texts: Is this experiment to check enzyme reaction rate according to substrate concentration correct?

texts:
We just had an experiment to check enzyme reaction rate according to it's substrate concentration.
In the experiment, we used a varying amount of substrate and the same amount of enzyme:

(1.5mm enz, 4.0mm water, 0.5mm subs)
(1.5mm enz, 3.5mm water, 1.0mm subs)
(1.5mm enz, 2.5mm water, 2.0mm subs)
(1.5mm enz, 1.5mm water, 3.0mm subs)
(1.5mm enz, 0mm water, 4.5mm subs)

We check the rate by looking at the optical density after 3 minutes.

Upon staring at this, I couldn't help but wonder: We don't only change the substrate concentration! We also change it's amount!

While 3.0/4.5 is a higher concentration than 0.5/4.5, it's also a higher amount resulting in longer reaction time for sure. If we check after 3 minutes, there's a chance that the 0.5mm subs would already be gone.

If we really wished to look at the rate according to concentration, shouldn't we have only changed the amount of water? It also changes the concentration of the enzyme but there is there any way to isolate either of them?


texts: How can I make legal mature female Cannabis plants to Flower in home during March (springtime)?

texts: In December 2019 I purchased 4 Cannabis seeds Legally in Canada.Two of my plants are now about 100 cm tall. I am using wide-spectrum LED grow lights and have fertilized them both. I started with 16 hours light per day and now have cut back to about 12 hours per day.I was told that these seeds were not auto-flowering.These seeds were from Tweed and were labeled "Baker Street Indica". The leaves are all healthy and dark green. Now I would like to stimulate flowering. As our days are getting longer I want to trick the plants into its Fall/Autumn flowering cycle. Any good ideas ?


texts: What evolutionary reason is there for having the urinary duct and reproductive organs so close together?

texts:
As the old joke goes, "God must have been a civil engineer. Who else would put a waste facility straight through a recreational area?"

But maybe it wasn't God. Is there any evolutionary reason (or background for) having the urinary duct and reproductive organs right next to each other (in both humans and many other vertebrates)?

To be clear, I'm not asking why isn't it elsewhere. I'm asking where the original "design" came from that spread everywhere.


texts: How to automatically obtain the "kingdom" of a species from its name?

texts: I'm looking for a simple way (such as a database) so that a program can get the kingdom of a species, knowing its name (such as "Prunus persica"). As a matter of fact the species I'm concerned with are the ones in the miRBase database.


texts:
A and B are two different proteins:
1- can they have same mrna
2- is it possible that the gene types which encoding the synthase are same ?

my answer is yes to both .
because after protein synthased cell can remove aminoacids with  post-transcriptional modification etc.


texts:
I've seen that at the earlier stage coconut is filed with water and, as time passes, the water inside the coconut escapes and a thick layer of white substance forms.

Is the water converted into that white substance?


texts: How can a continuous RNA be transcribed in the lac operon?

texts: The lac operon has 3 genes: lacZ , lacY and lacA. I have seen that the m-RNA transcript of these genes has stop codons in between. So, how can the RNA be made continuously? Won't the RNA Pol detach if there is a stop codon in between?


texts:
I have several mulberry seedlings that have popped up in my garden.

What species (or hybrid-species) are they?

Details:

The location is Toronto, Ontario
The date is July 18th, 2019
I have several different kinds of cultivated and uncultivated mulberries in the surrounding area that could have been the parents. I would list their cultivars and species names, but to be honest, I don't have much faith in them (I think they might just taint our analysis/identification).

Note: Here are some close-up photos of the plant in the bottom-right of the above photo:

https://i.stack.imgur.com/qi6dJ.jpg
https://i.stack.imgur.com/JlNh0.jpg
https://i.stack.imgur.com/rP2M8.jpg
https://i.stack.imgur.com/yWQGg.jpg
https://i.stack.imgur.com/vkH80.jpg
https://i.stack.imgur.com/ZJTx2.jpg


texts: Is this how female and male gametes look like in plants?

texts:
In the red box, the pink one is female sex cell I presume and the blue one is a male sex cell.

http://prntscr.com/dsii2x Am I right? or are these chromosomes.. I'm confused.

This is law of segregation.


texts: Is autoclaving sucrose solution necessary?

texts: I use 10% sucrose solution to feed lab mosquitoes. Until now, I mix sucrose in autoclaved water and use it directly for feeding mosquitoes. Is it necessary to autoclave the sucrose solution itself before use?


texts: Simple interpretation of effective population size?

texts:
I'm looking for alternate ways to explain effective populations size, in more conceptual terms. These need not be perfectly accurate "definitions" but should at least be generally accurate in non-edge cases.

For example, if I have a population with a supposed effective population size of 1000, what (if anything) can I conclude about the amount of genetic diversity present within a single individual sampled at random from the real (census) population?

Like, would it be overly simplistic to say that the sampled individual could be expected to contain ~1/1000 of the population's standing variation? Or to say that a given (observed) nucleotide state has a 0.001 probability of being   fixed?

Again, I'm looking for anything that is not the standard way to explaining Ne
to somehow get a student's head partly into the game without being wholly misleading. Thank you


texts:
As far as I know, humans are the only animals that use visual references to track prey that is not immediately visible to them.

Do any other animals do this?

I'm not referring to stalking prey that the predator already has in sight, like many big cats do, and not tracking prey, that is out of sight, by scent or other means, before switching to visual before the final attack.

Are there any other animals that primarily use visual information, such as tracks, shed fur, broken foliage, disturbed earth, etc., to follow or approach a prey animal that they can't already see?


texts: How was the resemblance between apes and humans explained in pre-Darwinian biology?

texts:
Humans and apes have somewhat obvious similarities, these must have been apparent to natural philosophers before the possibility of a common ancestry was first proposed in the mid-1800's. These proposals were not formally made in Darwin's On the Origin of Species (1859), but his general ideas of common ancestry were built upon in Thomas Huxley's Evidence as to Man's Place in Nature (1863) and then Darwin's The Descent of Man (1871).

How was the resemblance between apes and humans explained prior to this shift in thinking?


texts: Typically we determine the concentration of proteins using a 280 nm reading. However, it is reasonable to use 205 nm. I was curious about the effectiveness of this method.


texts: Do immature fruits perform photosynthesis?

texts: Most immature fruits are green: peppers, pine cones, plums, lots of them. I want to know if the green is from chlorophyll in the cells. Do the fruit cells perform photosynthesis? When you cover a green stem or leaf, it will turn pale and stretch. That is because the stems have little need for chlorophyll in the dark, which is why they are pale. They stretch because the auxins in the stems are not destroyed by the photons, and the stems stretch out and topple over. If a green fruit is covered, will it turn pale and stretch like that?


texts: The colour of aquatic plants found deep under oceans

texts: I have read that many aquatic plants found in deep oceans are red in colour, however, I do not understand why. As red is the color which gets the least scattered it should be the only light available to them. Thus reflecting red light would deprive them of any light. Yet they appear to be in red color. Why is this so?


texts:
We have those caterpillars with some sort of webbing on stinging nettles below some oaks.  Photographs I found in Wikipedia look quite hairier with long white hairs but maybe it's the molting level?

Or those guys are something less notorious.  This is in Germany, Northrhine-Westfalia.

And here is a video in case it helps.


texts: What's the difference between shotgun sequencing and clone based sequencing?

texts:
In a lecture during  my undergraduate degree we were introduced to the race to complete the human genome. Celera were competing with Sanger and collaborators to sequence the human genome. Celera wanted to patent some sequences, whilst Sanger et al. wanted to keep their findings in the public domain. Celera knew they couldn't compete with Sanger et al. with conventional cloning techniques which required a lot of man-power, "so instead opted for shotgun sequencing".

To me it seems like both clone based sequencing and shotgun sequencing could have been used together, however the lecturers semantics were a bit vague (...okay, I wasn't paying close enough attention!) and I didn't ask for clarification at the time.

Whilst I appreciate this is a large topic, what are the main differences between Celera's shotgun sequencing and Sanger's clone based sequencing during the late 1990s? Are "shotgun cloning" and "clone based sequencing" actually mutually exclusive terms?


texts: Can protein sample be made 2% Triton X-100 free?

texts: The protein I am purifying needed an elution buffer with 2% Triton X-100. I formulated the elution buffer not keeping the CMC in mind. My goal is to make my protein sample triton free to check its stability and quantify its concentration. Lately, I learnt that micelles can be broken down upon dilution. So, I've diluted my protein sample below triton's CMC and tried concentrating it using Sartorius Vivaspin 5K (PES resin). I loaded 500 ul of diluted sample and was left with 100 ul after concentration using vivaspin. But, this sample gave an abnormal reading of above 3 OD after blanking against the buffer it is in. I presume, triton's interference is causing these discrepant readings.


texts: Where are doxycycline's anti-inflammatory properties derived from?

texts: I have been looking at this antibiotic called doxycycline which is used mainly as an antibiotic. It has however some interesting anti-inflammatory properties. Does anyone know where these anti-inflammatory properties come from, chemically?


texts: Is it possible to sequence only the 16S rRNA component? If so, how?

texts:
There have recently been several papers on using 16S rRNA as a way of identifying species (here, and here). I'm wondering if it's possible to sequence either just that subunit of the ribosome or just the sequence of DNA that it comes from (probably not, I know). That way you can use only the sequence you need to compare against other 16S rRNA sequences to test for novel species.

If so, what is the process involved?


texts:
Do new neurons divide propotionally?

if i try to improve my reasoning skills,are the new neurons only made for that specific region of the brain that controls reasoning skill?
i have heard that one side of the brain controls the other side of the body, if i try to use my non-dominant hand(left hand in my case),are new neurons only made for right side of the brain,does it improve only some of the brain regions?


texts:
Functional connectivity may be defined as

  »the temporal correlation between spatially remote neurophysiological events, expressed as deviation from statistical independence across these events in distributed neuronal groups and areas«

or alternatively as

  »the presence of statistical dependencies between two sets of neurophysiological data«.

Images of large-scale brain networks typically show highlighted regions of interest that - in my humble understanding - are supposed to be functionally connected. But being highlighted means being active (at least more active than other regions), and thus functional connectivity seems to be mainly excitatory (even though only virtually).

But what about inhibitory functional connectivity? Can it be found by equal statistical means as excitatory functional connectivity - and how would it be "highlighted" in brain images?


texts: What are all of the currently known variations of the G zipper motif?

texts:
The G zipper motif is found in transmembrane proteins at an above random frequency and there are models explaining how it might help with multiple transmembrane intra-membrane helix bundle assembly.

However there are a bunch of different "flavours" of these G zipper motifs. Here are the ones I have come across so far:

GXXXG
GVXXGV
GXXXGXXXG
AXXXGXXXG
SXXXGXXXG
GXXXGXXXS
GXXXGXXXT

I don't think I am completely up to date so that is a non-exhaustive list. Have I missed any? Broadly speaking what accounts for their variation?

note: X refers to a non specific amino acid in FASTA protein sequences.


texts:
I have more than 10 cell lysate samples (70 µL each) whose concentration varies from 1.9 mg/mL to 4.8 mg/mL. I have 5X and 2X SDS sample buffers. I would like to prepare SDS PAGE samples in such a way that the final concentration of all the protein samples would be equal. I am struggling to deal with it.

What I know is while using 5X buffer, for 4 parts of sample we use 1 part of buffer to make it finally 1X. Similarly, for 2X buffer, we use equal amounts of buffer and sample to make 1X. Also, I would like to know will it be a problem if I make it more than 1X? Why we need 1X?


texts: Molecular Docking Enzyme Inhibitor Biosensor?

texts: I had some task to study Molecular Docking relations with Biosensor and I am really new with this discipline (beginner). I am docking C60 with Glucose Oxidase and my question is: what would happen if C60 inhibited the active site of enzyme? Can the protein still be used by the biosensor or would it be broken because of the active site used by C60?


texts: How does the partial pressure of oxygen affect mental focus?

texts: On this Wikipedia page it says that lower oxygen levels can cause light-headedness. Is there evidence that higher partial pressure of oxygen can improve mental focus?


texts:
I believe a "mechanistic study" means a study where a medicinal product is being used but the purpose of the study is to investigate the patient or disease, not the medicinal product.

How does this differ from any other type of study?  What is the purpose of this study?  Why would we not be interested in the medicinal product?

Please provide a very simple example that a non-scientist could understand.


texts: Does antibody staining / immunolabeling block or inhibit protein function?

texts:
In dissociated live cells, does staining them with an antibody block the protein's function?

I am sorting cells based on their expression of a few marker genes, and culturing them post-sort for several days.

How can one assess if the protein is still functional?


texts: How do people wake up just before their alarm goes off?

texts:
I can wake up less than 2 minutes before my alarm goes off regularly.
I read the common wisdom on the subject which says "circadian rhythm; PER proteins; internal clock". I am skeptical of this for two reasons:

I go to sleep at night at different times ranging from 11:00 to 2:00 and rarely check the time, so if I don't even know the sleep start time, how can my body measure out the duration of sleep and get the end time right?
People's chemical levels vary from day to day depending on a ton of variables (food intake, physical activity, stress, etc). It appears that we are not deterministic machines that are constant from day to day to that level of precision

I have a few hypotheses that I haven't heard before:

Maybe the subconscious is queuing off the light level in the room? (this a unique property of the specific minute of wakeup, as there would be less light a minute sooner and more light a minute later)
Maybe while sleeping, the eyes periodically open, view the clock, process the numbers, and wake up accordingly (just like people  can sleepwalk and use their eyes to process where the walls and doors are)

Any thoughts?


texts: Transcription by RNA polymerase in absence of inducer and activator

texts:
Does the presence of activator(CAP-cAMP complex) and inducer(lactose) only increase the likelihood that a particular gene(here operon) gets transcribed, i.e increases the rate of transcription of that gene?And transcription of some(assumption) genes always happen?

Because as I know basal level transcription is something that happens always,even without an inducer.


texts: Can multiple cetacean species communicate?

texts: It seems that individuals within the same species have their own communication, but is there evidence to suggest that individuals from different species are able to communicate?


texts: Can we see the cell cycle of the cells administered using IVIS-like device?

texts:
My question;

Can we measure the cell cycle of the administered cells from outside the body, while the recipient is still alive ?　Preferably, by using a device such as IVIS that can read fluorescent labelling in the body non-invasively.

In this paper, cells incorporating a reporter called Fucci are transplanted into mice in which a skin-flap window was created. The mice were observed in CLSM while alive through the skin-flap window. As a result, the cells were individually imaged at very high resolution.

Fucci-explessing cells change colour as the cell cycle progresses, so the researchers were able to visualise which stage of the cell cycle each transplanted cell was in.
However, this method is invasive. So we need a simpler method. The required resolution should  give what proportion of cells are in which stage of the cell cycle.　We don't need the single cell resolution.


texts: What happens if the queen ant is removed and taken elsewhere?

texts: Suppose I manually remove the queen ant from a colony, and take it to a completely different place (ant cannot visually travel back to its colony). Will it start a new colony in its new surroundings, similarly to the way in which it did after the nuptial flight? Or will it keep on looking for its old colony?


texts:
In the last weeks there have been a lot of news reports about the number of animals that died in the current wild fires. However, I was wondering, what that is as a percentage of overall animal population in Australia. So:

What's the total number of animals living in Australia?


texts: Do animals demonstrate target practice (i.e., playful accuracy behavior)?

texts:
Do animals demonstrate any sort of accuracy-motivated play? (please provide examples!)

Consider most human sports and related hobbies. Most share the common goal of hitting a target or being accurate, and in the case of organized sports, points are typically awarded for being accurate. Archery, firearm past times, football, soccer, basketball, hockey, baseball, tennis, billiards, bowling, darts, beer pong, horseshoes, and countless other examples all are based on competitive accuracy.

Humans seem to be obsessed with accuracy in our competitive past-times. Examination of more ancient sport interests demonstrate less preoccupation with accuracy (though of course there is variation between cultures -- see here or here, ), and perhaps just more with demonstrations of strength and dominance. However, competitive accuracy was alive and well in ancient times: boxing, sword fighting, lacrosse, hoop rolling, golf (and Chinese equivalent Chuiwan), and others already listed are just a few examples of accuracy games with more ancient origins. It seems, then, that the human species has  had a fascination with accuracy for a long time.

However, do animals have the same (or really any) preoccupation with accuracy? I've seen countless examples of animals 'playing' or competing (e.g., pets & captive animals playing with toys & enrichment objects,  young males of various taxa sparring or wrestling, whales playing with their food, monkeys sheep herding on dogs, etc.), but is there any evidence or example of wild animals playing 'games' based on accuracy?


texts: Can you increase the microbiota in an insect?

texts: I know you can suppress the microbiota of an insect with antibiotics, but I´m am looking for a way to increase it. For example, can I feed an insect with something that helps boost the bacteria like agar or something.


texts: In microarray normalization, why is the normalization factor this?

texts:
I am working on analysis of a huge number of microarray files. I was trying to understand the need for normalization in microarray data and was going through this paper by John Quackenbush(2002). In the paper, the author mentions that

  There are a number of reasons why data must be normalized, including
  unequal quantities of starting RNA, differences in labeling or
  detection efficiencies between the fluorescent dyes used, and
  systematic biases in the measured  expression levels

Then he talks about a simple normalization techniques. Assuming that  the total hybridization intensities summed over all elements in the arrays should be the same for each sample, he defines a normalization factor is calculated by
summing the measured intensities in both channels-

where Gi and Ri are the measured intensities for the 'i'th array element (for example, the green and red (or experimental and control) intensities in a two-color microarray assay) and Narray is the total number of elements represented in the microarray.

Then the author says this -

This is the part I don't understand. What is the need to introduce $G_k^{'}$, $R_k^{'}$ and why are they what they are? Most importantly, why is $T_i$ equal to $R_i/G_i$ first and then ($1/N_{total}$)*($R_i/G_i$)?

Any ideas?


texts:
What is MHC haplotype? I did check out the wiki article, but did not understand.

(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)


texts: Optogenetics - How do microbial opsins work?

texts:
I'm just introduced to the optogenetics method and am having some trouble grasping the genetics (of the optogenteics) part of things.

So we have Retinal and Opsin that form Rhodopsin molecule that serves as a light-gated ion channel (which is, needless to say, very cool).

What is the process in which a cell population is targeted and implanted with these Rhodopsins?

And where does the microbial opsin gets into picture?

My main resource, so far, was - Optogenetics - Method of the year/Nature.

Thanks!


texts: How does the immune system find the DNA code for antibodies

texts:
There are millions of possible antigens. To respond to each antigen, the immune system must quickly produce an antibody by modifying the DNA of a B cell.

I have no idea how this process works, but surely it can't be by trial and error.

So I thought how I would do it:

The part of the pathogens DNA that codes for receptors is copied
then an algorithm is applied that transforms this code into an antibody code.
This code is then pasted into the DNA of the B cell. So the B cell has antibody receptors that fit on the antigen.

But how does it work in reality?


texts: Why does the rabies virus have such a long incubation period?

texts:
So there was a case in India, where a man developed rabies 25 yrs after the dog bite. Source:
https://www.google.co.in/amp/s/m.timesofindia.com/city/goa/25-yrs-after-dog-bite-man-gets-dies-of-rabies/amp_articleshow/16415870.cms
I have the following questions:
1) what are the reasons behind such a long incubation pd?

2) in such cases, can vaccines taken years after the dog bite save the person? (Even though it’s advised to take it immediately)


texts:
I have the following example of how an equation for the production of mRNA in a particular organism could look like:

  Consider the following equation for the production of mRNA for a gene Y. Gene Y is expressed from a promoter that is repressed by protein R. For example, if Y is GFP above, then R would be TetR.
  $$
\beta_{Y m}=\left[\frac{\beta_{y \max }}{1+\left([R] /_{K_{R Y}}\right)}\right]
$$

And now I am trying to understand what the different variables of the equation are.

$\beta_{ymax}$ must be the maximum rate at which mRNA can be produced and $R$ is concentration of a repressing protein, but what must then $K_{RY}$ be? Is it as simple as that it is an inducer for the production of mRNA?


texts: How to detect Single Nucleotide Variants (SNVs)?

texts:
This image is obtained from this paper.

The description of this image is as follows:-
DNA-sequence reads from a tumor sample are aligned to a reference genome
(shown in gray). Single-nucleotide differences between reads and the reference genome indicate germline single-nucleotide variants (SNVs; green
circles), somatic SNVs (red circles), or sequencing errors (black diamonds).
(a)
In a pure tumor sample, a location containing mismatches or single
nucleotide substitutions in approximately half of the reads covering the location indicates a heterozygous germline SNV or a heterozygous somatic
SNV - assuming that there is no copy number aberration at the locus. Algorithms for detecting SNVs distinguish true SNVs from sequencing errors by
requiring multiple reads with the same single-letter substitution to be aligned at the position (gray boxes).
(b)
As tumor purity decreases, the fraction
of reads containing somatic mutations decreases: cancerous and normal cells, and the reads originating from each, are shown in blue and orange,
respectively. The number of reads reporting a somatic mutation decrease
s with tumor purity, diminishing the s
ignal to distinguish true somatic
mutations from sequencing errors. In this example, only one heterozy
gous somatic SNV and one hetererozygous germline SNV are detected
(gray boxes) as the mutation in the middle set of aligned r
eads is not distinguishable from sequencing errors.

This is my understanding below. Am I correct?

There are multiple reads that are aligned such that for a given location in the reference genome,(here fourth), if approximately half or more of the reads covering that location has a single nucleotide mismatch with the reference genome,then it is a heterozygous SNV.
Eg:-


texts: Are there animals that are present in two different classes?

texts: Are there animals that are present in two different classes, like amphibian and bird, reptile and mammal etc.?


texts: What determines whether the maternal or paternal allele is expressed?

texts:
I am taking cell biology and have this question:

During the process of gene expression, it is possible to express either the maternal allele or the paternal allele.

When and how is the determination made to express one allele over the other?


texts: Where to start understanding chemical principles of human body?

texts:
I have no background in chemistry.

What is a good way to start understanding principles of human body - how it works, determine which meals are good or bad for health. Maybe it is not just chemistry, but some other fields, too. I just want to know how human body works, lets say - improve health - but on my own. Knowing just that this is not good for health is not enough for me. I want to build deep knowledge.

I want to know how it is functioning at the lower level (based on chemistry).

Where to start?

(sorry for my incompetence)


texts: What's the mechanism for pain-induced swoon?

texts: Is it true that people will pass out when subject to pain too much to bear, or there's no such threshold? What's the reason for passing out under acute pain, even if no physical injuries occur (e.g, loss of blood, etc.)?


texts: Is exon order always preserved in splicing?

texts: Are there any cases in which the splicing machinery constructs an mRNA in which the exons are not in the 5' -> 3' genomic order? I'm interested any such cases, whether they involve constitutive or alternative splicing.


texts:
Nervous tissue includes Neurons and Glial cells. Neurons have soma and other projections (neurites) namely Axon and Dendrites. Axon or dendrites of a nerve cell covered with endoneurium
is called nerve fibre, a bundle of nerve fibres covered by perineurium is called
nerve fasciculus, many nerve fasciculi covered by epineurium form the "nerve". Is the "nerve", which is present in the PNS, will be regarded as a tissue or a cell?


texts:
I am little confused here.
I used the term adrenoagonist and sympatholytic to describe the compound.
However, my teacher says that the correct term here is adrenomimetic -term.

My understanding of Terms

Adrenoagonist says that to bind to adrenoreceptor which prolongs the effect of NE in receptor.
Sympatholytic - inhibition of postganglionic fibers of sympathetic nervous system
Adrenomimetic - mimic effects of sympathetic nerve stimulation on pre- / postganglionic fibers.

I still think clonidine is sympatholytic i.e. adrenolytic (not adrenomimetic).

How can clonidine be adrenomimetic?
Why not adrenolytic?


texts: Any examples of animal behavior in response to meteor showers?

texts:
I just spent two nights observing the Perseids and was wondering whether any animals have been recorded to exhibit unusual behaviour in response to meteor showers.

It is known that some animals change their behavior at night in response to moonlight and artificial illumination (e.g. eagle owls call more frequently at full moon), but I am not aware of any materials indicating behavioral changes in response to short-term lights like those produced by meteor showers or far away lightnings.

Any pointers would be appreciated.


texts: Hominidae is to hominid as Poaceae is to what?

texts:
I considered asking this on English.SE, but decided against it, since it strictly applies to biological nomenclature, which not many of them will know about - particularly that of plants.

So, in animals, all families end in the suffix  -idae - e.g. Hominidae, Apidae, Canidae or Laridae. When referring to members of a family, you can use the suffix -ids - e.g. hominids, apids, canids or larids.

However, plant families are usually named with the ending "aceae" - such as Poaceae, the grass family. If I want to refer to members of Poaceae (without just saying the common name), what do I say?


texts: What do the -30 to +60mm markings mean in this MRI scan image?


texts:
This plant came (seemingly by accident) with another pot plant a few years ago in a plant sale.  Unfortunately, we do not remember what the original plant was that it came with.

It was initially one of the small 'fleshy stems' you can see in the photos, about 2cm in length.
If you do not water it, the leaves fall off and leave the fleshy stems
If it is watered, a new section of stem is grown with leaves.
Its existing stems do not seem to regrow their leaves if they drop off.
It was acquired in the South-West of England.
It does not appear to be affected by the time of year.

Photos (click to enlarge):


texts: How can I find some pieces of the genome of a microorganism?

texts: I have figured out how to download the fasta of the genomes of microorganisms, for example the botulism bacteria and the spirulina algae. However, I want to find a fasta file for some significant extraction of those genomes - say, some important gene, some mutation, some protein that occurs in a microorganisms genome. What should I look for, and how can I find it in genbank?


texts: Can an influenza virus carry other infectors with it?

texts:
This idea came to my mind when thinking about how many people become ill in many locations with similar symptoms (fever and rough cough) from Influenza.

There are of course different types of influenza virus.

Can Influenza A virus work as a vector for other upper respiratory infections?
That is, much the same as the mosquito being a vector of malaria, can an influenza virus carry other infections with it?

If so, how? If not, why do some people get so sick from viral influenza, and not others?


texts: Converting Ensembl Compara gene tree DNA alignment to corresponding amino acid alignment

texts:
I have Ensembl compara gene tree alignments (Compara.gene_trees.57.fasta.gz downloaded from ftp://ftp.ensembl.org/pub/release-57/emf/ensembl-compara/homologies/) in nucleotide format. According to documentation, it says that the file "contains the peptide alignment for every genetree in fasta format".

I was wondering what might be a handy tool to obtain the corresponding amino acid alignments from the file.

Thanks,

Ikram


texts: Stable isotope sample preparation: Bone Collagen

texts:
I am performing research in which I need to extract bone collagen from the foot bones of American Beaver (Castor canadensis).  I have read through the literature fairly thoroughly on both the archaeological/anthropological side and the wild life side and have been finding a many tweaks to a fairly simple extraction process, but I still have a few questions.

When processing bone I split the bone and removed the center, which was red/ light pink, (I thought it was the marrow and wanted to make sure that I was getting collagen from only 1 part of the bone to not confuse my isotope data with varying tissues)
There is also some variability across papers in the time that people allow bone to demineralize in a strong acid  ranging from 20 mins to upwards of 10 hours.  Does anyone have any experience with this and size to which you ground your samples.
The literature has a variety of temps ranging from 58 C to 95C, it proposes to gellatinize the collagen in a weak acid over a variable number of hours (approx pH of 3), does anyone who has experience offer a temp and time that worked for them.

Any help is much appreciated, Thanks


texts:
What makes white phosphorous toxic?

I mean it causes liver and kidney damage, and altered blood coagulation, but it is hard to find anything about what biochemical mechanism this poison uses to kill liver and kidney cells and why the liver is not capable to neutralize it even in a 50mg/kg dose (LD50 in rats). It would take just a simple oxidation to convert it to phosphate, which is commonly used by living cells.

conclusion:

I think the main cause that white phosphorous is so toxic that it is not something common in the environment, so there was no evolutional pressure to adapt to it. The human body can deal with it relative fast, but it damages cellular organelles and causes possibly fatal liver and kidney damage in hours. Some of the metabolites are even more toxic and they can cause arrhythmia and disturb the CNS. Because the molecular mechanism of toxicity is still mostly unknown and there is only a short time to treat people before liver and kidney damage, currently I think there is no way to save somebody exposured to a high dose of white phosphorus.


texts: What is the significance to life of the anomalous properties of water?

texts:
I have heard that the anomalous properties of water - e.g the fact its solid form is less dense than its liquid form - is extremely important. In fact, some people have gone so far as to tell me it was crucial for the development of life.

What is the significance of the anomalous properties of water to life?


texts:
N,N-Dimethyltryptamine (DMT) is found, besides humans and other animals, in many plants(50+).
In humans (in the pineal gland) it is suggested that it is used for our immune system.

  Immunomodulatory activity may contribute to significant anti-inflammatory effects and tissue regeneration. [Wikipedia]

The question is, could it have a same function in plants or it has a more defending function, like other drugs that are derived from plants?


texts: People say the cardiac cycle depends on blood pressure? How so?

texts: I know what the cardiac cycle is. There are two phases diastole and systole. One is the relaxed, and the other is the contracted form of the heart. The diastole is where blood is pumped to the ventricles and systole is when blood goes to the aorta, and lungs. But what is the connection to blood pressure?


texts: Is organ transplantation race dependent?

texts:
I watched (IMHO canibalistic) movie "Seven Pounds" where protagonist donated many of his organs to other people and I noticed, that most recipients were black also as protagonist was.

Is race really taken into account when organ transplanting?

UPDATE

The question is not just about if interracial transplantation really good or bad. I can imagine, that transplantation is done same-race just in case, in favor of "do not harm" principle.


texts: Why Do we close our eyes while sneezing?

texts: Google says germs  may fall on eyes from our sneeze but it happens all the time . Also it says it a part of contraction. What may happen if we sneezing wirh our eyes open ?


texts: Say plant x has a dormancy period of y in location z, for instance in Sweden. We bring this plant to another location z', say France. Are there any results with respect to if/how the dormancy period would change? (I would assume such observations would be of interest to understand how plants adapt to/can cope with climate change.)


texts: How distantly related are eusocial insects? Aren't members of a species much more related than 1/4, 1/2, or 3/4?

texts:
Possible Duplicate:
  How many genes do we share with our mother?

I went to a lecture that talked about the behavior of social insects in terms of their relatedness of genes. For instance, workers were 3/4ths related to each other, so it was in their gene's interest to care for each other instead of having their own, half-related offspring.

However isn't it the case that members of the same species are much more related than 1/2 or 3/4s? I've read that we share anywhere from 95-99% of our genes with chimpanzees. Also I believe I've read (perhaps in Pinker) that we share some 60% of our genes with daffodils.

So when they talk about the relatedness of social insects, and they say it's 1/2 or 2/3 or 1/4, aren't they really talking about the 1% to 5% of genes that are in play in sexual reproduction within the species? In other words, aren't I 97% + 1/2 * 3% related to my sister, assuming human beings share 97% of our genes?


texts: Is the 6th rib attached to 7th rib, and 7th rib to 8th?

texts:
I'm just confused between a lot of pics that draw the thoracic cage in their way. what are these white things that I've shown?

or why the 7th rib is attached to the 8th?


texts: What are "+" and "Ar" in consensus binding sequence of amino acids?

texts:
So I was reading this paper and found a figure as below:

I understand that [LEAM] means any of LEAM residues, pS is phosphoserine and X means any amino acid residue.

What is [+] here ? Is both R and Ar arginine itself?


texts: lifespan of Nautilus compared to other cephalopods

texts:
Most cephalopods live uncharacteristically short lifes compared to other creatures of their size and intelligence. The octopuses with the longest lifespan for example, the giant pacific octopus, only live for up to 5 years.
This is quite long for cephalopods already, as some of them only live for as little as half a year.

The reason for this short lifespan is not aging itself (meaning loss of information in the epigenome and similar effects), but their reproduction. The maturation of their reproductive organs results in the deactivation of their degestive glands, so they basically starve themselves to death.
When the reproductive glands of an octopus are removed, their lifespan increases greatly.

Nautilus are an exception to this low lifespan of cephalopods. They live to be over 20 years old.
Why do nautilus live so long and is it possible to grow other cephalopods with similar lifespans by introducing nautilus genes?


texts:
I came across Lindeman's 10% law at school. It states that 10% of the total energy entering a trophic level is available for transfer to the next trophic level.

I was reading Ecology: Principles and Applications
By J. L. Chapman, M. J. Reiss and they mentioned two contradictory statements:

The 10% law, i.e. the trophic efficiency is always 10%
The trophic efficiency increases with trophic level (which was substantiated by data).

This is the statistics:

What is right? Is Lindeman's 10% law actually valid?


texts: How is NAD+ used in lactic acid fermentation after it is oxidized from NADH?

texts: I am confused with the whole process of glycolysis and the fate of the products of this reaction. So, I understand that anaerobic glycolysis results in 2 pyruvate + 2 NADH and 2 net ATP. Is the whole anaerobic purpose of glycolysis to make the 2 net ATP? Then pyruvate and NADH are waste products? Also, pyruvate then reduces to lactic acid. What is the need for this? NADH is oxidized to NAD+. How is NAD+ used? Also, lactic acid is eventually converted back to pyruvate through Cori cycle. How is that pyruvate used?


texts: Is a Ribonuclease Inhibitor protein the only mechanism employed by the human cell to protect cellular RNA from degradation by endoribonuclease?

texts:
Are there any other methods of protection for cellular RNA from degradation by endonuclease (specifically the Pancreatic Ribonuclease RNase II (Eosinophil-derived neurotoxin) and RNase III (Eosinophil cationic protein)) besides Ribonuclease Inhibitor Proteins? Perhaps a method that interacts with the RNA itself rather than compromising the RNase?

Would 5' end capping or 3' end polyadenylation which are normally used to protect from exoribonuclease also protect from endoribonuclease? Could a Ribonucleoprotein Particle (RNP) type strategy protect from degradation?

Thank you,

CDB


texts:
I want to measure metabolism in tardigrades (a jar of 30 tardigrades). I know that an easy way to measure metabolism is heat loss; I can just measure the temperature of the water before and after a certain period of time and take the difference. I have a few questions:

1) Is this a viable way?

2) Do I need to put the tardigrades in a controlled system (or is the outside environment a constant)?

3) Will the measurements be really really small (so I would need a very precise thermometer?)

4) How long should I wait between the two measurements?


texts:
When is colchicine added to dividing cells for karyotype studies?

I know that colchicine inhibits polymerization of microtubules.

2 So, why should it stop the cell cycle at metaphase when microtubules have already assembled and the next step(anaphase) requires depolymerization rather than polymerization ?


texts: I cannot find a clear explanation of what is mRNA expression level, and how to measure it. I would appreciate if someone explained it or gave a reference.


texts: How is output of DNA assembler measured?

texts:
I developed own DNA assembly pipeline. Input is set of reads and output is set of contigs.
Many papers measure own algorithms and compare it against each other. There are basic metrics like:

N50, N70..,
number of contigs,
genom coverage,
error rate

I download tool QUAST and there I can see metric N50, L50, where is easy to develop own computation. But how I can measure error rate of my output contigs? Is there any tool which can do it?
I searched in many papers but I cannot find way how they do it. I would like to compare with some assemblers with some general way. I found only hints that it should be done by aligning contigs to reference genomes but I do not know how and if it is right way.


texts: How to find the location of a gene, starting with the gene name and the DNA sequence of nucleotides?

texts: I'm not a professional biologist, I'm just trying to analyze some actual data. Where should I look up the location of a gene and nucleotides it consist of? How can I find it in DNA? Is there an algorithm that can be used?


texts: Why Only DNA can Contain Hereditary Material?

texts:
Well I'm well aware that it is proven that DNA contains  genetic material via transformation and Hershey-Chase Experiment of T2 bacteriophage. Still I was wondering what is the reason only DNA contains it and not protein or RNA.
What I've learned is that DNA is the most stable of all these molecules and it has the ability to replicate itself.
Other than this I can't find any solid answere.
Thanks!


texts: Is the chemical composition of urine detrimental or beneficial for a tree?

texts:
Seeing as a lot of people around the world urinate against trees it came to mind that I never thought about how the tree responds to this.
Is it detrimental for a tree if people urinate against them?

When looking on the internet, I found this explanation about urine:

  Human urine consists primarily of water (91% to 96%), with organic
  solutes including urea, creatinine, uric acid, and trace amounts of
  enzymes, carbohydrates, hormones, fatty acids, pigments, and mucins,
  and inorganic ions such as sodium (Na+), potassium (K+), chloride
  (Cl-), magnesium (Mg2+), calcium (Ca2+), ammonium (NH4+), sulfates
  (SO42-), and phosphates (e.g., PO43-). What Is the Chemical Composition of Urine?

Of course, it is possible that the small amounts present in urine are negligible in contrast to the amounts a tree absorbs on a daily basis.
What I am wondering: is the chemical composition of urine detrimental or beneficial for a tree?


texts:
When a bacteria A divides it produces two cells A', A''. Each of them receives a copy of the chromosome/plasmids. Now, DNA replication occurs way before division in a semiconservative manner. That is, each new chromosome has an 'old' strand and a 'new' strand. Since the polymerase is error prone, my belief is that both genomes can potentially have mutations. Now when people refer to the mutation rate/genome/replication, e.g. 3x10-4 , Does this mean that:

Only one of the resulting genomes have this mutation rate? (according to me not likely).
The mutation rate takes into account the total number of mutations in both new genomes.
Each of the genomes can potentially have independently as many mutations as the mutation rate specifies.


texts: The source of ABA for inducing stomatal closure in the detached leaves?

texts:
As you may know, when leaves detached from the whole plant close their stomata to maintain water and prevent wilting. Could you please let me know what is the mechanism of stomatal closure in the detached leaves? if it is induced by ABA, what is the source of ABA under these conditions?

Please provide me the corresponding links for your answers as I couldn't find an appropriate answer for the question.

Thanks


texts: Drinking and eating ability of infants soon after birth

texts: How do infants know how to eat, drink without being taught? How do they get this ability soon after birth?


texts: Need clarification on a sentence regarding vesicle-mediated translocation

texts:
I've chanced upon a passage that is not entirely clear to me:

In addition to conjugation, transformation and transduction, other less well recognised mechanisms of DNA uptake occur in nature, while other mechanisms of HGT are probably yet to be elucidated, in particular, DNA uptake by eukaryotes:
Vesicle-mediated translocation by a range of gram-negative bacteria such as Neisseria gonorrheae, E. coli and Pseudomonas aeruginosa, which can bud off vesicle structures that contain genetic material (e.g.antibiotic resistance and virulence genes) and then fuse with another bacterium (Dorward et al., 1989; Kadurugamuwa and Beveridge, 1997; Yaron et al., 2000).

(From "Risks from GMOs due to Horizontal Gene Transfer", by Paul Keese)
Is it the bacteria that fuse with another bacterium, or is it the vesicles that fuse another bacterium? I'm not sure.
I thought the vesicles were budded off in the first place so that they could carry gene material to another bacteria.

(asked a parallel question at ELL SE)


texts: why do marine organisms orient with their bellies facing downwards?

texts: why do marine organisms orient with their bellies facing downwards (like most creatures) given that they have relatively fewer constraints on their orientations than land or air organisms?


texts: Is spiders building webs on plants an example of mutualism or commensalism?

texts:
In one section of the GED study book I'm looking through to prepare myself for exams, they define parasitism, mutualism, and commensalism, and give examples.

One of the examples they give for mutualism is ants living in an acacia tree. The ants get a home, and they defend the tree.

One of the examples they give for commensalism is a spider building a web on a plant.

Is this actually an example of commensalism? This seems more like mutualism to me. The spider benefits from being able to put its web somewhere, and the plant benefits from protection from bugs (as the spider's web will catch them).

Is this relationship an example of commensalism or mutualism?


texts:
Turner syndrome is a chromosomal disorder where one of the X chromosomes is missing. For more details visit the Wikipedia page

I don't understand why missing one X chromosome would be harmful. In normal females one of the two X chromosomes is inactivated at an early embryonic stage to a Barr body. For more details visit the Wikipedia page on this.

This X chromosome inactivation can be beneficial. For example, women are less prone to sex-linked genetic disorders due to this X chromosome inactivation.

My questions are:

If only one copy of an X chromosome is active in normal human females, why would having only one copy of an X chromosome cause a disorder?
What does it mean to deactivate parts of a chromosome
Why would it be essential to have two copies of a gene, as only the dominant one is expressed?


texts: Childhood cancer is fundamentally a disease of dysregulated development. Why does it rarely occur during the fetal period, a time of enormous growth and development?


texts: What is this little (3mm) spotted insect in Northern Italy?

texts:
Every now and then I find one or two of these tiny bugs in my kitchen. They are about 3-4 mm long and seem to be very static on hard surfaces (furniture or walls). They rarely, if ever, more.
The one in the picture was found dead on the floor so I was able to take close-up pictures. The insect seems to have a very regular pattern of spots and presumably wings.
I tried to look online for Italian websites of "household bugs" but I could not find it.
Is it problematic, i.e. does it ruin food or something?
Location: Northern Italy, province of Vicenza


texts: Has Staphylococcus aureus ever been used against cancer?

texts: Treating inoperable tumors with bacteria appears to be very effective, albeit being toxic to the patient as well. Has (live attenuated) Staphylococcus aureus ever been used against cancer? If the answer is yes, can you give me a link to some papers on this topic as well?


texts: Artificial reduction of NADP into NADPH by means of an electrical current

texts:
I've recently been attempting to artificially drive the formation of NADPH via the NADP reduction mechanism utilized by Ferredoxin-NADP Reductase in the Light-Dependent Reactions of Photosynthesis in plants. My goal is to reproduce the synthesis reaction in vitro only by means of an electric current.

Is there any way to replace the electron pair supplied by PSI in vivo, with one from a current going through a wire? Would conducting electricity through a solution of Ferredoxin, FNR, NADP, and a weak acid yield any desirable results?


texts: Which trait does the given Pedigree chart show?

texts:
I have a doubt in this pedigree chart , according to me it should be autosomal dominant. But the ans given is X linked recessive , in the case of X linked recessive one daughter should be carrier and not affected , but in the chart it's shown the daughter is affected and not a carrier .
What should be  genotype of female parent ?


texts: Why is DNA replication  performed in the 5' to 3' direction?

texts:
DNA replication goes in the 5' to 3' direction because DNA polymerase acts on the 3'-OH of the existing strand for adding free nucleotides. Is there any biochemical reason why all organisms evolved to go from 5' to 3'?

Are there any energetic/resource advantages to using 5' to 3'? Is using the 3'-OH of the existing strand to attach the phosphate of the free nucleotide more energetically favorable than using the 3'-OH of the free nucleotide to attach the phosphate of the existing strand? Does it take more resources to create a 3' to 5' polymerase?


texts: Why does the body not recycle red blood cells?

texts:
This question is out of curiosity.

The life expectancy of a red blood cell (RBC) is approximately 3 months, and then RBCs are disposed of. Why does the body opt to build new red blood cells rather than using the existing ones? Do RBCs lose functionality/efficiency as they get older?


texts: Why can't NMR be used on large RNA molecules?

texts: While reading my Molecular Bio textbook, I came across a sentence that stated that NMR cannot be used on large RNA molecules to determine their structure. Why is this? Is it because RNA is single stranded?


texts: What is doubling of genetic material invented in flowering plants?

texts:
David Attenborough in his Kingdom of Plants 3D said, that flowering plants made two inventions: (1) doubling of genetic material and (2) symbiosis with animals.

What was meant by "doubling of genetic material"? Appearing of diploidy or something else?

UPDATE

Let me explain my doubts. Inventing of ploidy I regard as inventing of sex and syngenesis. This was done ~500 million y.a. in Ediacarian, if I am not mistake. Hence, this can't be done 140 m.y.a when flowering appears. I.e. both plats and insects had sex 140 mya.


texts:
I recently traveled to Japan, where I picked up a cast-iron kettle known as a tetsubin. When I opened it up, I found that the inside was heavily rusted. Rust is a result of various combinations of $\ce{Fe^2+}$ and $\ce{Fe^3+}$ bonded to different combinations of oxygens and hydroxides. Would it be safe to drink water boiled in this kettle? I know that Iron is a dietary supplement, but I am not sure in what form our bodies can use iron. Are these oxidation states potentially harmful for the human body? Additionally, is there anything else (such as bacteria) that I should be worried about? I assume that bacteria would be killed since I am boiling the water, though. I am not sure if this question fits withing the scope of the biology stackexchange and if not, where should I post this question?

By the way, I will take full responsibility if I chose to implement any suggestion on this page. If I were to blame anyone else for their free advice, that would make me a jerk.


texts:
I found this hawk(?) sitting on a fence near a small duck pond with a fountain near my workplace in Fort Smith, Arkansas, USA. There are some wooded hills (deciduous) nearby. It let me get within 3 meters or so before flying up to a tree across the pond. Based on measurements made of the fence it was sitting on, I'm guessing a height of 50 cm (20 inches) head to tail, I assume it'd have a wingspan of 60-70 cm perhaps (24-28 inches).

My best guess it either the Red-shouldered Hawk or Red-tailed Hawk. Unfortunately, I couldn't get a good picture of its back/tail. Any idea what species this is? I came across the bird during winter.


texts: How does the creative process of Biological Evolution work?

texts:
In order for nature to go from microbes to man, there needs to be new information. Where does this new information come from?

It is understood that Evolution basically involves three elements. Natural selection, genetic mutation, and time. The problem for Evolution, is that none of those three elements are creative. Natural selection is basically just a pruning process. It selects from what is there and advantageous, and prunes off what is deleterious to the organism as far as its fitness.

Genetic mutation is just errors in replication. So it creates nothing. It simply degrades. We have no new information, just an erroneous replication, and degradation of what was there before.

That is still true of gene duplication. We have an error that repeats the same information/genes. So we have two copies of something but there is still no new information.

This brings us to the second problem. What mechanism or process of nature/Evolution, carries out the instructions. What I mean by this, is that it essentially has to work like a computer. If I want my computer to have a more advanced program, I need to input new information, and its often codified in the form of say a disk, or installation file.

What is the equivalent of this installation file for Evolution?

For example. Say I'm a cephalopod. And I'm getting environmental pressure from predators and I want, or need, to advance my defenses, so I want to built some spikes on a hard outer shell. Where does the cephalopod get the new information, or rather, instructions, to know how to do this new feature?


texts: Insulin and leptin action on Anorexigenic Neurons in Hypothalamus?

texts:
Receptors for Insulin are present on liver, adipose tissue and muscles. In addition, there are Insulin Receptors present in arcuate nucleus of hypothalamus, which influences anorexogenic neurons through IRS2 and PI-3K signaling. They also causes the inhibition of Food intake by increasing the expression of POMC, and cleaving its protein to alpha melanocortio stimulating hormone (αMSH). This is however the same response produced by the release of "LEPTIN" that act on anorexogenic neurons, and stop eating behavior - similarly as insulin by producing (αMSH).

My question is: why insulin goes to brain and produce this effect when their was Leptin available to do the same task? What is the significance of Insulin action here?


texts: Like other animals, why humans don't have species & breeds?

texts:
Like other animals, why don't humans have species & breeds ?
 Even my pet dog is one type of breed, but we (humans) lack breeds & species?  What is the main reason?


texts: Do we have information on differential reproductive success for many species?

texts:
It has been claimed that human males have a successful reproduction rate of about 40%, whereas females have 80%. This leads to the claim that we have about twice as many unique female ancestors as male. My understanding is that this claim is based on looking at the ratio of the number of generations to our most recent female common ancestor and our most recent male one.

Do we have similar data for other species? I'm especially interested in whether there are species where the number of unique male ancestors is greater than the number of female ones. Is a role reversal, like in seahorses, is sufficient to invert the ratio? Does the ratio invert for bees and ants (species where I understand, each female mates with more than one male)?


texts: Testing monophyly from per site log-likelihoods without optimising branch lengths

texts:
How can I obtain per site log-likelihoods for a topology against an alignment without optimising branch lengths? (which software can I use to do this)

Per site log-likelihoods can be used for various tests of whether a topology fits the data in a multiple sequence alignment well using e.g. the Shimodaira-Hasagawa test, the AU test etc.

RAxML, Garli and FastTree and other software packages can calculate per site log-likelihoods given a tree, alignment and substitution model but all will automatically optimise branch lengths first.

I would like to test a tree in which a pair of sequences (A and B) are monophyletic, where in the maximum likelihood topology they are not. My problem is that when I infer a tree with a constraint requiring A and B to be monophyletic, the edge length is set to the minimum within the allowed precision. But having an edge length so close to zero does not make biological sense if the tree is describing a monophyletic clade for A and B: the minimum length of the edge must be equivalent to one substitution or character change, else A and B are in a polytomy containing clade with other sequences which is not the biological scenario I'd like to test (in that case there would be ambiguity regarding the relationship of A and B to other groups emerging from that polytomy).

So . . . I'd like to edit my constrained tree and increase the edge length to the A and B clade to the minimum one substitution length, then perform the AU test against the per site log likelihoods for that topology. But the above software optimises the edge lengths, resetting the edge length to A and B to effectively 0!

thanks


texts: How to get conservation of vaccine candidates between hundreds of bacterial strains?

texts:
We have identified vaccine candidates via an ex-vivo RNA-seq approach. Next step would be to perform conservation of these candidates (about 20) between multiple bacterial strains (about 200). I would like to know your suggestions to perform this step.

From my bioinformatic experience, it could be possible to start with a first rough screening using blastp or blastx against a multiple strain database, and more accurate approaches would be then performed to validate this results.

Please let me know your suggestions and possible references you might consider helpful to answer this question.

Thanks for your help. Best regards, Bernardo


texts:
Saw this bug in my hallway tonight, crawling alongside the baseboard, it didn't seem like it could crawl up the wall despite trying to countless times. Google wasn't much help, although I saw a weevil that looks sort of similar to it.

Location: Augusta, Georgia, US


texts:
Is it possible to completely cure myopia using natural methods (i.e. not with Lasik etc.)?.
I have seen websites claiming that exercising the eyes will help improve eyesight.

Is this true?


texts: How to find suitable qRTPCR reference gene for a inflammatory response experiment?

texts:
I have tried several housekeeping genes – Hprt, β-actin and GAPDH, to analyze the relative expression of a cytokine for measuring the inflammatory local response in mice ears. However, all these housekeeping genes show significant variation in both within and between different experimental conditions.

I really don't know how to solve this. I take the same amount of RNA (quantified by  nanodrop) to make cDNA so I guess I have the same concentration in all the samples.

Any suggestion of what can happens and how to solve it? Could I use something different to measure the relative quantification? (My cytokine of interest is TNF).


texts: Frequency modulation of parasympathicus and sympathicus

texts:
According to my literature, the sympathetic nervous system accelerates heart rate and modulates < 0.1 Hz, whereas the parasympathetic nervous system decelerates heart rate and is modulated 0.04 - 0.5 Hz.

According to this, heart rate accelerates in sympathetic which means the frequency should be higher than that compared to Parasympathetic. Though Parasympathetic starts with 0.04 it goes up to a value higher than 0.1Hz. Why so?

Here is the source (Physiological Sensing of Emotion by Jennifer Healey in the Oxford Handbook of Affective Computing):

  Since it is known that the parasympathetic nervous system is able to
  modulate heart rate effectively at all frequencies between 0.04 and
  0.5 Hz, whereas the sympathetic system modulates heart rate with significant gain only below 0.1Hz (Akselrod, Gordon, Ubel, Shannon, &
  Cohen, 1981; Berntson, et al., 1997), the relative strengths of the
  sympathetic and parasympathetic influence on HRV can be discriminated
  in the spectral domain.


texts: Neuroendocrinal mechanism of parturition

texts:
My book reads,

  "The fetus signals that it is mature by secreting certain hormones
  that diffuse across the placenta into mother's blood and cause the
  secretion of oxytocin from her posterior pituitary."

I would like to know what exactly are these hormones and their sites of production in the foetus, as well as their mode of action.

Also, I was wondering whether these hormones are released even during premature births? I doubt this because what I understand from the lines of my book is that it has to be a signal by the foetus that it is 'fully developed', whereas if it is not secreted it would not stimulate the secretion of oxytocin. This is creating a bit of confusion.

A detailed explanation would be a great help

Thank you


texts: Does melanin protect humans from gamma radiation?

texts:
It is known that radiotrophic fungi use melanin to make use of gamma radiation. It is also known that melanin protects human skin from UV radiation.

Thus I wonder whether melanin protects humans from gamma radiation as well?

Are the black people and tanned white people less vulnerable to gamma radiation?

http://web.archive.org/web/20080424001002/http://www.sciencenews.org/articles/20070526/fob5.asp


texts:
I'm reading the wikipidia page on Panmixia.

Panmixia (or panmixis) means random mating. A panmictic population is one where all individuals are potential partners. This assumes that there are no mating restrictions, neither genetic nor behavioural, upon the population and that therefore all recombination is possible. The Wahlund effect assumes that the overall population is panmictic.

In genetics, random mating[4] involves the mating of individuals regardless of any physical, genetic or social preference. In other words, the mating between two organisms is not influenced by any environmental, hereditary or social interaction. Hence, potential mates have an equal chance of being selected. Random mating is a factor assumed in the Hardy–Weinberg principle and is distinct from lack of natural selection: in viability selection for instance, selection occurs before mating.

Now, I would guess from this definition that Panmixia is a condition that almost never occurs, that in the vast majority of cases, there is some sexual selection going on which makes some pairings more likely than others.
But the way the page is written seems to suggest that this is a pretty normal condition of populations, or at lead doesn't mention that it is a "spherical cow" abstraction.
Am I missing something here?


texts: Why do wild lizards often tap with their front leg?

texts:
I have a lot of wild lizards (possibly Podarcis muralis) in my garden, and I have noticed some of their behavior I'd like to understand:

whenever they are in 'still' position on any surface, they are quite often 'beating' with one of their front legs on the surface

in some cases they put the tail of the mate in the mouth

What is this behavior? Some kind of communication?


texts: Can someone tell me what these cocoons are?

texts:
I am camping in Slovenia and have found some cocoon like materials.
They look like nests of some kind and are about 30cm long and 10-15 cm wide. Can anyone help me find out what these things are?
Found in Tolmin, Slovenia


texts: What is the impact of prolonged electromagnetic exposure on human health?

texts: What are the health effects of being exposed to a very strong electromagnetic field caused by  two resonating superconductive coils (not static magnets) for a period of years?


texts: Premise of life cycle synchronization between predator and prey

texts:
While reading about the predator satiation hypothesis of the periodical cicadas' 13/17 year life cycles, I started wondering about its premise. By the way, I understand the math behind the prime number life cycle. 13 and 17, being prime numbers are only divisible by themselves and 1, and thus have as few divisors as possible. But my question is about the premise of why a predator would even want to synchronize its life cycle with a divisor of the prey's life cycle in the first place.

If the predator has a set life cycle, but its individuals are evenly distributed in regards to their development within that life cycle at any given time (for example there could be roughly even amounts of mature and immature predators at any given time), then what difference does the life cycle make? Here I am assuming that eating cicadas is most beneficial to a specific developmental stage of the predators, which is the only reason I can think of why there would be an advantage to this synchronization. By the way, is this even a correct assumption in regards to this hypothesis?

To be clear, my main question is why life cycle synchronizations between predator and prey matter when/if predators aren't all undergoing the same stages of their life cycles simultaneously.

edit: To be even more clear, I am asking what the benefits are to the predator to synchronize its life cycle with the prey (the cicadas, in my example).

My reference: Wikipedia says the following: *It was hypothesized that the emergence period of large prime numbers (13 and 17 years) was a predator avoidance strategy adopted to eliminate the possibility of potential predators receiving periodic population boosts by synchronizing their own generations to divisors of the cicada emergence period.
Goles, E.; Schulz, O.; Markus, M. (2001). "Prime number selection of cycles in a predator-prey model". Complexity 6 (4): 33–38. doi:10.1002/cplx.1040.

I have interpreted "synchronizing their own generations to divisors..." to mean synchronizing the length of the life cycle. I am happy to hear of another interpretation.


texts: PCR limits of detection calculate method

texts: Is any standard method for use to gain PCR sensivity or limit of detection? my mean is not for RT-PCR or Real-Time or any other kind and just simple PCR. After making PCR product free of dNTP and Primers I have a microtube that contain 40ng/micro Liter dsDNA. My product size is 200bp. If I  should diluted it or any other standard acceptable method expain to me please.


texts: Chance of cancer as a function of smoking frequency

texts: I was wondering if there is some kind of known relation between the chance of getting cancer and the frequency of smoking cigarettes. A quick Google search did not yield results. Would any of you perchance know of a relation?


texts:
In my (albeit basic) biology classes in the past, we've learned about how, to reproduce, two organisms must have the same number of chromosomes. This has been verified by a few other websites I found. So- I've heard about various genetic disorders in which people can have fewer or more chromosomes than usual. For example, if a person had tetrasomy, they would have two extra chromosomes (48 in total). Chimpanzees also have 48.
Therefore:

If, hypothetically, a person with tetrasomy and a chimp's sex cells were combined, would it create anything?

If not, what are the other requirements for creating a baby organism besides the parents having the same number of chromosomes?


texts: What are the causes of the dimples commonly found above the buttocks?  They seem to be in line with the sacroiliac joints.  Do the joints have anything to do with them?


texts: Is reverse senescence/"anti-aging" actually scientifically possible among humans yet?

texts:
I have been very interested in this since I myself am interested in reversing my skin's aging/genes/damage/etc. I also am interested in volunteering any future genetic altering of skin quality.

Basically I've heard of experimental drugs called senoyltics that are believed to (and have actually done so) have the ability to truly reverse aging at the cellular level and/or aging damage of skin and etc.

I am very intrigued and want to know if this is feasible for humans yet -- or any such breakthroughs. I really want my skin's genetic quality to be enhanced, but reversing aging damage by genes will suffice.

So skin aside, in general, is reverse senescence (with or without senolytics) anywhere near possible to reach human success? I've heard of labs and etc. working on this for testing, but nothing more.

My question is basically: is it possible? Are we really in the near future to reversing aging in humans?

As a note: I don't mean "anti-aging" as in preventing death -- more so as in making yourself younger in a myriad of ways, such as by appearance and physical ability (like heart; brain; skin texture/youth; etc.)


texts: As Neanderthal DNA has been sequenced, is it possible to create a living Neanderthal?


texts: How does the spindle fiber find the kinetochore?

texts: I am curious if anyone knows the exact mechanism of how exactly does the spindle fiber find the kinetochore? it certainly seems like a fairly non-spontaneous reaction for a spindle fiber to reach all the way to a chromosome, how are these type of reactions carried out without producing new proteins? How Can cells execute complex "choreography" such as mitosis without making new proteins on the spot?


texts:
Is that because of evolution?
Does it have something to do with its amount in the universe?
Carbon compounds form the basis of all known life on Earth, and the carbon-nitrogen cycle provides some of the energy produced by the Sun and other stars as I know.


texts: Why does a fetus drink and urinate into the amniotic fluid?

texts:
I was reading this website saying that fetuses urinate into the amniotic fluid. It also mentioned that, because we drink the amniotic fluid, we’ve been drinking our urine for months.

However, why do we produce urine as fetuses? I always believed the placenta was our source of waste removal; then why have fetuses the need for filtering their blood through their own kidneys?

In addition, why would fetuses drink the amniotic fluid? Is there a benefit for doing that?


texts: Optimal agriculture: maximum yield with minimum environmental impact

texts:
I read more and more stuff about alternative method of agriculture such as permaculture. Howerver, I'm not an ecologist or biologist so I don't know where to look for really good and serious articles / paper on the subject. I am really interested in food production methods that may be efficient and respectful for both the environment and the health.
The question that interests me the most is the question of crop yield and environment. I wonder if there are studies that compares the crop yield of the different production methods AND if there are scientific researches on the optimisation of the food production under ressources constrains.
Do you have any reading suggestion? I'm mostly interested in scientific papers but I'm open to anything that may be interesting.


texts: What is the extent of the effect of Tris on E. coli?

texts:
I was a fool and dissolved my antibiotic (Kanamycin) into Tris Buffer rather than H₂O. The Kanamycin still seems to be active but a fellow labmate mentioned that Tris messes around with the membrane permeability of cells. I was curious to what extent this actually influences experiments.

Tris(hydroxymethyl)aminomethane buffer modification of Escherichia coli outer membrane permeability.


texts: Given the number of individuals who have a recessive disorder, how can one calculate the probability that the disorder was inherited?

texts:
Just to be clear, this is not homework.
Suppose a biological family has five children, two of whom have a certain recessive genetic disorder that is not sex-linked. The parents themselves do not have this disorder.
I want to estimate the probability that the parents are carriers. How can I do that, short of getting this probability directly from a lab study?

This problem appears to be where Bayesian statistics can help. All I need to know is:
1) the probability of the parents being carriers, given they don't have the disorder, but 2/5 of the children do.
2) The probability of the parents being carriers
and 3) The probability of the children having the disorder.

3 I can probably find without too much effort. #2, I'm guessing, is a Hardy-Weinberg problem - I just need to find the relevant statistics for people of the parents' backgrounds. But I have no clue how to start with #1.


texts: What is the relationship between UV wavelength and penetration depth into human skin?

texts:
Some background - Some recent research has strongly suggested that UVA penetration into the skin is far more dangerous than UVB, a very good example is this paper by Agar et al. (2004).

My query is, is there a measure that relates the UV wavelength with the penetration depth into human skin?  Related, is the answer to this related to skin types?

(I understand that this may be migrated to Biology.SE).


texts: What made this tiny honeycomb-like structure?

texts: I found this on the ground in Maryland.  I believe the twig is from a tulip poplar tree.  The structure looks like a tiny honeycomb except that the cells are individual tubes rather than a true hexagonal honeycomb shape.  It's one layer deep and wraps completely around the branch.  I assume it was made by some tiny insect, but what?


texts: What is the current molecular explanation of Mendel's pea cross?

texts:
With reference to the simplest Punnet square for Mendel's pea plant experiments it occurred to me that I could not connect the little I know about genetics to the little I know about molecules.

The mathematical model assumes that there are two factors (alleles) involved. With respect to Mendel's pea flower colors, to what do those alleles correspond at the molecular level? Genes--minimally it might be two codons, each with binary states so that a protein involved in the manufacture of color molecules changes at two specific amino acids.

Of course it is not so simple. But it must be true that there are two physical objects which in the aggregate have two binary states for this particular case. Do we know what they are, exactly, for Mendel's peas?

Thanks for any insight.


texts:
I'd like to perform densitometry on a Coomassie stained SDS PAGE gel to compare a recombinant protein's expression levels under two conditions. I'm using BioRad's Image Lab software.

My questions are about what estimates can be made, given that Coomassie staining can be nonlinear has protein-to-protein variability. Unfortunately, I do not have a standard curve, and the lanes contain total lysate.

Can I take the percentage of band volume to lane volume as an estimate of percentage of total cell protein mass? (25% vs 20% total cell protein)
Or would it more appropriate to take the band volume normalized to an arbitrary band in the lysate, and then report the percentage difference between conditions? (6 vs 4.8 normalized band volume, or 20% decrease in expression levels).


texts: Action potential changes in low sodium concentrations but constant osmotic pressure

texts:
If I bathe a squid axon in a fluid that has high sodium concentration , why does the duration of action potential decrease compared to a control experiment in low sodium bath but maintained at the same osmotic pressure with choline chloride? Why does the amplitude of action potential increase in the experimental set ?

In short-  In the experiment, when the neurons are bathed in low sodium fluid but constant osmotic pressure, amplitude of action potential decreased, but duration of action potential increased.

I wanted to validate this with Nernst equation and/or GHK equation .

The increase is action potential amplitude with high extracellular sodium ( more sodium influx,more depolarization ? ) is intuitive?
But again I am confused because the membrane is only slightly permeable to sodium such that increases in extracellular sodium won't really alter the membrane potential enough to generate an action potential.

Also how does the action potential duration decrease in high sodium ?

What should be done if I want to increase duration of action potential while keeping the axons in high sodium bath ?

  The duration of action potential is not the time to reach threshold voltage. It is the overall time the membrane stays depolarized.
  In other words, why are the axons slowly repolarized when bathed in low sodium concentration(and also maintained at constant osmotic pressure with choline chloride ) compared to high sodium bath axons that are rapidly repolarized ?

How do you think the answer would've changed if choline chloride was not used ?


texts: Are prions a recent biological phenomenon?

texts: Is there evidence to suggest whether prions have existed for a large portion of evolutionary history, played a role in evolutionary history, or could they actually be a recent biological technology invented by mother nature? Is there evidence or biochemical data that prions may predate cells?


texts: Why only human have noticeable difference in face?

texts: Our facial appearance is pretty much different from each other unless we are talking about twin. Credit goes to crossing over of chromosome. But why can't we distinguish between other animals of same species? Yes there are some very little differences but not that much clear and obvious difference like we have. Why is that?


texts:
I recently read about methanogens and methanotrophs. One converts CO2 to methane and vice versa respectively.
I can't get exact mechanism for the methanotrophs and I know they can't be reversed because this would result, in both directions being unable to produce energy.

Any information elaborating on the mechanism responsible for the generation is greatly appreciated.


texts:
I'm currently studying Robbins basic pathology, and I'm confused about a specific statement:

It states in the book that when hydrostatic pressure is low due to a lack of albumin synthesis, it leads to a net movement of fluid into the interstitial spaces.

However to me that doesn't make any sense: isn't the hydrostatic pressure the thing that facilitates the net movement of particles across the capillaries, so if there is a lack of it, shouldn't the particles not move across the membrane?

Any help appreciated


texts: How to tell if a beverage will hydrate or dehydrate?

texts:
Beverages of any type generally contain some measure of water. However, in the case of some liquids, the non-water components take more water from the human body to filter out than the water contained in the beverage.

The most-known example of this is salt-water from the ocean - there is too much salt so the body tries to use water from the body to "water down" the salt water.

Given a beverage with unknown additives, how would one determine if the beverage would actually hydrate or dehydrate a person?

If you knew the ingredients (and the amounts), could you tell that way?

Edit:comments seem to indicate that it depends on the solutes and tonicity of the solution: are there any other factors to be aware of?
What (common) solutes will have the largest affect on whether the human body will be hydrated and why?

if you need "common" to be defined, consider it defined as: contained in many[more than 3] store-bought beverages


texts: Would exposure to a strong magnetic field have deleterious effect on the human?

texts:
This article states of a 25T magnet, ".. If are ever caught in one of these devices, let’s just say you probably won’t live to tell the tale."

Is the above statement in order? What effect would exposure to such a high magnetic field have on the exposed human?


texts:
I seem to have come across two contrasting explanations for tinnitus induced by loud noises- i.e. damage to the hair cells in the cochlea.

On the one hand, I have read that damage to the hair cells results in them releasing excess glutamate, the neurotransmitter that carries the impulse from the hair cells to the neurones in the auditory nerve. This would result in the neurones constantly being excited, which I can understand would lead to constantly perceiving sound.

On the other hand I have read that when the hair cells are damaged, the auditory cortex is no longer receiving electrical impulses from the hair cells that detect those frequencies, and so the neurones start to fire (although I am not sure why no input would lead to neurones going off by themselves! Surely there must be some input to cause the initial depolarisation to cause an action potential?) and so you perceive a constant sound.

These seem to me to be two contrasting explanations. My only other guess on how these explanations overlap is that the excess glutamate being released causes death of the neurone, and therefore the neurones after that one do not receive and input and they start firing spontaneously (although again I would appreciate if someone could explain how lack of input results in neurones firing by themselves).

Thank you in advance!


texts: Can aptamers be used to identify the terminal amino acid residue of a peptide?

texts:
Suppose there were DNA or RNA aptamers that bind specifically to a certain terminal amino acid residue. Let's name it aaSA (amino acid specific aptamer). For example, the aptamer binding to terminal methionine residue is named as MetSA.

If such 20 aaSA all existed, then they could be applied to identify the terminal amino acid of a peptide. Concretedly, the peptide sample is immobilized to a solid surface, then all 20 aaSA are introduced and bind to the terminal residue. Extra unbinding aaSA will be washed away, and the binding aaSA will be separated later by another approach (like heating). And by sequencing the binding aaSA we can know the terminal residue of the peptide.

Either N-terminal or C-terminal is OK.

I know mass spectrometry is much more powerful in this task than the method I have supposed. But I still want to know if such aptamer exists or not.

I have searched in Google and Google Scholar, only to find aptamers binding to some intact proteins (rather than short peptides with terminal exposed). The binding site is unknown, possibly not in the terminal.


texts: Why do autumn leaves on the eastern sides of trees change and fall before the western leaves?

texts:
I've noticed that for the autumn leaves in my area (Great Lakes region of United States), if a tree's leaves are changing or falling asymmetrically, they almost always change first on the East-facing side of the tree.

I can't find any explanation for this phenomenon online; but in the spirit of "showing my work", I'll give some hypotheses from this non-biologist. :)

If there is a temperature at which direct sunlight destroys chlorophyll or reduces its effectiveness, there might be pronounced coloring effect on eastern leaves. The air temperature at dawn is usually 5-10 degrees Celsius less than at sunset.
If direct sunlight instead prolongs color change or leaf detachment, it could be that this asymmetry is caused by an increase in cloud cover in the mornings relative to the afternoons.

Any thoughts? I've noticed this in past years, but this year seems really extreme: many trees in the region have lost all of their eastern leaves but have a western side covered in bright orange leaves; they also had orange eastern leaves while the western sides were green, so wind gusts aren't the culprit.


texts: Why does squinting allow you to see objects more clearly?

texts: How does squinting alllow one to see clearer pictures? What are the harmful effects?


texts: What distinguishes "coding" from "noncoding" DNA?

texts:
I've been reading a bit about "junk DNA" and how much of our genome consists of this "non coding DNA" in comparison to "coding DNA".

I'm just an interested layperson but I thought all combinations of three base pairs encoded one amino acid, with some amino acids being encoded by more than one combination of base pairs.

But if that were true then all of our DNA would encode something.

Or if only a tiny percentage of our DNA is "coding" that would mean that the vast majority of possible combinations of three base pairs don't represent any amino acid.

Or it could mean that there are a small number of "meaningless" combinations of three base pairs, but that those combinations are vastly overrepresented in our genome.

Which is correct? What am I missing?


texts:
After researching the definition of Assay, I am left with the idea that an assay refers to scientific screening. It could be of chemicals, microbes, etc.

I understand that during drug-discovery assays scientists screen for chemical compounds that may make up an effective drug.

But could someone explain, or provide me with some links that further discuss the process of assays, or how they work or take place during drug discovery?
Frankly, I'm also still a bit confused about the definition of "Assay" itself.

Thank you.


texts: How is a portion of DNA selected and unwound from nucleosome?

texts: If I understand this correctly during interphase most of the DNA strand is tightly wound around histones in the form of nucleosomes, to conserve space in the nucleus. Yet RNA polymerase in order to work needs a part of DNA to be temporarily unwound. How does the polymerase find the particular part of the DNA (and especially the promoter for a gene coding the protein needed to be synthesised) in this mass of tightly wound DNA?


texts:
I was reading this article. In Risk Factors, it clearly mention "Being a male".

Why is Sleep apnea only risk to males?


texts: Understanding conclusions that functional regions are under negative selection?

texts:
I am reading in notes for a comparative annotation lecture that :

all DNA is subject to mutations
most functional regions are under negative selection (ie., mutations are often deleterious)

The conclusion was:

  that pieces of DNA with specific functions (especially genes) tend to be conserved against mutation more strongly than a DNA region with no specific function.

So if i understand it properly, since all DNA can accumulate mutations, the regions of genes that provide some fitness benefits avoid the negative selection of random mutations and are preserved (conserved?).

Also, the author placed in parentheses, (especially genes), therefore are there non coding regions that can provide benefits? Is he referring to "Selfish DNA" like Transposable elements that can have regulatory functions (or so i have heard).


texts: Are Asian people genetically predisposed to be shorter than Europeans?

texts:
People in different countries have different average heights. For example, Wikipedia's article on human height states that Australian men have an average height of 177.8 cm, and Australian women 163.8 cm, whereas Japanese men have an average height of 170.7 cm, and Japanese women 158 cm.

Are these differences in height due to environmental differences between people in different countries, or does genetic differences play a role?

In particular, are Asian people (people from Far East countries like Japan) genetically predisposed to be on average shorter than people who are of European descent?


texts: Do experiences shape actions of insects? Animals?

texts: Would an insect behave differently to stimuli depending on what stimuli occurred to them earlier (that only affects them cognitively or their conscience)?


texts:
This answer to another question satisfactorily answer one of my major confusion.

  The convention is that in indicating any sequence feature† in a protein-coding gene on double-stranded DNA, a single strand‡ is represented — the one from which the amino sequence could be read using the genetic code (conceptually, with T substituted for U). Like any other nucleic acid sequence§, it is always written in the 5ʹ to 3ʹ direction in the same manner as the mRNA transcribed from it, without this being explicitly stated.

But I have another related (and overlapping question): (I'm still looking for); is whether there is a standard and universal documentation for this particular convention (IUPAC/ IUBMB/ ICBN/ ICZN/ anything such); because "conventions" are human-made rules, and particularly in field of science (where nucleic acid research is a comparatively new and institution-based (not-folk or not-colloquial) study; without "declared, universally followed, and accessible" documentation; the conventions does not make a sense. It rather feels like a rumor or viral phenomenon. I visited the IUPAC and IUBMB website home pages but I could not locate the documentation from there. Also google keyword search did not found the helpful.

So I specify my question that I want to get the standard/ official source of this convention. I would be highly grateful if anyone kindly mention the source hyperlink.

N.B. This question is follow-up of a closed duplicate question,


texts: What virus transforms full grown plants?

texts: I read an article by a gardener describing how a virus had transmitted a negative trait to his plants. It rather shocked me, because I hadn't realized that a virus could transform an adult plant. I was aware of dipping arabadopsis flowers in agrobacterium tumefaciens, but the concept of non-reproductive structures being transformed seems fascinating. What kind of virus is capable of that?


texts: Failed attempts at changing ecosystem in order to preserve it?

texts:
Have there been any notable tries in the recent past (think 20th century or later) to purposefully change any ecosystem in order to save it or some particularly species in it, but which have instead produced the opposite effect? I am sure there must have been, but can't bring any to my mind at the moment.

Like, for example, if you have an island that has some large felines, which frequently attack sheep that are becoming scarce, so the felines are starving and becoming scarce, too. So you introduce feral goats, which were supposed to provide meat for felines, however, goats were (a) too nimble for felines to hunt well due to, eg. geography of the island (too many rocks that goats can prance about, but cats not so well), and (b) ate all the grass that sheep still had. So the net effect was that sheep died out, cats died out and there remained a few goats.

I am aware of a number of cases, where these things could have happened due to humans not aware or not caring about the problem (eg. introducing rabbits in Australia), but I am wondering specifically about misplaced efforts to save/stabilize an ecosystem.


texts: Alpine flower identification — Italy/France

texts:
I have been using the internet to try to identify alpine flowers photographed in July 2007 on a shortish walk above Chianale (1800 m), in the Italian Valle Varaita (bordering the French maritime alps).

I have managed all except the blue/lilac one shown below. It looks a bit like a scabious or perhaps a knapweed, but neither seem to correspond properly. Anyone know?

Group of flowers

Close-up with triply split petals indicated by red arrows


texts:
When i finish operation. My masterclave has smell, I think has media moulecular bind into the surface and microbial can live in. My labs don't have SOP to clean it. I promote use detergent but wonder it'll bad effect in the suface. Do you know how I can clean masterclave effective?

This's my masterclave


texts: Why is the ingestion of salt and water beneficial to muscle cramp

texts:
According to Wikipedia, muscle cramps are caused by the inability of myosin fibers to break free from the actin filaments during contraction, resulting in a prolonged contraction.

A lack of ATP would obviously produce cramping, as myosin requires ATP to become free from actin.

However, I have heard that potassium and sodium are useful for treating cramps and that their deficiencies can lead to cramping.


texts: Can animals that rely heavily on sonar sense colour?

texts:
Apparently there're species around as rely heavily on sonar to sense the world around them.

E.g. Bat, Dolphin, Whale ...

The humans, and other terrestrial beings in a lighted world are capable of distinguishing colour in varying degrees of acuity. Is this ability to sense colour in our environment applicable to species (terrestrial, avian, and marine) that rely heavily on sonar?


texts: When does BLAST fail to align 2 DNA sequences?

texts:
This is an assignment that had confused me for a long time.  So I think you guys who study computational biology might be interested. The original question is:

  Find the two most similar DNA sequences of length 20 that Blast using a word length of 5 will fail to align.


texts: Sensing weather conditions through bodily reactions (e.g. dry hands, arthritic pains)

texts:
Two fairly known examples of the effect of certain weather conditions on the body are dry hands due to decreased air humidity around us (more commonly in the winter, as described here), and flaring of arthritis immediately before or after it rains (as described here and here).

I was wondering if there are more examples of this kind, when what I am specifically looking for are bodily reactions through which one might be able to forecast or know something about the weather (i.e. if you have arthritis, you might be able to know it is going to rain sometime soon according to what you feel in your legs; if your hands are dry and chapped, you know that the air is drier than usual).


texts: What is the basis of the endocochlear potential?

texts:
I am learning about the endocochlear potential. According to different sources, the ionic composition of perilymph is about as follows (in mM): 150 Na+, 4-5 K+, 1.2 Ca2+, 1 Mg2+, 120 Cl−, and 20 HCO3−; and that of endolymph is 1 Na+, 157 K+, 0.02 Ca2+, 0.01 Mg2+, 132 Cl−, and 30 HCO3−.

This means (in a naive attempt to quantify ionic charges) that the sum of charges in perilymph is 150+4.5+2*1.2+2*1-120-20 = +18,9.
And in endolymph it is: 1 + 157 + 2*0.02 + 2*0.01 - 132 - 30 = -3,94.

From these numbers, it seems like perilymph contains more positive charges than endolymph. How is it possible that the potential of endolymph is highly positive (80-90 mV) compared to perilymph? Shouldn't it be the other way around?

I have searched the forum and the internet for answers, but my question seems so basic (or based on a very fundamental misunderstanding) that I can't find anything of help. The only explanation I keep seeing is that the high potassium concentration accounts for the potential. However, isn't that outweighed electrically by the excess of negative ions in contrast to the perilymph?


texts: If nerve consists of many axons, where are then their soma located?

texts:
This question has haunted me for two years.

Wikipedia mentions :

  A nerve is an enclosed, cable-like bundle of axons (the long, slender projections of neurons) in the peripheral nervous system. A nerve provides a common pathway for the electrochemical nerve impulses that are transmitted along each of the axons to peripheral organs.

Okay, my book also defines like that. But if the nerve runs only with bundles of axons, where then are their soma located?

They say nerves are formed of many axons bundled together. Now, if there are axons, there must be soma, but they do not form nerve & hence are not present in nerve. So, where are they? Are they present at the beginning of the nerve?

Also, nerves communicate with each other. Books picture this as two neurons one above other; the above one sends impulse through its terminals to the dendrites of the neuron below it. So, how do these two neurons constitute a nerve?? After all, they now contain the cyton?? So, how do neurons one above other form nerve as they now contain the soma??

PLz explain.