person’s gut microbes?

texts:
You are your bacteria! The probiotics and the antibiotics...

There has been on going discussions about how our gut bacteria is important for a healthy lifestyle.

  Figure 1: Schematic diagram illustrating potential or known mechanisms
  whereby probiotic bacteria might impact on the microbiota. These
  mechanisms include (1) competition for dietary ingredients as growth
  substrates, (2) bioconversion of, for example, sugars into
  fermentation products with inhibitory properties, (3) production of
  growth substrates, for example, EPS or vitamins, for other bacteria,
  (4) direct antagonism by bacteriocins, (5) competitive exclusion for
  binding sites, (6) improved barrier function, (7) reduction of
  inflammation, thus altering intestinal properties for colonization and
  persistence within, and (8) stimulation of innate immune response (by
  unknown mechanisms). IEC: epithelial cells, DC: dendritic cells,
  T:T-cells. For further details, see main text.

Also, an online search provides numerous articles about diet aspect that alters our gut bacteria.

e.g.

1.A New Diet Quickly Alters Gut Bacteria-(not sure about the credibility and relevance to humans as the study is on mice)

2.Artificial Sweeteners Change How Our Gut Bacteria Work, Paving The Way To Diabetes And Obesity

3.Changing gut bacteria through diet affects brain function

As far as the GIT is concerned, health, lifestyle, eating habits and the environment a person is living may be at large influence and affect one's gut microbes.

Are there day to day encounters, in-depth examples and references that can prove the factors which influence our gut microbes the most?


texts: Book Recommendations: GRE Subject Test In Biochemistry, Cell And Molecular Biology

texts:
There are probably a lot of really good answers that may vary significantly in terms of content.  I'm looking for a set of books that I can read in preparation for the GRE Subject Test In Biochemistry, Cell And Molecular Biology.  I have a Bachelors of Science degree, but never really studied any of the material on this exam (it's in a field which is not really related).  I'm interested in applying for a doctoral program in Biology, and would like to add something to my application so that it doesn't appear to come out of "left-field", as they say.  When I look at the questions from the sample exam in the link above, I can't tell whether they are introductory in scope or would require advanced study in particular areas.  Could somebody recommend a set of textbooks that would cover all of the ground for this test?  If one textbook exists which is sufficient, that would be wonderful, but I'm guessing that multiple texts will be required.  My goal is to learn the material necessary to do well on the exam as thoroughly as possible.

As an aside, I tried looking for study materials in online bookstores, but wasn't able to find anything that consistently got good reviews.  I don't think Princeton Review or Barron's have books on this subject, unless I overlooked something.  At any rate, I'm okay reading through a set of undergraduate university textbooks, but I really have no idea which ones would be good.

Thank you in advance!

Edit:  I just changed the word "efficiently" to "thoroughly".  Sorry about that...  This more accurately reflects the goal.


texts: Are there any examples of proteins with no or minimal sequence identity, but highly similar structure?

texts:
What are they, and do they share a common ancestor? How far back in evolutionary time must we go to find them?

If none are known, what computational tools might be used to search for such examples?


texts: What does phasing mean in genetics/informatics? I've heard that a phased file is a file that has genes separated by chromosome, but can someone give a concrete definition of what phasing actually means?


texts:
What is supposed to fall under the title Bionomics (The study of an organism and its relation to its environment; ecology.)?

Suppose we are dealing with a vector, Anopheles sp. are the following going to be included in its bionomics:

Life cycle
Interaction with parasite (Plasmodium sp.)
Mode of transmission of parasite by this vector
Control
Diseases caused ?


texts: Can antibodies be formed against white blood cells after blood transfusion?

texts: If antibodies are produced against other blood groups' red blood cells, why can't antibodies form against white blood cells, of any blood group? (even the same one, as MHC will be different in almost all individuals)


texts:
I've found it in my kitchen. It seems to be that he flew through the window from the street.

The country is Russia.


texts:
Uracil, the RNA base, has been replaced in DNA by thymine, (which has the same base-pairing with guanine). However the synthesis of dTTP (more usually written TTP) requires dUTP:

To what extent is dUTP (mis)incorporated into DNA?


texts: How does herpes (HSV) infection suppress HIV?

texts:
HIV compromises the human body to defend against infection. Yet people who are infected with herpes are at less risk of developing AIDS.
How does this work?
This question comes from this paper, which is hard for me to follow since I am uneducated on this field. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716975/


texts: Is there a specific terms to describe variant of existing genes in bacteria?

texts:
I have a question regarding a specific term that describes the variant of existing genes. I am analyzing whole-genome sequencing of a bacterial isolate. I found there are a large number of genes that have partial sequence identity or subject/query coverage to the known reference genes.

Now I know that by looking at sequence identity and coverage may not be enough to analyze the genes. I know some gene can have 30% sequence identity and still folded the same way as the original genes. However, let's say these genes are truly variant of the existing genes based off sequence identity. What is the term to call them?

My PI told me they are rapidly evolving genes. I searched some paper and found rapidly evolving genes are genes that are subjected to positive selection. While I agree for some of these are rapidly evolving genes as they probably subject to positive selection, I cannot see that all of the genes actually undergoes selection at same time. I am wondering if there is another term to call these gene variants. If there is any paper to define them that will be great.

Thanks


texts: Transfering Odds Ratios to another SNP with high LD?

texts:
I have the Odds Ratios (OR) for a particular risk allele in a SNP (I'll call it SNP1).  That SNP was unfortunately not genotyped in my data, but I don't want to throw it away.  I have looked up the SNP on LDLink and another SNP (I'll call it SNP2) is in high linkage disequilibrium with SNP1 (R2=0.94).

How do I transfer the OR from the SNP1 allele to the corresponding SNP2 allele?

I know it is something similar to log(OR)*sqrt(R2) but I'm not entirely sure.  Could somone please clarify if this is the correct formula?


texts: Is it the case that all changes in phenotype during life are not inheritable?

texts:
This came up in a talk with a friend. I wanted to clear this doubt. I've read about it before and did again after her remark (my thoughts didn't change: her concept is Lamarck's, not Darwin's), but wanted to clarify.

Regarding Evolution, nothing, absolutely nothing, that a person does to herself in life can be genetically inherited. It does not matter how much this person drinks, the changes they do to their body,  how dark their skin gets over life etc. Such changes can not be transmitted to their offspring in any way, correct?

*Summary:*Is the assertion "You can not change in life what will be genetically inherited in any possible way" true?


texts: Download FunCat Database for Programmatic Access

texts:
I am enriching RNA-seq data for the fungus Neurospora crassa and would like to be able to search the genome by functional category, determine similarity of genes by category membership, and any other information I find interesting in Python or R. There are many websites that have this information, but the most comprehensive appears to be Pedant.

I would like to download a SQL database, a JSON file, or even a text file that contains the information on these sites without having to use a web interface for everything.

The data I need access to is gene code, gene description, DNA sequence, FunCat category, GO category, and maybe others on the Pedant site.  Is there anyway to to programmatically access these fields or download all of them in bulk?

Note: I have been using the python bioservices module, but it only gives access to KEGG, which is missing information on many of the genes in the N. Crassa genome.


texts: What is the number of cells in a line of a fingerprint?

texts:
I have been reading a little about the size of cells and was curious as to how small they really were.

I have noticed that on my finger, the outlines of the fingerprint are made up of thin lines. In fact, some of them are so thin that I have difficulty imagining anything thinner I can make out with the naked eye.

I have read that the naked eye has a resolution of 0.1 millimeters = 100 micrometers, whereas eukaryotic cells range in diameter of 10 - 100 micrometers.

Putting this information together, would it be reasonable to conclude that the lines on my fingers have a width ranging from 1 - 10 skin cells? Is there any satisfactory method to verify this without fancy equipment? Is it even true?

P.S.

Are there also more scientific names for these "finger lines" so that I can look it up somewhere? Googling "finger lines" brings up a lot of stuff about palm reading.


texts: What are these caterpillars eating a potato plant?

texts:
I saw these caterpillars rapidly consuming a potato plant in Central Texas:

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

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

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

What are these caterpillars? How do you kill them?


texts: Do the primers used for Covid-19 test work with all new strains?

texts:
We keep reading news of new Sars-CoV-2 strains, some of them allegedly able to evade vaccine-induced Igs. That's not unexpected, specially for a single-stranded RNA virus. However, it seems to me that the tests (RT-PCR) are being done exactly as they've been since early 2020, all around the world.
Therefore, my question is about the primers used: how can we be sure that there are not new strains with sequences not complementary to the primers? Does the current covid19 test target highly conserved RNA regions? If that is correct, how do we know that those regions are highly conserved?


texts: Physiological indicators of happiness and well being

texts:
If I understand it correctly, levels of serotonin in the brain can indicate if a person is happy. What other physiological measures indicate happiness or well being for a humans?

I am looking for indicators which can be measured quantitatively but don't be very strictly correlated with 'happiness'. And on the flip-side is there physiological  indicators that a person is/not depressed?


texts: Which biological process causes the feeling of having "Butterflies in the body"?

texts:
If someone is under stress, he or she may feel a strange feeling in the belly; it can be said that he or she feels that butterflies spread through the belly.

For other emotional reactions like being in love, similar, but different feelings can be caused.

What causes this symptoms? Is it because of the muscle tension varies, is it an electric current through the nerves?


texts: Does anyone know good software for producing tanglegrams?

texts:
I'm trying to look at relationships between parasite and host phylogenetic trees. I have done a bit of searching for software with which to do this, and I have tried using Dendroscope and TreeMap, but can't get to grips with them.

I want to produce something along the lines of this;


texts:
Coming out of the pool the other day, I felt very cold because I was wet and the wind picked up. My idea is that a "cold" feeling should be associated with low temperatures, but it's indeed wrong.

Why do we perceive wind at a farely normal temperature as cold?


texts: What is the minimum water consumption for Arabidopsis and other plants?

texts:
I'm working on a project to design a self-contained plant growth environment for germinating and growing plants in space. It's important to know the absolute minimum amount of water and nutrients required to keep the plants alive and healthy over the course of 30 days, since we have very little space to store the water.
The plan is to use a single water reservoir to feed three separate growth chambers by injecting nutrient-rich water directly into a soil medium, similar to the ISS Veggie environment. We want to find out how much water we need to inject and how often.
I've looked over the literature as to what previous astrobotany projects have done. While they are typically very clear about the nutrient composition of the water, I have yet to find one that clearly states how much water the plants were given, and how often.
I focused my search on Arabidopsis thaliana to start, but ideally we would like to know water requirements for all major groups of small plants.
This seems like it shouldn't be a difficult question to answer. What am I missing?


texts: Are there examples of human genes using meiotic drive?

texts:
Meiotic drive is a type of intragenomic conflict, whereby one or more loci within a genome will affect a manipulation of the meiotic process in such a way as to favor the transmission of one or more alleles over another, regardless of its phenotypic expression. More simply, meiotic drive is when one copy of a gene is passed on to offspring more than the expected 50% of the time.

But do humans have such genes?


texts: What causes a polypeptide to fold into an Alpha helix over a Beta pleated sheet

texts: I know how they fold, but what causes some polypeptide chains to preferably fold into Alpha-helix rather than Beta-sheets (or vice-versa). What force makes it fold into one conformation over the other?


texts: Does an annealing temp higher than primer's Tm contribute to primer dimer?

texts:
I am attempting to reproduce results from a number of journal articles all referring to the same SNP. In doing this I'm using the same primer set outlined in the articles. When I attempted a run the other day I experienced what I can only assume was primer dimer (~40bp product, bands not visible at expected bps.) While the primers and restriction enzyme were the same among numerous articles, the annealing temperatures in the reaction varied a fair amount (52-59C). All were above the individual Tms of the primers which struck me as odd.

Calculating the Tm via primer blast here are the numbers:

Forward Tm: 50.14  [5'-GCTCTACTTCCTGAAGACCT-3']

Reverse Tm: 51.67  [5'-AGTCTCACTCACCTTTGCAG-3']

Other sites gave slightly higher numbers (54-55) but they are still below the 57C that I used in my reaction. I do not have access to a gradient thermocycler otherwise I would have tried a range myself.

If an annealing temperature is chosen above the individual Tms how do the oligos have a chance to anneal with the template and eventually extend? I remember hearing the Tm calculation is more involved and includes finding where the melting curve changes direction. But on the surfance I would think the primers would never have a chance to anneal at such high temperature? What is wrong about my interpretation?


texts: If rabies always kills its hosts, must there be some animal that is an asymptomatic carrier?

texts:
I searched a lot on the Internet, but I am not clear about the spread of the rabies virus. As I understand, rabies kills any animal it infects—cats, dogs, foxes, bats, humans. If it kills all of its hosts, then where does it stay?

So, if all rabies-infected animals die, but in order to transmit the virus, every rabid animal has to bite some other animal or have rabies without symptoms, must there be some animal that is an asymptomatic carrier?


texts: Using Height and Area for plotting histogram of each marker in FACS

texts:
I had a flow cytometry experiment. After normal filter with cell debris and doublet cells, I would like to gate the cells by different markers. However, I get confused to use which parameter to plot out the histogram/ scattered dot plot. More specifically, for each fluorescent channel, there are 3 options: height, width, and area. I know that width is only related to the cell size while height and area both correlate with the signal intensity. I would like to know which measurement (i.e. height or area) should I use to plot the graph?
Someone suggested that if I am analyzing different cell populations with different shapes/sizes, I should use the height. I wonder whether this is true.
Thanks!


texts: When gene editing are both chromosomes in a pair changed?

texts:
Sorry for the possibly confused question, my knowledge of genetics is limited to medical training only but I have a question.

Are gene editing techniques such as CRISPR used on both of the chromosomes in a pair or just on one of them?

Some of the general searching I have done suggests that it can hit one or both. Is there a preferred outcome?


texts: Identification of a segmented black insect in France

texts: Found in the Lot department of southern France.


texts:
This is an excerpt from a paper:

  T>C mutations at NpTpN trinucleotides, also found in hepatocellular carcinomas, shows strong transcriptional strand bias with more T>C mutations on the transcribed than untranscribed strands

What exactly is meant by "transcribed" strand: the sense strand or the template strand ?

I tried looking up for it but couldn't find any definition.


texts:
A common question posed is, "how did the eye evolve?", because the eye is so complex.  However, this has been answered rather clearly and there are several examples around the world of animals in which the eye has evolved independently.

The human brain, however, only seems to have evolved once in the history of life on Earth - a brain which is capable of advanced speech, predicting the future given information on the past, producing art, imagining advanced abstract concepts such as algebra, creating advanced tools, etc.

How, then, could the human brain have evolved?  What stimulus was there for progressive Homo individuals to have brains that were slightly more advanced than the previous one's?  I've heard Richard Dawkins summarize it as "big brains are sexy", but that's a comment made in hindsight (and not even shared by all members of the human species today!)  At the time, why would a human female choose a male with a slightly larger brain, so slightly larger that the increased intelligence probably wouldn't be noticeable?  Or why would such an individual have an evolutionary advantage?


texts: Difference between taking tissue of cancer from secondary place or primary place

texts: Are there any differences when a surgeon takes tissue from secondary place (for example from metastasis) rather then from primary place (from an organ where cancer is) for morphological research?


texts: How does the sensitive plant detect vibrations?

texts:
The sensitive plant (Mimosa pudica) is a remarkable little plant whose characteristic feature is its ability to droop its leaves when disturbed:

Apparently, this ability to droop rests on the cells in the leaves of the sensitive plant being able to draw water out of themselves through changes in intracellular ion concentrations, which makes the leaves less turgid.

What I'm hazy about is how the plant "senses" vibrations. Plants don't really have a nervous system to speak of; how then does the sensitive plant "know" to droop when disturbed?


texts: Recently, I have been reading Janeway's immunobiology and had a question on immunoglobin A. I read that IgA activates the complement pathway using the Fab fragment of the IgA. How does IgA do that? I can't seem to find an information on that in  the book or online.


texts: What neurons' projections comprise the olfactory nerve (Cranial Nerve 1)?

texts:
Recently, I have been learning about olfaction. To my surprise, I am having a heck of a time finding explicit information regarding which neurons' axons are comprising the olfactory nerve. I am aware that there are several cells types that are relevant in the olfactory bulb: mitral cells, olfactory sensory neurons, tufted cells, and many more. However, I have not been able to find any source that definitively states from which neuron type the projections that comprise the olfactory nerve arise from.

I keep seeing articles that seem to imply olfactory sensory neurons comprise the olfactory nerve, but this doesn't seem right to me. My understanding is that the projections that emanate from the olfactory bulb and terminate in the brain constitute the olfactory nerve. The only thing I can think of is that the "olfactory bulb" is actually being considered "part of the brain"...in which case, the olfactory sensory neurons are technically peripheral neurons.

If that is the case, what exactly are the olfactory bulbs? Are they part of the telencephalon? Are they an outgrowth similar to how the optic nerves are outgrowths of the telencephalon and therefore not "true nerves"?


texts: Chromosomally different D. melanogaster sperm

texts: I know that D. melanogaster have 4 pairs of chromosomes and crossing over is absent in males. Denoting autosomes as Ai,j where i is chromosome no. and j are homologues (1 and 2) I am solving the total no. of chromosomally different sperm as 8. I am assuming it as 2x2x2. Can anyone verify my answer?


texts: Why do hair on head not get pilo-erected?

texts: Whenever we have "goosebumps", there is a momentary piloerection, due to which hair on our elbows and legs get "erected" and "stand" almost perpendicular to the surface of our skin. But why do our "head hair" not get erected ?


texts: Help identifying what this is in Crayfish gills?

texts:
this is my first time posting here. I was in my Zoology lab doing a dissection on a Crayfish when I noticed these hairlike structures within the gills. They were very "snappy" and fine, and would break off if I pulled hard enough. I put some on a wet mount under a dissecting microscope, but my Lab prof and the parasitologist could not identify it. We put it under a compound microscope and thought maybe it is an animal but we couldn't definitively say it had no cell well. My profs thought it was an animal, with setae, but I would really like to know what it is

Edit here are the images:


texts: Estimating RNA concentration from Specific Activity of Labeled RNA

texts:
The question reads, Using T7 RNA polymerase to transcribe in vitro a 100-nt RNA off a DNA template. This RNA contains 19 Adenosines. In your 100 uL transcription reaction you added 1.00 µL of α32P•[ATP] that had a specific activity on its reference date (May 6th) of 10.0 µCi/µL. The concentration of "cold" (non-radioactive) ATP in  your transcription reaction was .500 mM. At the end of a 2.00-hour transcription reaction, you run a calibration curve using autoradiography on standards of radioactive ATP plus 2 µL of your reaction to obtain the following data:

Sample-------------------------------------------------------------Pixels

1:1000 dilution of α32P•[ATP] Stock (10.0µL)-------------3.211x10^7

1:10,000 dilution of α32P•[ATP] Stock (10.0µL)-----------2,483,565

1:100,000 dilution of α32P•[ATP] Stock (10.0µL)---------299,215

1:1,000,000 dilution of α32P•[ATP] Stock (10.0µL)-------31,444

Your transcription reaction (2.00 µL)-------------------------102,784

-

Estimate the concentration of RNA (in pmol/uL) that exists in your remaining 98 uL of the reaction.

I am using the equation: S.A = (Chn*(.5)^d/14.3 *Vhn * N * cf)/
                                        Vt*Ccn

where Chn = concentration of the S.A. of the α32P•[ATP] in µCi/µL =10 µCi/µL

Vhn = volume of α32P•[ATP] used in the labeling reaction =1.00 µL

N = the number of A nucleotides in the NA= 19

cf = calibration factor from the standard curve (“pixels”/µCi)= 10278.4 pixels/uCi

Vt = volume of the reaction=  100µL

d = number of days past your isotope’s “reference date” = 7 (May 6th to May 13th given in problem)

Ccn = concentration of cold ATP in the labeling reaction (pmol/µL) =.500 mM =500pmol

After I calculate the S.A. how do use that to estimate the concentration of RNA that exists in my remaining 98 uL of the reaction. I am beyond confused, any help would be greatly appreciated.


texts: Does the sun light have to have *direct access* to fruits to make them sweet?

texts:
I understand that sun light is needed for fruits to ripen. In the years with less sun light, the fruits are usually not so sweet. So the sun light is needed to make the fruits sweet.

Where and how does the sweetening process occur? Does the sugar in the fruits come from the photosynthesis occurring in the green parts of the plant (leaves) and is then conducted to the fruits, or is the sugar produced in the fruits themselves? Does it matter whether the sun shines directly to the fruits, or is it enough if just the leaves have enough sun light and the fruits become equally sweet even if they are hidden under the leaves?


texts: I am a graduate student volunteering in a professor's lab being tasked with finding out how to dispose of certain hazardous materials. I have encountered a problem with disposing of Bradford's Reagent. I have checked online, but am running into problems due to the methanol component of this compound. Can someone help me with the proper disposal procedure? Thank you in advance.


texts: Why doesn't local anesthesia affect muscles?

texts:
While having a dental surgery, I've got this question that why I can still talk, open/close my mouth, move my lips and so on while I can't feel anything at all in my mouth?

If the local anesthesia interrupts the alert that goes through brain, how is the muscle still functional? Is it some sort of one-way interruption which only disables the alert that go "from" the nerve "to" the brain? Or are there different nerves for this task?


texts: How many virus infections does the average human have?

texts:
According to the WHO:

67% of the population  are infected with herpes simplex virus type 1 (HSV-1)

Presumably there are other viruses as well that infect a lot of people. How many infections does the average person have?


texts: This insect was found in India. It looks like a hawk moth to me, but I still can't get the exact name for this species.


texts: Interplay of neuritic and synaptic growth

texts:
Let me try to give a picture of my understanding of neuritic and synaptic growth and their interplay.

Pick two neurons in corresponding areas of opposite hemispheres which are connected by a synapse (and a rather long axon).

Both neurons were originally born at approximately the same time t during brain development in a given distance d, without already having neurites.

They necessarily have a latest common ancestor (stem cell), which doesn't have to be the same parent cell, but maybe the same grandmother or great-grandmother cell.

Now several processes start with different delays and at different speeds:

the two neurons wander away from each other
they specialize thus expressing specific "markers" on their membranes
their axons grow
their dendritic trees grow

Case 1: If neuritic growth is fast enough, the two neurons can meet and build a synapse early (recognizing each other by markers they have in common due to their common ancestor). While wandering away from each other, the neurites have to grow accordingly.

Case 2: If neuritic growth is too slow, and the neurons wander away from each other too fast, the growth of axons and dendrites at least has to be guided somehow (by glia cells or by molecule gradients?) such that later they have a chance to find each other. Finally they recognize each other by markers expressed eventually during specialization.

I could imagine that both cases do occur purely, but even that they can be somehow intermingled.

Question: Is this picture essentially correct or flawed? (A yes/no answer would suffice!)

  Furthermore, I am looking for a concise presentation of (resp. gentle
  introduction to) these processes (and maybe others?) and their
  interplay that lead to specific synaptogenesis.


texts: From where did the selfish gene get its selfishness?

texts:
This is in reference to the book The Selfish Gene by Richard Dawkins. Further,

Because there is a law such as gravity, the universe can and will
create itself from nothing. Spontaneous creation is the reason there
is something rather than nothing, why the universe exists, why we
exist. It is not necessary to invoke God to light the blue touch paper
and set the universe going.
— Stephen Hawking and Leonard Mlodinow, The Grand Design, 2010

What was the spontaneous creation that led to this selfish gene?


texts: What controls the feeling of discomfort/comfort before and after sleep?

texts:
I'm interested in which biological systems or hormones are involved in the following phenomenon:

Before sleep it may be difficult to find a comfortable position, and muscular aches and pains are more evident.

After 8 hours of sleep, many more positions are comfortable, and muscle aches/tension are non-existent. Some time after awakening, the feeling disappears.

What causes the difference in feeling between prior to falling asleep and after? Are there some hormones involved? Is it caused by some form of thought/feeling inhibition (e.g., part of a brain "falls asleep")?

If I remember correctly, after long running muscles accumulate some compound that is a result of metabolizing energy without enough oxygen, which causes muscles to ache. Could a similar process be involved?


texts: tandem repeat sequence; causes of contraction and/or expansion question

texts:
Question:

Which of the following events, occurring within a tandem repeat sequence, will cause an expansion or contraction of the array?

A) Endoduplication    B) homologous recombination    C) Unequal
   crossing-over   D) Error-prone DNA repair    E) Inversion

I know for a fact that upon replication, tandem repeats of DNA (specifically trinucleotide repeats) can form loops which are repaired by mismatch repair enzymes (MSH2-MSH3); and failure to correct this would lead to an expansion of the array post-replication. However, this answer was incorrect.

Could someone assist me with this question? I read up on the topic but its not clear to me why DNA repair defects do not suffice as an answer. I don't also necessarily understand the correct answer (C)

Thanks so much

-Chris


texts:
How many times can a human get chicken pox?
For example: I got chicken pox, and recovered. If I was infected with HIV, and I am exposed to chicken pox again, can it infect me second time?, According to what I've heard, chicken pox comes only one time, because of the immune system of humans. But if I am infected with HIV and so definitely have immune system damage, will chicken pox come a second time, or will the immune system still protect the body from chicken pox?


texts: Can the natural loss of memory be modeled with a continuous function?

texts:
Disclaimer: I have little to no background in biology, so this question is based on anecdotal evidence. I've tried to spell out all of my suppositions, but please let me know if I'm making any leaps I'm not explaining.
Some Context/My biology assumptions
There are some things I can recall very clearly and quickly, other things that are maybe a little fuzzy and take me a second to remember and others still that will feel "on the tip of my tongue" for minutes before I can recall them. And then there are things that I don't remember at all or that I know I knew but can't recall.
To me it seems there's a range of how "clear" or easy a memory is to recall. This clarity and "recallability" seem to decrease over time (assuming I don't use the memory) and it seems there's some minimum clarity/"recallability" that is required for me to recall a memory. Can the clarity and "recallability" of my memories be modeled with a continuous function? And if so...
A (maybe false) Conclusion
According to the Intermediate Value Theorem,

if a continuous function, f, with an interval, [a, b], as its domain, takes values f(a) and f(b) at each end of the interval, then it also takes any value between f(a) and f(b) at some point within the interval."

So if we can model the clarity and "recallability" as continuous functions, and I can perfectly quickly recall a memory at one point and not recall it at all at another, then there should exist times with every flavor in between.
If this is true, would it be true to say that there existed a moment when my clarity/"recallibility" of a memory was high enough for me to recall it should I have chosen to and there is another moment when it wasn't (where these moments are some small distance apart)? Or is my understanding of memory incomplete to where this is all horribly wrong?
To put it in other words, how small can the time be between when you are able to recall something and when you no longer can? And following my logic, could this time be seconds or moments?


texts: What would happen if one eats silica gel?

texts: What happens if one actually does go about eating the beads in those "do-not-eat" packets?


texts:
If isozymes are seperated using electrophoresis, which of the following will be the principle of separation ?

A.charge density

B.molecular weight

C.polarity of molecule

I think it should be B.


texts:
The Mymaridae are the smallest insects. This video explains their numerous adaptations to being as small as 140 microns yet still complex, such as smaller cells with as little cytoplasm as possible, denucleated neurons, loss of several body parts (including eyes and hearts, depending on the species), and parasitism as an alternative to insects' usual level of nutrition in eggs. My question is why natural selection would favour their being so small in the first place.
Since few extant species have been extensively observed, this question may require some "just so story" speculation, hopefully informed by other examples of organisms becoming unusually, almost prohibitively small for their taxa. On the other hand, their fossil record covers about 100 million years, so perhaps the time and place of shrinking intermediates would suggest specific explanations.


texts: Can a bacteriophage be used to treat bacterial diseases?

texts: Some bacteriophages reproduce using the lytic cycle which ends with the destruction of the host bacterial cell. I was wondering if theoretically this could be used theraputically to treat bacterial diseases.


texts: When a 'v' letter should be changed to 'w' in botanical nomenclature?

texts:
When should be 'v' changed to 'w' in botanical names? (especially ones derived from names originally written in cyrillics).

The International Code of Nomenclature for algae, fungi, and plants says that

  The letters w and y, foreign to classical Latin, and k, rare in that
  language, are permissible in scientific names

  When the original publication of a name adopted a use of the letters
  u, v or i, j in any way incompatible with modern nomenclatural
  practices, those letters are to be transcribed in conformity with
  modern nomenclatural usage.

Where should I look for the rules on such usage?


texts: RE: Fasting gastric pH vs Normal gastric pH

texts: If fasting gastric pH values are more acidic then why is it recommended to eat no more than three hours before bed time to prevent reflux. It seems at some point during sleep the stomach would become more acidic therefore make reflux worse.


texts: Memory capacity of the human brain in bytes?

texts: Is there an estimate out there for how much memory (in bytes) an average human brain can have? Is there a physical limit?


texts: What will happen if mitochondria had a structure like lysosomes?

texts: I wanted to know an explanation how the structure of mitochondria affects its function. Therefore, how would it turn out if its structure is like the structure of lysosomes, what is going to happen?


texts: Impact of Alan Turing's approach to morphogenesis

texts:
Shortly before his untimely passing, the computing pioneer Alan Turing published his most cited paper The Chemical Basis of Morphogenesis (1952).

The central question for Turing was: how does a spherically symmetric embryo develop into a non-spherically symmetric organism under the action of symmetry-preserving chemical diffusion of morphogens (as Turing calls them, an abstract term for arbitrary molecules relevant to development)? The insight that Turing made is that very small stochastic fluctuations in the chemical distribution can be amplified by diffusion to produce stable (i.e. not time varying except slow increases in intensity; although also potentially time-varying with 3 or more morphogens) patterns that break the spherical symmetry.

The theory is beautifully simple and abstract, and produces very important qualitative results (and also quantitative results through computer simulation, which unfortunately Turing did not get to fully explore). However, even in the definition Turing discusses some potential limitations such as ignoring mechanical factors, and the inability to explain preferences in handedness. The particular models he considers -- a cycle of discrete cells and a circular tissue -- do not seem particularly relevant. As far as I understand, the key feature is his observation of symmetry breaking through small stochastic noise and instability.

What was the most important contribution of Turing's paper to developmental biology? Is his approach still used, or has the field moved on to other models? If his approach is used, how was the handedness problem resolved?


texts: I understand why dogs pant and humans transpire, namely for temperature homeostasis. So why don't cats need to do either, even after expending a lot of energy on a hot day?


texts: Can virus survive dessication (and come back functional after rewetting)?

texts: I am thinking of ideas for disinfection that can be done by the average person. So, this is one question I have: Can a material/surface be effectively disinfected (I am more interested in virus) by drying using low/medium heat + wind (or any other less thermally-intensive means)? Would the virus be only temporarily inactivated and is able to come back functional?


texts: How do traits with no negative effects get "weeded out" via evolution?

texts:
If only those who are most fit to reproduce are the ones reproducing the most, it makes sense that traits that prevent one from reproducing would eventually disappear from a population.

But what about traits that have no effect on reproduction, like the presence of wisdom teeth? Humans don't need them, but they don't inhibit us from reproducing either. So how do humans evolve past the point of having wisdom teeth or other similar traits with no negative effects?


texts: Book recommendation: protocols and recipes handbook for molecular biology / biochemistry

texts:
I'm a 5th-year PhD student in chemical biology. I've mostly been doing computational work, so my bench skills are rusty. To help me, I'd like a handbook of common techniques -- transformations, ELISA, protein purification, DNA extraction, SDS-PAGE, column chromatography, etc. I'd especially like a collection of recipes for buffers, etc.
I can find some protocols, but it's hard to find ones covering the more basic methods, and I'd like something cohesive. And there's something satisfying about an actual book.
I found these (and browsed through them in an HHMI library once):

https://www.amazon.com/Kathy-Barker/dp/0879697083/
https://www.amazon.com/Lab-Ref-Handbook-Reagents-Reference/dp/1936113791/

But they're pretty out of date! Most of the techniques are still valid, but I know many have been superseded. There are still a lot of radioligand assays (which are now uncommon in most labs).
So, can anyone recommend a book that could help someone relearn basic techniques?

My experience is that techniques are almost most often taught by hands-on, one-on-one training -- you find someone who knows the technique and ask them to show you, but COVID-19 distancing protocols make that nearly impossible. (The good news is that I often have the lab to myself and an underused supply of chemical stocks and reagents.)


texts: Why is saltatory conduction in myelinated axons faster than continuous conduction in unmyelinated axons?

texts:
How does spacing apart sodium and potassium channels allow the action potential to travel faster down the axon? This is the reason always cited for saltatory conduction and myelination, but my mental model of conduction tells me that the density of ion gates along the axon should not affect the speed of the AP.

To illustrate, consider a myelinated axon. A wave of Na$^+$ from action potential site 1, a node of Ranvier, rushes into and quickly diffuses down the axon. (It travels in both directions, but backwards is still in the refractory period.) It diffuses through the myelinated region, its concentration always diminishing. Before it attenuates too much, however, it happens upon node of Ranvier 2, where it triggers another action potential. A new wave of Na$^+$ rushes in and the cycle repeats. This should be plain so far.

Now imagine that there is actually a node of Ranvier halfway between node 1 and 2, called node 1.5. The wave of Na$^+$, on its way to node 2, happens to trigger an action potential at node 1.5, from which a wave of Na$^+$ pours in and either boosts the original wave or replaces it by taking its momentum. Now the reinforced wave proceeds to node 2 and triggers it just as soon as, perhaps even sooner than, if node 1.5 had not existed. Repeatedly insert nodes at higher densities until the situation is simply lack of myelination, and we conclude that unmyelinated axons can transmit an action-potential-triggering wave of Na+ as fast as or faster than a myelinated one.

In short, my point of confusion is this: I cannot see how a higher density of gated channels can possibly slow down the wavefront of Na+ that triggers action potentials. If anything, the additional influxes of Na+ should speed up the all-important wavefront, assuming that new waves really "either boost the original wave or replace it by taking its momentum", and also assuming that the wavefront of Na$^+$ is really all-important for signal transmission, and also assuming that the mere presence of (voltage?) gated ion channels in the membrane does not significantly retard the wavefront.

But the usual explanation for why saltatory conduction is faster than continuous conduction (a fact I hope is empirically and unambiguously established) relies on the putative slowing effect of ion channels on the signal fore. Please explain this effect in more detail, if it is not a misconception.


texts: Why are 2 electrons transported from photosystem II at the same time?

texts: I only know that electrons are captured by the primary electron acceptor and then go through the electron transport chain, ultimately ending up at photosystem I. But why do 2 leave photosystem II in the first place? I thought the oxygen-evolving complex only replenishes the electron hole one-by-one?


texts: Identification of colorful jelly-like marine creature

texts:
I'm on my trip to Gulangyu Island, Xiamen, Fujian Province, China. Today(4th February 2017), at 12:13 A.M., I saw a beach filled with huge rocks on which various dry shells reside. Among the shells, I spotted a colorful eye-like marine creature.

To figure out what it is, I torn it off from the rock. (don't worry, I've put it back after taking this photo)

Also, it feels soft when I poked it, and its size is approximately 1cm to 1cm. Could anybody please tell me what I've found?


texts: Evolutionary rationale behind migration proteins

texts:
Tumor cells are able to migrate due to specific migration proteins.
What is their evolutionary origin?
Or are they simply deregulated?


texts:
I found a rather strange invertebrate...something... outside my home this evening, and I have no idea what it might be. It looks kind of like a small brown lobster, without the claws. I think it has 8 legs, making it an arthropod(?), but if I've misidentified that, please correct the tags. It's 4 or 5 inches long, head to tail. It was found in south-eastern Massachusetts. Potential nearby habitats are open grassy fields, a forest, and a cranberry bog, if that helps.

The picture is kinda fuzzy, I think the video is better.

Any ideas?


texts:
Seems to me that these two sources (M. Whitlock, B. Wallace) use different definitions of soft and hard selection.

M. Whitlock: Soft selection occurs when the relative fitness of an individual is calculated relative to the fittest individual of the local patch. Hard selection occurs when the relative fitness of an individual is calculated relative to the fitness of the fittest individual in the whole metapopulation.

B. Wallace: Soft selection occurs when the relative fitness of an individual is calculated relative to the fittest individual in the population. Hard selection occurs when the relative fitness of an individual is calculated relative a hypothetical fitness. Therefore, extinction only occurs under hard selection but never (except eventually when all individuals have fitness of 0) in the soft selection case.

Are there other definitions? What is the most common definition?


texts:
I would like to know how long it takes for the human body to absorb / digest a 10mg zinc capsule?

Note: It is recommended to take zinc  an empty stomach to gain the maximum effect. Regarding to that I think it's also a disadvantage to eat something right after taking zinc?

greetings


texts:
Blood is removed from meat before it is consumed. Below is, for example, how chickens are processed from Wikipedia.

Removed from transport cages
Hung by the legs on a shackle, mounted on a conveyor chain.
Stunned using an electrically charged water bath
Killed by cutting the blood vessels in the neck
Bled so that most blood has left the carcass
Scalded to soften the attachment of the feathers
Plucked to remove the feathers
Head removed
Hock cutting to remove the feet
Rehung in the evisceration room
Gutted or eviscerated to remove the internal organs
Washed to remove blood and soiling from the carcass
Chilled to prevent bacterial spoiling

Why is the blood removed? Does it just simply taste bad? This might be a stupid question but being vegetarian, I may not know.


texts:
I always wondered why gametes from two different species dont fuse together to form an offspring. eg a donkey (sperm) and a female dog (egg)

I know this is not possible but I'm just curious.


texts:
Chromosome X in female sperm is heavier than male Y chromosome. Does it causes difference in fertility of sperm and heavier female sperm is unable to fertilize better than male sperm?

This is given in AK Jain of physiology, chapter on reproduction.
I doubt this explanation.


texts: Why do we feel cold in the lower part when we lie down?

texts:
This question is based on my personal experience. But I believe that this common for many of us.

Let us say that I am sitting on a chair in normal indoor dress. Then, if I lie down on bed, I will feel the need to cover the lower portion of my body.

As I have seen at home, I am working sitting on a chair. Then I lie down in the same dress, and i feel the need to cover my lower part. When traveling in some sleeper train, people ask for blankets when they lie down, not while they are sitting. It is not that they change their dresses when they lie down, they are in the same dress.

Why does this happen? Why do we feel colder, specially in the lower portion, when we lie down?


texts: Importance of knowing GC Content of an organism

texts:
I was looking at the GC content percentages of few organisms. I also know calculating the GC content percentage. But, what I want to know is, what information would we get., let us suppose if human genome has 40% of GC in the genome.

Does it help us compare the number of genes between different species, for example, a bacteria has less GC content than human, so does it mean Human produce more genes than bacteria?

or Is it that the 40% of the genome,has coding regions in them and more genes are found in those regions? What is the number "40%" actually indicate us?

Please help me understanding the concept. Would be thankful your answers and suggested reading.

EDIT: My question is what does knowing percentage of GC content help us knowing? If the GC content is 40%, does it correlate to number of genes in the genome?
Regards,
Prakki Rama.


texts: How can you explain the origin of life out of nonliving matter (abiogenesis)?

texts:
According to biochemist Robert Shapiro, the "primordial soup" theory is as follows:

Early Earth had a chemically reducing atmosphere.
This atmosphere, exposed to energy in various forms, produced simple organic compounds ("monomers").
These compounds accumulated in a "soup", which may have been concentrated at various locations (shorelines, oceanic vents etc.).
By further transformation, more complex organic polymers – and ultimately life – developed in the soup.

From: en.wikipedia.org/wiki/Primordial_soup

I don't understand how in step four life forms out of nonliving organic polymers. Could you explain this process? Can it be reproduced in the lab?

Louis Pasteur already disproved Spontaneous Generation: The law of biogenesis


texts: Why can oligo-U not be used to isolate mRNAs, instead of oligo dT?

texts: dTTP oligonucleotides are used to isolate mRNAs because mRNAs (in eukaryotes) have a poly A tail which binds to the complementary oligo-dT. However, why can we not use oligo-U instead (uracil)? I would guess it is because ribonucleotides have the additional 2' OH which is reactive, so less desirable, but is there any other reason?


texts: The apple pictured is a of the Gala variety,typically striped.The stripes swirl around a brown protrusion. The protrusion is flexible,in the way a leaf is flexible. The flesh underneath is not discolored or soft. The apple is not misshapen,the seeds are not un-developed or underdeveloped. What is this brown protrusion called and what causes it?


texts: Is it possible to conduct scientific research without actually getting close to the sample/specimen?

texts:
For example, I have never get closed to a whale. The only source I have is research from who has get close to it. If I read their research and find a new thing, would my "discovery" be scientific? If yes, can you give some example of such research?
There is a related question in Philosophy SE: “Dinosaurs did exist once”. Is it knowledge or is it only justified belief? However this question is more about the knowledge directly produced by field researchers, while in this question I focus more on researchers who can only access secondary research. Plus that dinosaurs extincted, so in a sense I and a paleontologist are equal: neither of us can have direct experience to a living dinosaur. But whales are still living, and that equality is gone. So maybe the threshold for scientific research between a living organism and an extinct one is different?
See also: Is it possible to have a scientific review of a method if the author doesn't have direct experience of it?
Some may say this question is opinion-based. But there are good subjective questions as well.


texts: Is the whole MHC haplotype expressed and so their proteins are exhibited on each nucleated cell membrane?

texts:
Am I correct if I guess the following (?):

If we inherit both maternal and paternal MHC haplotypes, the functional (non-pseudo)genes are expressed and all of their products (MHC molecules) are exhibited on the cytoplasmic membrane of any nucleated cell.

In case of MHC type I molecules our all nucleated cells bear one (or more? how many?) types of polypeptide(s) (corresponding to and) encoded by the inherited allels of each of A, B, C, E, F, G MHC-I genes.

In other words each nucleated cell expresses all MHC type I molecules encoded by our inherited MHC haplotype.

Is it true?

Thank you.


texts: Do acetyl-CoA, acetyl-CoA carboxylase and acetyl-glutamate carry any charge?

texts:
Do the following compounds have any charge? If not, then why? If yes, is there any database that would give me this information if the compound is negatively or positively charged?

The compounds are as follows:
Acetyl-CoA
Acetyl-CoA carboxylase
Acetyl-glutamate

I have searched and somehow I am getting more confused.


texts: How to integrate transcriptomics data with kinetic metabolic models?

texts:
I have created a convenience kinetics† model. Now, I want to integrate the transcriptomics data with my convenience kinetics model for altering/weighing the kinetic parameter values. I have read some publications related to this work but can’t get a satisfactory idea of how to do it properly.

Details

I've got a pancreatic model for the study on type 2 diabetic patients. It has a few compartments and the reaction pathways; the species are metabolites. All the reactions are convenience kinetics based. Enzyme is a constant factor, so its production and regulation is not considered. From my model, I'll get the Vm values for all the reactions and then I'm supposed to get the Vm (Vmax of Michaelis-Menten kinetics) values for the type 2 diabetic patients by somehow integrating the transcriptomics data with it. I was asked to use the fold change values but I couldn't find any relevant publication on this topic (my PI has suggested me these but hasn't worked in this area before).

Any leads or references will be highly appreciated.

† You can call convenience kinetics rate laws as approximate rate laws or you might have heard about "modular rate laws", they are more or less the same. We use this approximate rate law approach in cases where we don't have the experimental data for all the true rate law parameters.


texts: Is the motor cortex identical to the sensorimotor cortex?

texts: As far as I understand, the primary motor cortex (M1) and primary sensorimotor (SM1) are notations for the same cortical area in the brain. Am I right that there is no dedicated motor cortex, and that M1 actually processes both sensation and movement functions?


texts: Why does the DSC peak have a bell shape?

texts:
I am studying Differential Scanning Calorimetry (DSC) and am not quite understanding why most proteins have a bell shape when the heat capacity is plotted against the temperature.

Also, I would appreciate if you could provide good sources on this topic (books, articles, etc).


texts: What is the meaning of "leukemic cell recovery" in an abstract?

texts:
An article abstract:

  Significant predictors of treatment outcome are poorly defined for patients with T-lineage acute lymphoblastic leukemia (T-ALL). A high WBC at diagnosis, which has traditionally been a predictor of poor response in T-ALL, has considerably weakened prognostic significance in the face of modern, more intensive chemotherapy. To test the hypothesis that bone marrow stroma-supported leukemic cell recovery might identify children at high risk for relapse, we measured the ex vivo recovery of T-ALL lymphoblasts from 29 newly diagnosed patients using a stromal cell co-culture assay. In all cases the T-ALL lymphoblasts showed an increase in recovery of T-ALL cells (RTC), ranging from 4 to 343%, in comparison to samples maintained without stroma. Since we were blinded to patient outcome in this case-control study, we then correlated patient outcome with RTC. The RTC for 18 patients in complete continuous remission (CCR) for greater than 4 years was stochastically larger than for the 11 patients who eventually relapsed (P = 0.011, by the two-sided Wilcoxon test). Furthermore, 100% of patients with an RTC of more than 26% had a CCR greater than 4 years while 78% of the patients with an RTC of less than 25% relapsed within 4 years. This is the first report to show that higher lymphoblast recovery may predict a more favorable outcome for children with T-ALL. A prospective study is needed to test whether stroma-supported leukemic cell recovery might serve as a basis for assigning risk-adjusted therapy.

What is the meaning of recovery here? It puzzles me as a non-native speaker of English. Do the authors simply mean "the number of cells that survive"? Or is there some "recovery process" - if yes, what is the nature of this process?

P.S. The question arose from a question asked by a fellow translator. She translates a text in which T cells transduced with gene for a receptor against leukemic cells are co-cultured with such cells, after which

  "T cells transduced with the receptor markedly reduced leukemic cell recovery".

The translator has trouble understanding how to put it in Russian, because translating "recovery" verbatim would imply some process in which a cell recovers, say, from injury.

Is "recovery" just "the percentage of cells that survived, relative to the overall number of cells"?


texts: What is the closest relative to odd-toed ungulate?

texts:
I have seen about 3 variation of phylogenetic tree about odd-toed ungulate and I don't know which one is really updated or outdated or which one have more backed up theory

First is odd-toed ungulate are closest to even-toed ungulate

https://en.wikipedia.org/wiki/Odd-toed_ungulate#Outer_taxonomy

Second is odd-toed ungulate are closest to carnivore

http://www.ultimateungulate.com/FamilyTree.html

Third is odd-toed ungulate are closest to Hyrax and Elephant

http://tolweb.org/Eutheria/15997
http://www.newworldencyclopedia.org/entry/Eutheria

Second or Third

https://research.amnh.org/paleontology/perissodactyl/node/55

Could anyone please ordering the actual relativity of each branch in the most reliable theory in present. And also could anyone please explain why there was such a very confusion in evolution of odd-toed ungulate specifically?


texts:
It is known that HIV is usually transmitted by direct blood or body fluid contact between an infected individual and a healthy person (like blood transfusion or needle sharing):

Suppose a mosquito bites an individual suffering from AIDS and in the process sucks up some T cells infected with HIV along with RBCs. Then it bites another person not suffering from the disease, and transfers these infected T cells. Isn't there a high probability of the second individual contracting HIV?


texts: In biological nitrogen fixation, the electrons required to reduce dinitrogen to ammonia are provided by which compound?

texts:
The reaction is as follows:

N2 + 16ATP + 8e- + 8H+ → 2NH3 + H2 + 16ADP + 16Pi

From where are the 8 electrons coming from?
We know that in photosynthesis, the electrons are supplied by the oxidation of water to evolve oxygen gas. What about here?


texts:
I have learnt that there are 2 types of hormones:

peptide hormones (hydrophilic, mostly bind to receptors on cell membrane)
steroid hormones (hydrophobic, can pass through cell membrane and bind to receptors on nucelus membrane)

I know that steroid hormones are enclosed by a protein (Is it lipoprotein or others?) when transported in blood. But I think the protein should be

relatively big
outer layer should be hydrophilic (since it can dissolve in blood easily).

If these 2 descriptions are true, then how can it EASILY pass through the cell membrane and enter cytoplasm directly?


texts: What is the highest competency possible for E coli?

texts: I am looking to find a highly competent E coli strain.  I am making a library of a ~6.6kb plasmid and I am not getting high enough efficiency.  Does anyone have a suggestion of a strain/protocol with ultrahigh efficiency (>1010).


texts: Why is there a notch in the Na curve for an action potential?

texts: Just out of curiosity, why does the Na curve dip down like in the figure below? I can't seem to find an explanation!


texts: Is it true that; when you apply your own saliva to a mosquito bite it would stop itching ?


texts: Which is harder to contract - HIV or AIDS?

texts:
I am working on mathematically modeling HIV and Tuberculosis Co-infection dynamics, and am working with 12 differential equations describing the behavior of all of the compartments and parameters.

Anyway, I just have one question:

Which is harder, in general: For a susceptible person to contract HIV, or a HIV+ person to contract AIDS?

Please pardon my ignorance.

Thanks.


texts: Have there been any measurements on the genomic differences between cancer cell DNA and healthy cell DNA?

texts: I'm loooking for simple stats like the average number of base pair differences to normal cells, average diversity between different cancer cells, etc.


texts: Spider Identification: Is this an Arizona Recluse?

texts:
I found this spider in my toilet bowl. It was after dark. We live in Prescott Valley, AZ at around 5100' elevation at the edge of a development fairly close to the mountains in grass land.

I'm concerned its an Arizona Recluse (or Desert Recluse). We saw a few of these around the house during the warmer months; this is the first I've seen in a while since its gotten cold, but my wife just did some extra cleaning.

I don't see a violin shape, but this article points out that desert recluse's don't have a noticeable violin. It also looks like it has 3 sets of eyes, but the 4th may just be hidden due to the angle since it looks like the 3 I see in the pics aren't centered quite right. Anyways, if anyone has some insight I would be happy to know. The leg span was a bit bigger than a penny.


texts: What are primary reasons for the failure to localise/anchor sequences in genome assemblies?

texts:
My question concerns the incorporation of individual sequence reads into chromosomes during gene sequencing projects, especially those with larger genomes such as Drosophila melanogaster or Homo sapiens.

There are some sequences or short contigs that it has not yet been possible to incorporate into the larger chromosome assemblies.

What are the reasons for this failure?


texts: What sequences are between adjacent genes?

texts:
The human genome has a lot of non-coding regions, which include regulatory elements, repetitive DNA, and introns. Suppose there are two adjacent genes on a chromosome, and their positions on the chromosome are, say,

For the first gene: 11,785,723 to 11,803,245 bp.

For the second gene: 11,806,096 to 11,806,143 bp. These values include their regulatory elements, promoter and introns as well.

So what sequence is present between bases 11,803,245 and 11,806,096? Are they satellite sequences? Is this non-coding, non-regulatory region 11,803,245 to 11,806,096 bp heterochromatin?


texts: Why don't we see new diseases more often? Or, ever?

texts:
It seems like every disease we ever hear about is something that's been around since ancient times, since thousands of years ago. Of course new diseases were catalogued over the course of the past couple hundred years, but they weren't actually new diseases-- they just hadn't been previously classified/identified.

Given that (in my understanding) viruses and microbial lifeforms can evolve and change considerably more rapidly than higher order organisms, why don't we often/ever hear about completely new diseases that have never been seen before? Diseases that may have only just been born.


texts: Why do different pain killers have different effects on people?

texts:
I've noticed some pain killers working great for me, while others have no effect.

Works for me

Aspirin
APC †
Naproxen

Doesn't work for me

Paracetamol
Diclofenac
Tramadol

I doubt there is much of a placebo effect at work, since most of these either did or did not work when I first took them, without having expectations either way.

Whenever I have a head ache, I take an APC. I suspect it's actually the aspirin in there that does the job, since when I take just paracetamol, it doesn't do squat. As a kid I got children's aspirin, which worked.

I once had a severe back ache. I was prescribed diclofenac (a heavier variant than the over the counter one), which didn't work. I was then prescribed tramadol — same results. I then tried naproxen, which worked rightaway.

Why do some pain killers work while others don't?

Is there an underlying mechanism, that explains why some of these work while others don't? Does that predict if pain killers that I haven't used yet will work?

Please note that I'm not looking for medical advice on which pain killers to take; I'm just curious about how my body interacts with the various ones.

†: the one consisting of aspirin, paracetamol, and caffeine, not the one containing phenaticin. Think Excedrin.


texts: Pre-linnaean names, where can I ask about current IDs?

texts:
I run a large website with lots of historical herb books. For the older ones, finding out current botanical names is very difficult.

Can I ask here? If not, does anybody know where I could ask what any given plant is, with or without images, usually with descriptions and pre-Linnaean names?


texts: Evolutionary reasons why you cannot tickle yourself but masturbate

texts:
There are obviously good reasons that explain why you cannot tickle yourself (see e.g. here). This got me thinking why it is possible to masturbate...

Wouldn't it make more sense to not being able to do that so that you are more inclined to have real sex. Individuals who were not able to relieve themselves in this manner should have been more actively producing offspring. And the tickling example shows that self-produced sensations can be inhabited.

Does this make sense? I know that it is always hard to reconstruct evolutionary processes but are there reasons that explain this?


texts: Hi could anyone explain the biological basis behind romantic love. What is the biological basis of falling in love?I know that serotonin and dopamine are secreted when we first fall in love. What happens after that as we move on to the more advanced stages of love. Why is it that after some time, we no longer feel the initial feelings of love. What is the biological basis behind it. And also why do we feel so heartbroken if we happen to fall out of love? What is the biological basis behind it?


texts: How do you differenciate between the eukaryotes and prokaryotes?

texts:
I wonder how we differentiate between the eukaryotes and prokaryotes.

Eukaryotes:

  Eukaryotes (also spelled "eucaryotes") comprise animals, plants, and
   fungi—which are mostly multicellular - as well as various other groups
  that are collectively classified as protists (many of which are
  unicellular).

Prokaryotes:

  Prokaryote (also spelled procaryote) comprise any organism that lacks a
  distinct nucleus and other organelles due to the absence of internal membranes. Bacteria are among the best-known prokaryotic organisms.
  The lack of internal membranes in prokaryotes distinguishes them from
  eukaryotes.

Isn't there any other method to know what organisms are eukaryote or prokaryote?


texts: How can you tell if a protein-coding gene is nuclear or mitochondrial?

texts: New to genes, and have to read literature to find candidate genes for a particular study. I cannot for the life of my understand if all genes are placed into either the "nuclear" or "mitochondrial" category...are there more categories? Some are easy, like cytochrome subunit genes are always written as "mitochondrial" and then rhodopsin are written as nuclear...but other genes like ATPase etc. don't have those descriptions. When I search online further, it still does not clarify, so I am wondering now if there are just more categories to this?


texts: Measuring depolarizations over the membrane

texts:
Measuring the rest potential of a membrane is relatively easy and straight forward: put one electrode inside the neuron, the other one (the "counter electrode") outside the neuron.

Because everything is at equilibrium (steady state), it's not important where exactly inside the neuron you place the first electrode, and even less important where outside the neuron you place the counter electrode: in the extracellular fluid next to the neuron or inside a container filled with extracellular fluid placed anywhere. One may even connect the other electrode to the ground (a lightning rod), if one does it consistently (over all measurements).

But now consider you want to measure the spread of depolarization along the membrane by measuring the membrane potential at two different locations of the membrane: You place one electrode underneath the membrane at point $p_1$ (and its counter electrode to the ground). And you place another electrode underneath the membrane at point $p_2$ (and its counter electrode to the ground).

Now it seems possibly important where exactly inside the neuron you place the two electrodes: the distance from the membrane might make a significant difference. (But maybe not.)

What probably would make a significant difference: Since the ionic compositions of the extracellular fluid in the vicinity of $p_1$ and $p_2$ will differ, it might be important to connect the counter electrodes not to the ground (or to some volume of normal extracellular fluid) but to corresponding points $p_1'$, $p_2'$ directly opposite to $p_1$, $p_2$ on the other side of the membrane.

I emphasized might be important because in practice it may be not important. That's what my question is for:

  Is it OK, even for the measurement of the dynamics of depolarizations,
  to connect the counter electrodes to the ground (if only
  consistently). What would be the difference in the measured voltages,
  and can these be determinstically be cancelled out?


texts: Why are X-linked illnesses less common in females if females have X-chromosome inactivation anyway?

texts: I have read this post but am still slightly confused about this. Do tissues in the human body not all develop from the same cell(s) in the embryo? If so, I do not see how the cell 'mosaic' would be grainy enough to mask the fact that half of the female's cells are not working properly. For example, all liver cells come from the same cell in the embryo which has an inactivated X. In that case, there is a 50% chance that the females liver is dysfunctional. So I would predict that some females would exhibit X-linked disorers even if they are heterozygous, but I haven't heard of this being the case...


texts: What are treatable foetal conditions during pregnancy?

texts:
What are different foetal conditions during pregnancy that could be treated with appropriate prenatal genetic testing?

I only know that pregnant women are encouraged to take certain supplements to make sure certain conditions won't develop in the foetus, and which are apparently also the case for deficiencies in human growth hormone, but I imagine there must be other specific cases that are treatable for specific conditions diagnosed to only a small number of cases?


texts: Does DNA being circular or linear directly affect the speed of DNA replication?

texts:
Let's say we have two DNA molecules of equal length, one belonging to a prokaryote and the other to an eukaryote. It's known that replication of the eukaryotic DNA is faster in this case. One clear reason for this is that linear DNA has multiple origins of replication whereas circular DNA only has one.
Now back to the real question: Does it matter for rate of replication whether the DNA is circular or linear? Does it contribute to eukaryotic DNA replication being faster in our specific case?
One thing I found in an old revision of this Wikipedia article is as such:

One reason that many organisms have evolved to having linear chromosomes is due to the size of their genome. Linear chromosomes make it easier for transcription and replication of large genomes. If an organism had a very large genome arranged in a circular chromosome, it would have the potential problems when unwinding due to torsional strain.

What I make out from this is that the rate of replication isn't directly affected. It's more closely related to avoiding other issues that arise from eukaryotic DNA molecules being typically longer than prokaryotic ones. But in our case where we declare both DNA to be of equal length, I'm assuming circular vs linear has no bearing on the rate of DNA replication.
So am I correct on my assumptions?
Edit in response to the answer below:

It's known that replication of the eukaryotic DNA is faster in this
case (where DNA molecules are of equal length) because eukaryotes
have linear chromosomes whereas prokaryotes have circular ones

If it makes sense to form a sentence like this, presenting linearity as the cause, then it's enough to satisfy my definition of directly affected in this case. For example, it's easy to make this claim if you present the number of origins of replication as the cause. I looked at the textbook you mentioned and the quantity of origins of replication is in fact mentioned this way.
Conclusion:
I went ahead and did a bit more reading in that textbook. What
I've understood is: An eukaryotic linear chromosome has multiple
replication origins rather than a single one in order to compensate
for its much larger size. So while the shape might be a factor
(possibly, not certainly), the primary and "direct"
reason is the difference in size, not the shape.


texts: Empirical evidence for species selection

texts:
Do we have any empirical evidence in favor of species (or lineage) selection? Do we know some cases that can only be explained (or seem to be only explained) by lineage selection? What are today the best study cases in favor of lineage selection?

If not, how could we find any evidence for lineage selection?

Note: I call lineage selection a differential in speciation and/or extinction rate that drive the proportion of lineage (species for example) displaying a given trait (emergent traits or not) to increase or decrease over time.


texts: How does Humira work when injected into patients with rheumatoid arthritis?

texts:
OK, I have rheumatoid arthritis and I've been injecting Humira 2 times a month for the last 8 months.

As far as I know rheumatoid arthritis is simply an immune system disorder which makes the immune system produce more proteins called Tumor Necrosis Factor alpha which regulate body disorders.
When I inject Humira I actually import a protein called Adalimumab which is a TNFα inhibitor.

So far so good but my question is

Does my body throw this protein away after some time? How is this protein removed from my body?

What about the way Adalimumab inhibits TNF, does it bind to TNF?

Also the details of how rheumatoid arthritis appears are not well known but the main reason is because of the patients DNA isn't it?


texts: Why do emperor penguins breed during the antarctic winter?

texts:
No land animal, and I think no sea animals either, stay in the antarctic during winter - except for one: The emperor penguin. These penguins not only stay there, but their prolonged stay involves 4 months of harsh winter, averaging -70$^o$C, no sunlight and no food for that period of time. And if that wasn't enough, then it's during that time that the emperor penguin male incubates the egg alone, left by his female mate. The male emperor penguins gather together to endure the antarctic winter.

My question thus becomes very obvious: Why does the emperor penguin stay in Antarctica during winter at all, and moreover, breed there during that time and incubates a precious egg in the harshest conditions on earth, while all other animals flee for their lives?


texts: Structure of RAP Antibodies (Specifically RAP-5)

texts:
[EDIT] - Have just found not one but two papers that address my structure problem. However they concern RAP-1A, so I guess my question is now what is the difference in  structure and function of RAP-1A and RAP-5? Does anyone know of X-ray structure analysis being used to examine RAP-5?

original question

I'm a University Physics student writing a mock review article on what to me feels like a very 'un-physicsy' antibody - RAP-5.

Although my knowledge of Biology is pretty poor, research is going quite well. I've found a lot of papers from the 80s talking about conducting immunohisto(/cyto)chemistry experiments, most of them finding that RAP-5 can be used to determine whether a cell has the ras in it, so they are able to measure the percentage of cells that are neoplastic (I believe this means cancerous) and contain ras and the percentage of cells which are normal and contain ras. (the ras-gene being a proto-oncogene which on mutation can result in permanently switched on ras proteins (p21?), which results in proliferation of cells and therefore can cause tumors). This is all very nice but on first glance immunohistochemistry doesn't seem to involve a huge amount of physics (for my bio-physics assignment), apart from using an optical microscope.

I was hoping to be able focus a section of my article on the physical techniques involved in determining the structure of RAP-5. Although there seems to be plenty of literature on uses of RAP-5, I am struggling to find anything on the details on why it is able to be used in such experiments. In other words, I presume that its function is to bind on to an epitode specific to the ras protein (amino acids 10 -17 have popped up a few times) but I don't know if there is any imaging one can do to have a look at the structure and conclude 'yes this is why it binds to ras proteins and not to others'. Is there a technique that is likely to have been used to examine the structure of RAP-5? Is it's tertiary structure likely to be 'Y' shaped like other antibodies? Does it differ in structure from RAP1-4? (this book informs me that RAP1 and RAP2 have 60% sequence identity, but most sources seem to leave out RAP3-to-5, some evening telling me that the RAP family consists of RAP1A/B, RAP2A/B/C and no others!).

Also, if RAP-5 is an antibody, does this mean that it is produced in the body and gets involved in the ras protein signal pathway in order to reduce too much ras expression? (am I right in saying the amount of expression is the amount of protein the ras-gene is producing?) or is it only synthetically produced and used in experiments to measure the amount and location of ras proteins?

Also there seems to be little differentiation between the differences in the functions of each RAP. RAP-5 seems to be used quite a bit in experiments involving Ha-ras - but not exclusively. Do the different RAPs bind to different variants of ras? Ha-ras being the one unique to RAP-5.


texts: making antibodies rather than buying them

texts:
I need large amounts of anti-CD20 and anti-pan-cytokeratin antibodies. At DAKO, they go for >$1,500/mg, and I need >100mg, hence a purchase is out of question.

Instead, I plan to make a homebrew antibody. I have been producing monoclonals from hybridomas and from HEK cells for a decade, and my lab avails of all necessary equipment (Äkta, cell culture, etc.) and expertise.

What I have never done, however, is to start with a published sequence and create (and express in suitable mammalian cells) an artificial antibody H+L gene. Specifically, I was thinking of pulling a sequence from a patent filing, as these tend to be quite precise for legal reasons, making a synthetic gene, and expressing it in HEK.

A nice precedent for that would be for example http://www.ncbi.nlm.nih.gov/pubmed/25451031. Here, the author of the original publication refused to provide (or even sell at any price) the ICSM18 antibody, for reasons that he did not disclose (but which we can all imagine, given that the primary paper was published in Nature and a refutation would be seen as a dishonor). As a result, Colby lifted the sequence from the patent, and made the antibody in their kitchen! (I must say that I love democracy in science!!!)

My question is:

might you be able to direct me to good, high-affinity antibodies to
CD20 and cytokeratins whose sequences are retrievable? The latter is
true only for a minute minority of all available antibodies


texts: What is the purpose of ethanol in a DNA extraction experiment?

texts:
We were doing a lab experiment in biology class in which we extracted DNA from a banana-detergent solution mixture.(The detergent solution was made of 100ml of detergent, 90ml of water, and 5g of salt.) We then added ethanol to the mixture.

I know detergent breaks down the lipids in cells and salt takes away the moisture from cells but how does ethanol affect cells?


texts: DNA extraction kit for microbial mats, rocks, and soil in a remote area

texts:
I am hoping to perform a metagenomics study of samples from a lava tube. It will be in a remote area (with no large scientific equipment) and I would need to bring all scientific equipment myself. For the sequencing, I plan to use either the Field Sequencing Kit or the Rapid PCR Barcoding Kit from Oxford MinION. However, I am unsure how to extract DNA before using the Oxford Minion kits (and in a manner, of course, that complements it).
Are there DNA extraction kits that can followed up Oxford MinION kits and can be performed without heavy equipment for the following sample types?
a) microbial mat
b) soil
c) lava rock
Thank you for sharing your advice!


texts: What happens when a human ingests a large meal, and after a short time follows it up with a large amount of indigestible carbs?

texts: A human eats a large meal and indigestible carbs (IC) with such a timing that the IC arrive to the small intestine when it is already full and busy breaking down and absorbing the meal. What would happen to the IC? Would they stay there until the digestible meal is digested, or would they somehow be moved along? Would they start fermenting if they are stuck there for some time? Would they push the unabsorbed remnants of the meal out as the body tries to excrete IC? Would they hamper absorption or aid it?


texts: What dangers would the wireless transmission of power through microwaves pose to living organisms?

texts:
If we were one day able to harness the power of "wireless electricity", and INTEGRATE it into society, what disadvantages and/or dangers to living organisms would become relevant at that point? To my understanding, the power would be transmitted through microwaves, which may or may not be correct.

The example I will use in regards to "wireless electricity", would be... The transmission of power from one source to another without the need for power cords, or power lines.

One such instance, according to "http://phys.org/news/2015-03-japan-space-scientists-wireless-energy.html", states "The idea, said the JAXA spokesman, would be for microwave-transmitting solar satellites—which would have sunlight-gathering panels and antennae—to be set up about 36,000 kilometres (22,300 miles) from the earth."


texts: What specific mutations can cause an apoptosis mechanism to malfunction?

texts: What specific mutations can cause the apoptosis mechanisms in a cell to malfunction? Are any such mutations 'reversible' , somehow or are they generally permanent? what kind of mutations can happen without disrupting the apoptosis mechanisms?


texts: How can I generate a random DNA sequence?

texts: I've found this paper which involves the construction of 19-bp random DNA sequences, but I don't know enough biology to understand how this method works.  Could someone explain it to someone who is highly technical, but has knowledge of only introductory, undergraduate biology?  How do the authors know that their resultant sequence is truly random?


texts: Is NADPH salt still usable after an hour at room temperature?

texts:
I accidentally left a delivery of NADPH Tetrasodium Salt (Santa Cruz Biotechnology) at room temperature for a little over half an hour.

In addition, when I opened up the package, I briefly held the bottle by the body instead of the cap (which would have prevented body heat from contacting it).

It was packed with airbags, but no ice packs, which is why I am asking this: is the powder still stable and usable?


texts: This strange looking thing was on the leaf, can you identify what this is?

texts: I found this today on one of the plant that I grow in the container at home. I cannot identify what kind of insect it is.


texts:
Noted for their thick skin are both rhinoceroses (1.5 to 5 cm) and hippopotamuses (6 cm).  They are further noted for their symbiotic relationship with bird called an oxpecker:

  Both the English and scientific names arise from their habit of perching on large mammals (both wild and domesticated) such as cattle, zebras, impalas, hippopotamuses, or rhinoceroses, and giraffes, eating ticks, small insects, botfly larvae, and other parasites.
  Oxpecker, Wikipedia

I feel like the thick skins of rhinoceroses and hippopotamuses would make them invulnerable to many parasites (such as those listed above), so I'm interested in finding out more specifically what oxpeckers eat from the skin of these two mammals.

Question: What do oxpeckers eat from thick-skinned hippopotamuses and rhinoceroses?

In the case of hippopotamuses, I feel like their semi-aquatic lifestyle would further impact many parasites.


texts: What is meant by translational repression by an upstream open reading frame?

texts:
The NCBI report on the human huntingtin gene contains the following statement:

  “This gene contains an upstream open reading frame in the 5' UTR that
  inhibits expression of the huntingtin gene product through
  translational repression.”

But no specific reference it given. Can anyone explain what this means.


texts: What is the most complex biological organism (or precursors) that we have been able to synthesize from raw materials?

texts:
In the Miller–Urey experiment they produced several amino acids.  I'm not sure if there were other similar experiments that got further.

http://www.jcvi.org/cms/press/press-releases/full-text/article/first-self-replicating-synthetic-bacterial-cell-constructed-by-j-craig-venter-institute-researcher/ is a reference to making a cell, but they really injected an engineered genome into an existing cell (which is pretty amazing!)

But I'm interested in work to make completely synthetic life with no preexisting biological components.


texts: We prepare buffer solutions with concentration in terms of x, for example 50x TAE buffer. How do we come up with x? Is x related to molarity in some sense? And how much can we concentrate the solution. We have 50x TAE but usually 10x TBE buffer, why is it so?


texts:
I found a short video on the Internet of a toad and I wonder if anybody could identify it?

It was posted on a social-media/blogging website called 'Tumblr',

so I don't know much about it (e.g., where the video took place).

EDIT: The original link is no longer active. Here's an alternate link.

Useful for hearing the specimen's "squeak"/scream.

EDIT 2: Here's a gif of some frames from the video for permanence on this site:

P.s. I think it's a toad. Please, don't hesitate to correct me/edit my question, if i'm mistaken.


texts: Programmatic way to differentiate homodimers from heterodimers?

texts:
For pdb files is there a simple programmatic way to determine if the file is made up of homodimers or heterodimers.

I have many files so an online tool or some psuedocode/scripts would help more than manually assessing each one.


texts: Is the Andraka pancreatic cancer test real?

texts:
In the wikipedia article about Andraka's pancreatic cancer test there are some controversial statements.

On one hand there are many glorious words about the method, also some awards, also some astonishing comparisons with other methods.

On the other hand, there is no proof, and also some evidence against its efficacy.

Also, I can't find any signs of Andraka's test in reality. For example, there is no such product in drug stores.

What is the proof or evidence that Andraka's method is really working and can feasibly exist in the near future?


texts: How is the effect of proof-reading on error frequency during DNA replication determined?

texts:
An article in Nature Scitable on DNA Replication and the causes of Mutation states that:

  When an incorrect nucleotide is added to the growing strand, replication is stalled by the fact that the nucleotide's exposed 3′-OH group is in the "wrong" position… During proofreading, DNA polymerase enzymes recognize this and replace the incorrectly inserted nucleotide so that replication can continue. Proofreading fixes about 99% of these types of errors

I am interested to know how this value of 99% was determined, and this is not explained in the article.


texts: experimental procedure regarding AceCS1 overexpression

texts:
I'm new to biology and was just as to curious on how one can experimentally prove/disprove that AceCS1 overexpression in mammalian cells would yield enhanced rates of fatty acid synthesis through acetate.

Thanks.


texts: Unsaturated fats contain double bonds like carotenoids (which is an antioxidant), and from my understanding, what makes carotenoid an antioxidant is that its double bonds allow it to undergo oxidation, hence they can donate electrons to free radicals. Therefore, would this suggest unsaturated fats (especially those with more double bonds) are also antioxidants?


texts: Calculation of the bacterial growth rate from a spectrophotomer growth curve

texts:
Typically the microbial growth in liquid cultures is monitored by turbidity. Data is obtained with a spectrophotometer to measure optical density at 600nm. The slope of the bacterial kinetic curve in exponential phase is the growth rate.

But I have seen two ways of calculate the growth rate:

Growth rate = Maximum slope value of the Kinetic curve
$Log_{10}$ transformation of the growth data and then calculate the slope.

I think the second one is right if you want to calculate the generation time:

generation time = $\frac{ln(2)}{Growth rate}$.

What is the correct way to calculate the growth rate and then generation time?


texts: When does the vertebral column finish chondrifying and begin to ossify?

texts:
I have read many articles on vertebral column development in embryos on the internet.
Different articles give different time periods for the end of chondrification of the vertebral column and the beginning of ossification.

Some websites and books(like The Developing Human: Clinically Orientd Embryology 10th edition) say that 'the 2 centers in each centrum fuse at the end of the embryonic period to form a cartilaginous centrum', which is rather confusing since they also say that ossification begins in the 7th week. How can ossification in the centrum begin when the chondrification centers in the centrum have not even fused yet? Why does it takes so long(2 weeks) for the chondrification centers to fuse?

When is the chondrification of the vertebral column complete and when does ossification start?


texts: Why do the COVID vaccines contain the cationic lipids they do?

texts: Why did Moderna & Pfizer specifically pick their SM-102 and ALC-0315 cationic lipids with tertiary amines, branched tails, long linker chains, and small hydroxyl head groups? Are the large tails and packing parameter to keep the lipid from leaking out of the liposomal membrane? Why not use any other large hydrophobic groups? Thanks!


texts:
When I researched I found  different reason for this, the  popular
ones are

1) white matter is mylinated .this reason was given in reference books and   this website

while others say

2)cell body concentration causes grayish appearance ,as in brain the cell body is concentrated outside. As mentioned in this .i.e cell body orientation.

also my teacher agrees with 2nd one, that the nissls granules contribute to the grayish appearance.orientation causes the effect of gray matter and white matter

I feel 1st reason to be more appropriate as there are billions of it couldn't be arranged as depicted in the second reason.

kindly help  me out to choose the accurate one, with appropriate reason of-course!


texts: What is the difference between "physical interaction" and "genetic interaction"?

texts: I searched sac1 in uniprot to know more about this gene. in interaction I selected this link and there I see that this gene has some "physical interactions" and "genetic interactions". I am wondering that what is the difference between "physical interaction" and "genetic interaction"?


texts: Troubleshooting bioconjugates migration in a SDS-PAGE gel?

texts: We do a lot of bioconjugation chemistry (click chemistry in particular but also NHS and Maleimide chemistries). Our method to valid the conjugation reactions have been to use SDS-PAGE gels followed with densitometry. However one particular challenge with such analyses is that proteins conjugated with non-proteins like DNA or PEG migrate with an inconsistent MW and also in a smear making it hard to isolate the relevant bands. I assume that this has to do with having a poly-disperse radius of gyration. Are there tricks that I can do to get tighter bands?


texts: Tea that makes everything taste like dirt

texts:
My highschool biology teacher once gave us (her class) a tea which made everything taste like dirt. I remember that chocolate candies, spicy hot sauce, and salty crackers all tasted the same after drinking the tea. The effect only lasted a minute or two. It's been a long time, and I can't remember the name of this tea - can anyone identify it?

(I am not certain if this question is appropriate for this SE, please let me know if it is not.)


texts: I know that we can get hydrophobic amino acids, but are there any proteins in the body whose surface is hydrophobic? If so what is their typical function and where can they typically be found and if not why not?


texts: E.O. Wilson on sociobiology and the origin of morality

texts:
Somewhere in E.O Wilson's writing, he discusses how human values are rooted in our nature as a specific kind of animal. He argues that we have an identifiable optimal living place -- a grove at the top of a hill, with surrounding grassland give an area of clear view, overlooking a body of water. He then goes on to further make this case by imagining that naked mole rats have risen to intelligence. He pens a speech that such a being might give on some patriotic holiday. And boy howdy, it sure does not sound like any epideictic speech you could imagine a human giving. The use of shit as a metaphor for sustenance alone is sufficiently jarring, but there were a bunch more, all firmly anchored in aspects of mole rat biology and social structure that differ from ours.

I would like to cite and quote this passage. I thought this was either in Biophilia or Consilience, but I have not been able to find it in either book, or in a bunch of other searches via google scholar, and through my own books and ebooks of his.

Does this sound familiar to anyone? Can you point me toward where I would find it?


texts: Is there a plant particularly suitable for absorbing Hydrogen Sulfide

texts:
I live in an area with some open sewers and in the morning I can usually can smell the gas inside my house.

There are many plants like snake plant which improve indoor air quality but I was wondering if there are any that are particularly useful for absorbing sewer gas (hydrogen sulfide)


texts: Does physical exercise following lack of sleep increase the risk of sudden cardiac death (SCD)?

texts:
Is there any scientific evidence supporting the hypothesis that physical exercise following lack of sleep increases the risk of sudden cardiac death (SCD)?

The only relevant research I could find is: Reddy PR, Reinier K, Singh T, et al. Physical activity as a trigger of sudden cardiac arrest: The Oregon Sudden Unexpected Death Study. International journal of cardiology 2009;131(3):345-349. doi:10.1016/j.ijcard.2007.10.024. However, it only points out that 5% of the SCD cases in the sample took place during vigorous physical activity, which does not directly answer my question.

I am not a biology professional, so please pardon me for any misunderstanding, and, when possible and reasonable, please avoid using too many biological jargons in the answer.


texts: How is achieved the loss of heat through vasodilation?

texts: I know it is the widening of blood vessels, loosing heat in this way. But is it achieved through: sweat evaporation, the increase of cardiac rhythm, the increase of respiratory/ breathing rhythm or frequent urination?


texts: How do gain-of-function alleles help with problems caused by genetic redundancy?

texts: Genetic redundancy masks the gene functions (eg it masks diverse functions of the tumor suppressor gene). I have read on the internet that gain of function alleles can solve a such problem caused by genetic redundancy and would like to know how.


texts: Dawn simulation - does color change affect waking up?

texts:
just curious. Are there any works or research results related to the influence of light color used for dawn simulation? I mean those wake-up lights which try to simulate dawn to make waking up better for you.

The cheap ones only use one color - those "warm white" LEDs - and only change brightness. However the more expensive ones also change color like the sun during sunrise.

I am just curious how much important could be the color change. :-)

thanks


texts: What do we use as baseline to determine what genetic segments are "mutations" (and what are not)

texts:
In order to determine whether a particular segment of the genome is a mutation, there must first be a baseline code on which that code looks somehow different.

How has the baseline genome been determined? Did someone dig up a _very_old_ human skeleton which was subsequently DNA-analyzed to be used as the baseline?

Or do mutations contain some kind of fingerprint that tells researchers that "it is not the original genome"? If so, how does that fingerprint look like?


texts: Has anyone tried using luminescent conjugated oligothiophenes to detect cellulose in a microbial biomass? If so is it accurate?

texts: I recently found this paper http://www.nature.com/articles/srep35578 which describes a "new" method for detecting cellulose. As I'm not an expert in the field I was wondering if other people have used this to detect cellulose in microbial biomass (specifically E. coli biofilm) and not just plants. It seems like it should work but maybe I'm missing something.