texts: How to prevent HL-60 cell contamination?

texts:
I have thawed Hl-60 cells from liquid nitrogen chamber two times in RPMI 1640 media (containing 10% FBS, L glutamin, penicillin/streptomycin). In the first day the cells remain okay. But when subcultured from the first flask to new flasks (cell solution : media= 1:3) all the flasks became contaminated on the 2nd day of culture. Cloud was found in both time. It can be mentioned that I used sterile one-time usable pipettes and uncoated flask for growth. All the transfers to other flasks and media addition were done very carefully and done inside clean bench. Before using clean bench, it was sprayed by 70% EtOH.

Has anyone experienced like this problem?  Please share and if have, please give some valuable suggestions or references.

Thanks


texts: Are all 23 chromosomes connected as one long strand of DNA?

texts: This has perpetually confused me. Is our genome made up of two long strands, each strand made up of 23 continuous chromosomes that bind together, or are they 23 free floating separate pair of chromosomes? I think it's the latter because I just learn that genes on different chromosomes assort independently, which would be hard if the genome was a long string, but I'm still not sure.


texts: I am trying to express a protein in K. lactis Protein Expression Kit (E1000S - NEB) in the way that the protein is secreted into the medium. I know that I can get some protein but it is not active. As the protein is secreted into the medium, I am not sure if doing expression for 24 h at 30°Cis a good idea. I am wondering if there are people here with some experience in this protein expression kit and, if so, what are the conditions for protein expression that worked well for you? Did you use ammonium sulphate precipitation to purify the protein from the medium or some other method?


texts: How statistically significant was the "sweaty T-shirt" experiment?

texts:
An Overview of the Experiment.
In 1995 there was an experiment that involves young people smelling T-shirts worn by another gender and rating their preference. The researchers found that people preferred shirts belonging to people with a dissimilar Major Histocompatibility Complex (MHC). Another interesting finding was that this preference reversed for the women 'sniffers' that were using oral contraceptives.
Here is a link to the wikipedia entry.
These findings were reiterated by a study in 2005.
My Question.
I'm very ignorant in the subject of pheromones, particularly in humans. For those of us not 'in the know' a result like this seems like magic! I want to get a better grasp on how set in stone pheromone preferences like this are.
Unfortunately I do not have access to these articles at the moment. The actual statistical difference in populations isn't mentioned in the abstracts  (the cynical sceptic alarm bells are ringing!) other than the 2005 one stating that the total sample size was 58, which sounds low given that the total population is split into two.
Generally I'm looking for any supporting or opposing critiques of the study, specifically I want to know more about the statistics of the studies.
My question is:

What statistical validations and scores appear in these studies?

I also am willing to accept answers discussing validation in similar studies. I'm after a number or quantification for how consistent pheromone preferences are.


texts: How to pipe Bwa-mem output without saving SAM file

texts:
I'm trying to find circular ARN using the program CIRI2. CIRI2 takes as input SAM file from BWA-mem, but I would like to go straight to CIRI2 output without saving SAM file.
Is there a way to achieve this?


texts: What pigment is responsible for the formation of blue skin color in some animals?

texts:
Not long ago I read about Vervet monkey. Here's picture:

My question is what causes this blue coloration of the scrotum? I don't mean evolutionary need  (e.g. attracting females), but what pigment or other factor is responsible for this color?


texts: Can sleep be replaced by chemical supliments?

texts: If adenosine makes a person sleepy to rebuild chemicals in the brain, than is it possible to inhibit adenosine and externally produce and inject the needed chemicals?


texts: what is the effect of soda water on digestion?

texts: what is the effect of soda water on the process of digestion? As it has been seen that after drinking soda the process is increased...I just want to know that what is the chemistry behind this?


texts: Why exactly are the reflections of sunlight in this dragonfly's eye hexagonal?

texts:
I photographed a rather cooperative, large dragonfly today and after getting back to my desk and looking closer at the images I realized that the reflection of the Sun in its eyes produced large hexagonal bright spots that are:

much larger/wider than if the eye surface were smooth specular reflector
relatively uniform in brightness all the way to the edge
have very sharp edges, transition from bright to dull red is very abrupt.

I'm aware that the components of compound eyes are usually at least roughly hexagonally packed, but what is happening here is something more than that.
What is it about a dragonfly's compound eye that can account for all three of these characteristics of reflected sunlight?
Presumably this is the same red dragonfly species as is seen in Identify these two large, colorful dragonflies in Taiwan? It's the same area and time of year.

Two more taken at different angles relative to the Sun. (click for larger)


texts: Microbiology- Pseudomonas aeruginosa, BSAC data

texts: I tested Pseudomonas aeruginosaagainst various antibiotics, using Stokes and Kirby-Bauer. When I compared my results with BSAC data it was completely different (understandable) but why for a lot of the antibiotics did BSAC state 'no information available'?


texts:
What is this fruit (round, 3 cm diameter, yellow outside, 1 black seed, found on Easter Island)?

Some fruits may have more than one seed:


texts: I recently got  and would like to know if this is a real species. It doesn’t look quite like a Styracosaurus, but is close. Can someone identify?


texts: If you add type A blood to type B blood, is there a visible reaction?

texts: I read that the original discovery of blood types was because they combined random blood samples togethers and noticed a reaction. I was wondering if this was a visible reaction? Or is anti-A or anti-B serum explicitly required?


texts: Is CRISPR being utilized when scientists use the CRISPR/Cas9 system to edit genes?

texts:
"CRISPR" and "Cas9" are different things. When a virus attacks a bacteria, the bacteria stores the viral code of the virus in CRISPR. And when the virus attacks again the Cas9 protein uses the RNA in the CRISPR to find the viral DNA and then destroy it.
So, what is the use of CRISPR when scientists use the CRISPR/Cas9 system to edit genes, as we have already given the Cas9 protein a guide RNA?
Sorry if this is a stupid question, I am new to genetic engineering and couldn't find the answer on google.


texts: What is the exact concept of "Repulsion" and "Coupling" (Genetics)?

texts:
From all sorts of books including standard books (like those by Tamarin, Griffith etc) as well as internet; I could not clear-up many things about "Repulsion" and "Coupling". Such as:-

Is "Coupling" an exact synonym of "Linkage" ? and is "repulsion" an exact synonym of "recombinant"? No-where I could yet found mention of it.
What are they telling as coupling-"phase" and repulsion-"phase"? Are there 2 different "step"s or "time-frames" or "generations"?
Coupling and repulsion- are they indicating to a "phenomenon"? or the Genotypic "state"?
according to Griffith's introduction to genetic analysis (7th Ed)

  Now let us consider what may be learned by repeating the crossing experiments but changing the combinations of alleles contributed as gametes by the homozygous parents in the first cross. In this cross, each parent was homozygous for one dominant allele and for one recessive allele. Again F1 females were testcrossed:

  The following progeny were obtained from the testcross:

  Again, these results are not even close to a 1:1:1:1 Mendelian ratio. Now, however, the largest classes are those that have one dominant allele or the other rather than, as before, two dominant alleles or two recessives. But notice that once again the allelic combinations that were originally contributed to the F1 by the parental flies provide the most frequent classes in the testcross progeny. In the early work on coupling, Bateson and Punnett coined the term repulsion to describe this situation, because it seemed to them that, in this case, the nonallelic dominant alleles “repelled” each other—the opposite of the situation in coupling, where the dominant alleles seemed to “stick together.”

From this paragraph; it strongly seems to me; repulsion is not opposite word of coupling; rather it is synonym of coupling; where we started the breeding experiment with such parents those contained Dominant allele on one locus and recessive allele in the other locus for all the chromosomes.  As a result; parental combination  Pr+ and vg trended to stay together "coupled" (965 progenies at testcross output) and similarly parental combination pr and Vg+ stayed "coupled". Have I understood it correctly? or I'm missing certain significance of the concept of repulsion?


texts: Why is the manchineel tree so poisonous?

texts:
The machineel tree is incredibly toxic to humans. What advantage could Hippomane mancinella have for being so poisonous? It's name even apparently translates to “little apple that makes horses mad”.

Is it an incidental toxin, or an evolutionary hangover from a previous predator, or is it still actively predated by a species with high immunity?

I ask because this seems somewhat paradoxical; the tree has fruit, yet is toxic to animals.


texts:
If a B cell contains two mu chains and two lambda chains and is self reactive can it go back and rearrange its kappa light chains? I'm not sure if it can only try to rearrange its lambda light chains or if it can go back and try to rearrange kappa chains as well.

Background info: the light chain is the smaller of the two types of polypeptide chain in an immunoglobulin molecule. There are two classes of light chain known as the kappa and lambda light chains. During B-cell development the light chain genes rearrange. First one kappa gene is rearranged; if this doesn't produce a functional protein then the kappa gene on the second chromosome is rearranged; if a functional protein is still not produced then the lambda gene is rearranged one chromosome at a time until a successful rearrangement is produced.


texts:
My question is what does the word 'factor' mean in words like transcription-factor or nerve growth-factor? What is similar between these different compounds such that they deserve the word 'factor' in their name?

Edit: My confusion comes perhaps from the use of the word 'factor' in statistics, where it refers to a variable that can take on discrete values (e.g., the factor Gender takes on values 'male' and 'female'). Here a different meaning of the word seems to be used.


texts: I am going through a paper where they have done DNA-cellulose chromatography to study the interaction between protein and DNA. They are adding the protein to the column and eluting with high salt concentration.


texts: Why does a wound itch while it's healing?

texts:
During healing of wound (almost in final stage) it begins to itch a lot around wound.

I wondering what the reason for this is?


texts: Transfect Mammalian Cells with Single Stranded DNA?

texts:
Agrobacteria can deliver parts of their DNA to plant cells as T-DNA, transfer DNA. This DNA is delivered as a single strand and can be integrated into the plant genome or can be converted to a double stranded molecule by priming the T-DNA to make it a substrate for a DNA polymerase. This article describes the process, but Nature makes getting to the article hard, sorry.

What I'm interested in is delivery of DNA to mammalian cells. I tried to find articles that used single stranded DNA in mammalian cells, but couldn't find much. Maybe I didn't spend enough time searching. I saw some suggestions that single stranded DNA could trigger apoptosis, or that single stranded DNA could be used to manipulate DNA repair mechanisms to cause integration into the genome.

However, is there any way to deliver a single stranded DNA, and have it converted to a double stranded plasmid in situ? Would probably need an RNA or DNA primer, but I don't see why you couldn't pre-bind the primer and deliver the whole complex.


texts:
I was reading about nephrons in my physiology book when i came across this-

The efferent arterioles and peritubular capillaries technically constitute a portal system

But according to Wikipedia, renal portal system is absent in mammals. Can someone please explain this contradiction?

Edit 1: Could it be that humans are an exception to the case and do contain a renal portal system?

Edit 2: When we were discussing this in class, the my lecturer did say, "They are like portal sytems."

Why is human renal portal system not considered a portal system? Although, it connects two capillary beds (efferent arterioles and peritubular capillaries)

Edit 3- Some sites do say that the capillary beds that connect generally belong to different organs. Could this be responsible for exclusion of human renal portal sytem?


texts: Is there a term for the entire system of moving oxygen around?

texts:
The respiratory system brings oxygen to the blood, and also can include stuff like nicotine from smoking.
The circulatory system brings oxygenated blood (and all its little friends) to wherever they're needed.

Both the respiratory system and circulatory system are extremely important in keeping hypoxia from happening, but I'd like to focus specifically on the system of oxygenation.  I don't want to include the systems of smoking, or moving around nutrients.
Is there are term for the "oxygenation" "stop hypoxia from happening" system?  Basically just the parts of the respiratory and circulatory systems that move oxygen?


texts:
I am just starting to learn to use bioinformatics tools.  My university has a limited and expensive bioinformatics team, so I'm mostly on my own except for big questions.

I am planning to use GATK to run 58 cancer control/normal pairs of Exome sequencing data (Illumina) from FASTQ or BAM file format, through the pipeline, with an output of a VCF & MAF format for analysis.

The current GATK pipeline is used for disease but not cancer, so I was wondering if anyone knew if there should be changes made for cancer.  Here's the current pipeline starting with BAM files:

(Non-GATK) Picard Mark Duplicates or Samtools roundup
Indel Realignment (Realigner TargetCreator + Indel Realigner)
Base Quality Score Reacalibration (Base Recalibrator + PrintReads)
HaplotypeCaller
VQSR (VariantRecalibrator and ApplyRecalibrator in SNP and INDEL mode)
Annotation using Oncotator (?)

I'd like some verification that this pipeline will output what I need to run my samples on MuTect, MutSig, or some other analysis program.  I appreciate any advice.


texts: Reference for most up to date sport physiology

texts:
I currently have

  Exercise Physiology Nutrition Energy And Human Performance, 7th Edition, 2012, McArdle et al.

as my reference book for Exercise physiology. However, based on a question I recently asked here on this very same board, I realise the book sometimes takes shortcuts and does not provide a complete explanation. Plus, the structure is sometimes a bit difficult or not to my liking.

I saw that the 8th edition (2014) has been issued. I don't know if it is significantly different from the edition I have.

Would someone have another solid reference for Exercise physiology? I am particularly interested in the energy pathways and their training.


texts: What is the frequency distribution of each base in a DNA sequence?

texts:
Can we say that the frequency distribution of each base in a DNA sequence is equiprobable?

After the negative answer; i rephrase: Is there a use case in which the frequency distribution of the bases is equiprobable?


texts: Is there an 'opposite' neurotransmitter to dopamine?

texts:
Dopamine is a neurotransmitter  (i.e. chemical) in the brain that gives us great feeling. From here:

Dopamine plays a role in how we feel pleasure. It's a big part of our unique human ability to think and plan. It helps us strive, focus, and find things interesting.

Is there any chemical(s) released in the brain that have an opposite effect to dopamine, that is, some chemical that makes us feel bad?


texts: If the average resting potential of a neuron is -70 mV, why is there such a high ratio of potassium ions inside relative to out?

texts:
My bio teacher was discussing the ratios of different ions inside versus outside the cell.

$$\text{OUT:IN}$$

$$\text{K}^+ (1:20)$$
$$\text{Cl}^- (11.5:1)$$
$$\text{Ca}^{2+} (10000:1)$$
$$\text{Na}^+ (10:1)$$

Can someone provide specific details as to the relative quantities of these different ions relative to each other? In other words, given these ion ratios, provide me with how much of each type of ion there are and show why this adds to to -70 mV. I just want to make sure I have a realistic picture of the concentrations.

I think I am mixing up concentration with the ratio between inside and out. Although for every potassium ion outside there are 20 inside, the charge from the total number of potassium ions must be less than that of chloride or it would not be negative inside, right?


texts:
What is the lowest pressure at which plants can survive? How the plants behave in a Martian-type atmosphere? Is there any plant that can survive such atmosphere?

Can a lichen grow at Martian pressure?


texts: Do blood cells immediately die after leaving the body?

texts: I am wondering, do blood cells die right after they leave the body?


texts: Why pentoses are absorbed by facilitated diffusion in intestine? Wouldn't it be futile because , when the pentose concentration is lower in intestine, the pentoses would diffuse back to the intestinal lumen? So does our body looses them? If not then what is preventing this backflow?


texts: What species is this yellow flower of angiosperm from Morocco? I photographed it in spring. I estimate the diameter of a flower to be 1.5 cm.


texts: What is the "stimulus" that initially triggers an action potential?

texts: There are many steps detailing the depolarization and repolarization of axon nodes to describe how an action potential is transmitted from a neuron. But, after looking at many different sources, I still see one clear thing missing: what causes the action potential in the first place? Every source simply says something vague like "stimulus" or the ever redundant "depolarizing current." But, how is this stimulus generated, and what exactly does it do to which chemical to start the chain reaction of moving sodium ions to create the depolarization in the first place?


texts:
I was attending a talk related to neurogenesis. So one professor was asking a question related to biochemical cues and mechanical cues (related to signaling pathways I believe). Cue as far as I understand is a signal, right? Biochemical cue is understandable for me.

But what does mechanical cue mean?


texts: Are scientist able to correct mutiple gene defect in our body by using CRISPR

texts:
Are scientist able to correct mutiple gene defect in whole body by using CRISPR recently?

AS i know, it is in a beginning stage


texts: Evolution of Homo Erectus to Homo Sapiens

texts:
I just read an article on Wikipedia and noticed that some similarities between Homo Erectus and Homo Sapiens in the "Comparative table of Homo species". My question is;

Is it possible to say that some members of Homo Erectus species
have survived up to now and they are living in modern world as members
of Homo Sapiens?


texts: What's the difference between protein and DNA behaviour during agarose gel electrophoresis?

texts:
I'm planning a science project about gel electrophoresis, and I'd like to know if there are any measurable, quantifiable (for example, things I could represent in a graph or chart) differences between the behavior of protein and DNA during agarose gel electrophoresis.
Detailed inputs and useful links are greatly appreciated.


texts: What type of Interspecific relationship does this graph depict?

texts:
The other day in class, our AP Biology teacher presented us with the following graph and asked us to determine which of the following interspecific relationships it represents:

(A) commensalism
(B) predation
(C) mutualism
(D) competition
(E) parasitism.

She explained to us that since there is not enough information in the graph to explain why species A suddenly drops off after time "x" and species B suddenly rises after time "x", the best answer out of the choices is (A) commensalism.
But to me, that seems to be a faulty line of thinking. After all, my teacher arrived at that answer only under the assumption that the graph/question itself is good to begin with. I tried finding graphs of commensalism using Google Images, and I actually found the original source of the graph that our teacher presented us.
Now, the question on Regentsprep actually gives us a point of reference and states that we are considering two herbivores in a grassland environment, so in my opinion it's reasonable to conclude that the relationship between species A and B is competition.
The problem is that my teacher never gave us a frame of reference: she just told us to identify the relationship in this graph without any "backstory". So what are your thoughts: is it possible to conclude that "A" is the best answer choice if we are not given any information aside from the graph?


texts:
While trying to understand DNA supercoiling, I came across these lines in the book Genetics by Ursula Goodenough :

  All natural DNA is superhelical. The axis of the duplex itself follows
  a helical path in space. For virtually all DNA, the sense of the
  superhelical turns is opposite to that of duplex, thereofer, they are
  negative supertwists.

I am unable to understand these lines. Specially, the second one.


texts: How does the brain train its neural network?

texts:
One question that came up learning how artificial neural networks are working was how the brain can train its neural network?

When we say we have an artificial neural network, the problem behind it is a typical, but uncommon minimizing problem. The math behind it is logical and pretty easy. But it's math, so an computer can calculate it by doing millions of iterations. But the brain can't do that (I would be surprised)

So, how does the brain solve this task. Trial & Error, we don't know or is there an even more complex system behind it?

Thanks in advance.
GA


texts:
Is there anything similar to this in Java (especially the circular map sequencing along with hover effect)?
For information I would like to convey that I am using Plasmapper and BioJava for achieving this, but, as the output is in image format, so I am not able to achieve the above said requirement.
Thanks...


texts: How can I reduce the background gradient in phase contrast microscopy?

texts:
I'm looking for ways to set up a phase contrast microscope to reduce the brightness gradient that appears across the background of my images.

I use phase contrast to find the outlines of cells in my images. My problem is that the automated processing algorithms I use get confused by strong brightness gradients in some images. Post-processing of the images disrupts the continuous nature of the histogram, again throwing off the algorithms.

Does anyone know why these gradients appear and how to reduce their formation?

Thanks,

Oliver

Edited the question to clarify that I am interested in microscope usage, rather than image manipulation

Sample image:

The image background is darker at the left of the image than at the right


texts: How can individual strands of coat hair have only a single color when considering codominance?

texts: I understand how codominance works. We have two (or more) alleles for one gene, neither having dominance over the other. They are both expressed independently, which means that different phenotypes are visible simultaneously. However, I'm not sure how it really works when we take, say, coat color. If both alleles are active, assuming each one produces a different pigment for each color, that means there are both pigments in a cell. What I see explained is that, if you look closely, each hair has a different color, and when you see it from far away, it gives the impression that the coat is made of one single color. But how can one hair have the same color all throughout? How can the different pigments be aggregated like this? As in, how is it that they do aggregate like this?


texts:
Can I ask what is the species of this bacteria? A comment there says that it is probably E. coli.
Disclaimer: I don't have an idea about the given video of bacteria as we are asked to solve for the number of them after 24 hours.


texts: What are the metabolic consequences of negative mechanical work in muscle contractions?

texts:
When a muscle contracts while it shortens (concentric), it consumes ATP I believe primarily due to cross-bridge shortening to remove the myosin head from it's attached state.

However, when a muscle contracts while it lengthens (eccentric), it must absorb negative mechanical energy. Is this negative mechanical energy absorbed used to disengage an attached cross bridge and thus doesn't require as much ATP?

If fatigue of concentric muscle contraction results from a shortage of ATP for contraction, is there a similar rule for eccentric contractions. Since it is known that eccentric contractions cost 5x less metabolically then concentric contractions, where do these savings come from?


texts: Combining gene expression data from two species

texts:
I currently have two sets of gene expression data. The first is a dataframe of genes identified by Annotation id CG numbers (for example "CG10005") in one column and a numerical variable of interest associated with each of those genes in the other (the important part is that the genes are identified by the CG number). The second dataset is this study from multiple species where genes are identified by "GLEANR" ID's like this one: "dsim_GLEANR_10060".

I would like to extract all of the values from this study for the D.melanogaster and D.simulans data, then link that to the Annotation ID's in the first dataset (to connect my variable of interest to the sex bias in expression for each species). The trouble I am having is connecting the orthologous genes within the second study to each other, and then connecting them to the CG identifiers in the first study.

Does anyone have any suggestions on resources which can be used to get this all to link up?


texts:
My recent post was tagged as unclear so I wanted to re frame my question. Though I am a layman, I would love to read books and find the stuff, if I get an overall picture of intelligence factor. My question is, how come evolutionary mechanism of protecting ones species made them adapt to their environment ?

The answer comes by the genetic mutation, the switch genes and so on. But how are these cells intelligent to cause such mutation ? For instance, cells don't have intelligence of their own, so presented a situation where in you have to see, but have no eyes, or have to walk but have no legs, how come cells know that they have to work against gravity and develop such structures and hollow bones in birds to make the flight easier ? Does it mean that nature is intelligent ? How come matter itself create gravity, space etc., on one side, and creating beings to overcome it ? Isn't the matter altogether ? If that's the case, imagine a thought experiment, where in we all have dangerous predators which are 4D beings. So since our cognitive and visual percepts  are just designed to perceive 2 dimensions at a time, we being 3D creatures. So over thousands of years, since we have to live and survive, would we develop a vision that can see 3D ? It would be amazing then. It then means that there is an intelligence factor in nature that tells the creatures how to change !

Please do answer, and again repeating I want to hear, how Genes know that they have to work against gravity, or develop a particular efficient thing, that can solve the problem. Otherwise it's as if Genes permute infinitely, and then develop all possible models, and only those which serve the purpose will stay.

Please do clarify.
Thanks !


texts: Why aren't hybrids of different species of felinae (say, hybrid of domestic cat with manul, cheetah, ocelot, puma or panther) widespread? Why were they not artifically created?


texts: Where can I find and download HMMTOP training set?

texts:
I would like to perform redundancy reduction for my test set for membrane topology prediction. I checked the 1998 paper and website of the HMMTOP server but haven't found any download links for the dataset that they have used for training.

Links:

paper
server

In the Appendix Section of the paper, there is a table of entries and topologies.  Below, there is a note:

  *Entries which are included in the initial parameter and
  pseudocount settings from the 83TMP set.

Please correct me if I'm wrong, I suppose these those 63 protein entry names with an asterisk are the data used for training?


texts: Can warm blooded vertebrates other than humans act as reservoir hosts for malaria parasites? I'm mainly interested in Plasmodium vivax and possible reservoir hosts in the wider area of Europe/ Eurasia.


texts: What is this brown insect with a large wingspan?

texts:
I found this dead creature on my window last night and spent hours looking for something that could explain what this is. I was unable to inspect it in person though, because opening the window would make the creature fall down.

It is roughly three inches in length and has a wingspan of five inches. I found it in the UK in August.

Here are some pictures:


texts: Reasons why this protein is not suitable as an immunogen?

texts:
In a paper entitled "Progress and Prospects on Vaccine Development against SARS-CoV-2", the authors write the following in section 2.5:

"Compared with S, N, and M protein, E protein is not suitable for use as an immunogen. For one reason, it consists of 76–109 amino acids in different coronaviruses with channel activity, thus the immunogenicity is limited. Studies have shown that SARS-CoV E protein is an important virulence factor, and the secretion of inflammatory factors IL-1β, TNF, and IL-6 are significantly reduced after
knocking out E protein"

Question

Why does the fact it consists of 76–109 amino acids in different coronaviruses with channel activity imply its immunogenicity would be limited?


texts: What determines the perceived pitch (frequency) of tinnitus?

texts:
I noticed that every time I suffer temporary tinnitus after going to a very loud concert, the frequency I perceive is identical. I'd put it somewhere around 17 kHz, but it's difficult to pin down with any real accuracy due to the dulling effect it has on external sound sources.

Is this frequency constant across all humans? If not, what determines the frequency? Note that I'm only interested in tinnitus caused by exposure to loud sounds, not other types of tinnitus such as idiopathic tinnitus or tinnitus caused as a side-effect of medication.


texts:
ATP Synthase is ubiquitous throughout life on earth and so most probably evolved within the last universal common ancestor (LUCA) before that lineage diversified into the various kingdoms of life.

It is suggested that the functional domains comprising the ATP Synthase complex were cobbled together from pre-existing sub-units, each with with a related activity (e.g. the union of a proton motor with a DNA Helicase with ATPase activity), which seems reasonable, although a bit vague in the details.

The fact that a primitive ATP Synthase arose in the first place suggests that ATP already had a central role in cellular metabolism and so begs the question, what preceded ATP Synthase in the role of generating ATP in the LUCA cell?


texts: Does the human eye’s field of view shrink when focusing on far away objects?

texts: It seems like the lenses of the eye is like a fisheye lens that flattens out to a normal lens when looking at far away objects. Does that also mean that the field of view gets narrowed down as well? Or is that not how light works?


texts:
Friends of mine recently came back from a visit in kenya and on the kenyan beach they said they found several jellyfish with "sails" on their head. We tried finding out what they were and found one image online that was exactly the type of jellyfish they found:

What kind of jellyfish is it?

The guide told them that they're dangerous and those are just the corpses without stings or something, but nobody knew it's name.


texts:
If you're standing and holding your nose closed, it becomes quickly uncomfortable; although you can breath fully through your mouth, it still feels like your lacking air since you're naturally trying to breath through your nose and you can feel the restriction.

On the other side, when swimming with a nose plug, you can have your nose totally shut down, breath only through the mouth and somehow you do not have the feeling of nose obstruction blocking your air intake.

Why is this?


texts: Determining the osmolarity and tonicity of a cell

texts:
Consider a cell with urea concentration inside being 2mmol/L and outside being 2.5mmol/L. The cell itself is permeable to both urea and water. Ignoring the effect of other osmolytes,

A) Urea flows in, water flows out

B) Urea flows in, water flows in

C) Urea flows out, water flows out

D) Urea flows out, water flows in

I'm confused because I thought water would simply flow out of the cell to equate the concentrations inside and outside such that there is no net flow in urea.


texts: What is a common body composition in mammals?

texts:
The Physiology Of The Racing Greyhound states that most species have about a 40% muscle mass to body mass ratio. Understanding Body Composition puts "optimal fitness" in humans at 16-25% body fat for women and 12-18% in men. These add up to pretty much anywhere from 50% to 65%, leaving 35-50% as more or less unaccounted for. In looking, I have been unable to readily locate any further breakdown, let alone any source that provides a full breakdown. At least Wikipedia is lacking in specifics in this regard.

In adult, healthy mammals, what is a common body mass breakdown into muscle tissue, fat, bone, and internal organs, by percentage of total body mass?

I am particularly interested in wild carnivores, but almost any mammalian species will do in a pinch. Specific examples and citations are appreciated.


texts: Could humans choose to establish fibre digesting colonies in our guts?

texts:
Humans don't digest fibre, and nor do any animals, but some creatures have micro-organisms (bacteria, I'm guessing) in their gut which digest fibre for them.  My question is, could humans take some sort of pill and establish our own fibre-digesting colonies in our intestines?  Has this been tried?  Supposing it could be done, would you suppose it would have any negative effects on our health?  (i.e.. would those whose gut digested fibre for them be stuck on a low-fibre diet?).

Purpose of question: just wondering.  It would be cool to be able to eat bark.


texts: Difference between the inactivation of neurotransmitters and hormones

texts: Neurotransmitters must be somehow removed from the synapse once they’ve produced a post-synaptic potential, whether it be through enzymatic breakdown, diffusion, reuptake or another mechanism. However, I rarely see such mechanisms mentioned when discussing hormonal communication. I assume hormones just diffuse away from their receptor and do not continually stimulate the cell. However, there does not seem to be an urgency in breaking it down. Why is there this urgency, then, in the case of neurotransmitters, but not with other first messengers, like hormones?


texts: Can someone help me answer or explain how to answer questions about DNA coding capabilities?

texts: How is it that a DNA coding system with only 4 bases can yield so many possibilities? Also, how many unique coding sequences can there be with a DNA code that is 8 base pairs long? Hint: 4^n combinations. I've gone through this in my textbook, but I don't understand how to get the answer for it.


texts:
It's the age old question, why can't we tickle ourselves? If you rub your fingers along your skin, sure there's sensation but you don't break down into a laughing fit (at least I don't :P), if someone else does it to you, you're rolling around on the ground begging them to stop tickling you.

Why is it that other people can tickle us but we can't tickle ourselves by touch? (I'm aware that if you use a feather or foreign object on yourself you can be tickled by it so that doesn't count.)


texts: How are some people able to continue growing after reaching maturity?

texts:
This is technically a cross-post of a question posted last year concerning gigantism and how certain people are able to grow far past expectations after it's assumed they've reached maturity.

How are some people still able to grow after reaching adulthood? Someone gave the answer in the old post that epiphyseal growth plate closure is caused by testosterone and not growth hormones. Is it a lack of testosterone, or an excess of testosterone? If it's a lack, why are women usually shorter than men and stop growing sooner? If it's an excess, does that mean basketball players produce less testosterone than average height people?

There are a number of cases of pituitary gigantism out there, but these are the best examples of what I'm asking:

Väinö Myllyrinne was 2.22m at the age of 21 but is described as having "experienced a second phase of growth in his late thirties", attaining a height of 2.51m by the time of his death at 54.
Adam Rainer at the age of 18, he was only 1.22m. However, he had a growth spurt in his 20's, reaching a height of 2.18m at the age of 30 and 2.34m by the time of his death at age 49.

What could have caused these men to grow so much after modern medicine tells us our growth plates have closed? Is there a possibility of replicating their late growth for people who suffer from hereditary short stature or other growth-related problems? And would it be safe?

EDIT: Although my question is different in many ways, here is the original question.


texts: What are the uses of centrioles and matrix of centrosomes?

texts:
In centrosomes, the gamma-tubulin ring complexes (gamma-TuRC) located on the surface are essential as the nucleation site for the growing (with polarity) of microtubules.
However, I see that there is also a centriole (made by 2 centriole units in T-shape structure) and a centrosomal matrix. According to Wikipedia, it seems without centrioles, the cells can still function normally and grow (please correct me if I am incorrect), and it seems I cannot find much information in the internet suggesting the use of both centrioles and centrosomal matrix.
Therefore, I would like to ask what are there functional significance? And I would like to ask if we are able to make a synthetic sphere with many gamma-TuRC on its surface (without any rejection), can the cell perform a normal cell cycle?


texts: Why do insects (flies) put their legs together when they die (as if they're praying)?

texts: Other animals don't seem to have an organized pose to die in. Or do they?


texts: Are All Taxonomic Groups Uniquely Named?

texts:
The Linnaean classification system classifies and groups organisms into taxonomic groups: Kingdom, Phylum, Class, etc. Obviously, a clade at any taxonomic level is uniquely determined by its classification at this level and all its parents in the hierarchy, e.g., Kingdom = Bacteria, Phylum = Firmicutes, Class = Clostridia uniquely identifies a group of bacteria. But is this group also uniquely identified by just Clostridia? Or are there situations where two Phylums might both contain Classes with the same name?

Since Genus & Species are typically used to identify organisms, I would assume that combinations of these at least are unique. As @Jam pointed out in the comments, Species alone is not enough. Note, however, that I am not asking about the binomial name for a species - I am asking about uniqueness among higher levels of aggregation, such as Class, Order, and Family.


texts: Why do cats sleep in a curled up position?

texts: I've noticed that cats will usually sleep curled up like ball, heads down and titled, with tails near their face. Is there any specific reason that cats would have a tendency to sleep this way?


texts:
I'm trying to find homologs of a set of proteins using BLASTp. I'm working with custom databases.

I'm using evalue of 0.00001 as threshold.

I would like to filter queries having hits with >90% identities. Because BLASTp output is based on HSPs, I cannot filter by %identities/query, only by HSP.

I would like to know how to do this and also if I'm following a reasonable strategy.

Here is an alignment example: qcovs=100 but qcovhsp lower.

qseqid           sseqid         pident length mismatch gapopen qstart   qend  sstart    send   evalue bitscore qcovs qcovhsp
HPNK_01698      HAPS_0519       81.88   596     75      5       630     1225    615     1177    0.0      889    100     49
HPNK_01698      HAPS_0519       49.17   301     115     8       84      366     201     481     2e-56    214    100     23
HPNK_01698      HAPS_0519       53.64   261     61      6       436     684     616     828     6e-49    191    100     20
HPNK_01698      HAPS_0519       46.61   251     62      3       332     510     584     834     6e-46    181    100     15
HPNK_01698      HAPS_0519       53.27   214     79      4       1       194     1       213     1e-45    180    100     16
HPNK_01698      HAPS_0519       55.96   218     60      8       550     764     643     827     1e-40    164    100     18
HPNK_01698      HAPS_0519       51.56   225     61      7       516     731     642     827     1e-38    157    100     18
HPNK_01698      HAPS_0519       49.57   230     77      6       484     713     643     833     1e-37    154    100     19
HPNK_01698      HAPS_0519       57.89   76      26      1       364     433     760     835     1e-13   76.3    100     6

Code used

Make database

makeblastdb -in $Hparasuisfastadatabase -out H_parasuis_strains_gb_ALL.fna_databaseBLAST -dbtype prot -parse_seqids

Run BLAST

blastp -db H_parasuis_strains_gb_ALL.fna_databaseBLAST -query 'out_2.fasta' -out HPNK_selected_vs_H_parasuis_strainss.tblastn -evalue 0.00001 -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovs qcovhsp" -max_target_seqs 50

Thanks, Bernardo


texts: Can Escherichia coli survive on glucose and water alone?

texts:
I am novice to biochemistry and biology in general. I am reading Lehninger Principles of Biochemistry, and I found the following sentence at the beginning of the chapter on glycolysis:

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

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


texts: What are the lifetimes of cellular components on organelle or molecular level?

texts:
I was thinking that even though I know how generally the cell works, I don't really have a feeling of how volatile it is.
I want to know what is the lifetime/turnover rate of different constituents of the cell.

On the molecular level what are the lifetimes for various proteins, for ribosome, lipids, carbohydrates, DNA and RNA. What about aminoacids, nucleotides?

On the organelle level what are the lifetimes of the mitochondria, golgi apparatus. Does nucleus or ER ever change if not during meiosis.

I understand that the lifetime depends on the context. For example, for DNA, cells that replicate, half-life is about one replication as a whole new strand is generated. In neurons, that don't replicate for decades it's not the case. But the DNA can't just sit there. It is constantly unraveled, transcribed, damaged and repaired. So it has a different time constant.

I am still very interested to know any specific numbers.


texts:
I live in NYC and these fellas started popping out near my computer screen and desk. They don't seem interested in food as my sister usually leaves candy wrappers around. They however are stinky, I tried to catch one with a tape and I can smell the odors they give off like 4 inches away. They got these stingers on their butt so I think they could be a species of fire ant. They're also really tiny. As shown on a q tip here.

(click to enlarge)

Finally could these be bites? They are really itchy and I get them overnight.


texts: Is some of the energy of food lost during digestion?

texts:
I know that chemical energy of food is converted to heat energy to be used by the body in many metabolic reactions. Specifically, I know that the breaking down of bonds is what releases energy.

Does that mean that some of the energy of food is lost during digestion as enzymes breakdown large food molecules into smaller soluble ones? Or is it the common concept of losing energy during digestion because not all the food is absorbed and some are egested?


texts:
What is meant when asked write molar ratios in 3 parts? For example I am currently assembling a vector that requires annealing several oligos to two pcr fragments prior to ligating them into my vector; which will be used for future transformations. I was told to "assemble the annealed oligos with the 2 pcr fragments. Use a 100:1:1 molar ratio of annealed oligos:each pcr fragment." I'm thinking this means- concentrated oligos:diluted pcr frag #1:diluted pcr fragment #2. I am confused about how to determine the final concentrations of my pcr fragments in relation to the concentrated/undiluted annealed oligos. Why? Because I only know their concentrations as ng/uL not as 5x, 2x or 1x. Should I calculate it as 1(part) divided by 102 (whole) for each fragment? Then multiply that number by the actual concentration of my pcr fragments.

I am sure the answer to this is probably simple but I'm sorry I don't understand it and am hoping someone helps me with understanding calculations of this sort. Thanks.


texts: Are Y spermatocytes faster but less resilient than X spermatocytes?

texts:
I have heard somewhere (but did not find any suitable reference) that spermatocytes carrying a Y chromosome are usually faster but less resistant than those carrying an X chromosome.

Is this true? If so, which are the actual reasons?

There is a remote but theoretically plausible explanation indeed for the difference in speed, as the Y chromosome is much smaller and lighter and thus would make the Y spermatocytes less heavy than the X spermatocytes. Possibly, the larger number of genes on the X chromosome (missing in Y spermatocytes) could imply that they can still have some incremental translational activity.


texts: Function of the alpha subunit in mitochondrial ATP-synthase?

texts:
Within the catalytic core of mitochondrial ATP-synthase there are two different types of subunits; $\alpha$ and $\beta$. From what I have read, the catalytic sites occur only in the $\beta$ subunit so clearly it is in these where ATP is synthesised.

However, I can't find what the function of the $\alpha$ subunit is. A source would be appreciated.


texts: I added ethanol to my TRizol RNA extraction

texts: I added ethanol instead of chloroform to the cell suspension in Trizol. Can I still obtain my aqueous phase?


texts: Found in Russia, in the kitchen. It is about 1–2 cm length.


texts: Why don't restriction endonucleases digest transformed plasmids?

texts: In the textbook that I'm using, it explains that bacteria does not digest its own chromosomal DNA because the sites that would be cut by its own endonuclease are methylated. Is there a similar mechanism involved for protecting its own plasmids? If so, how are plasmids cut while serving as vectors?


texts: Pharmacodynamics of Ethinyl estradiol + Drospirenone and interactions with istotertinoin

texts:
Does pharmacodynamics of Ethinyl estradiol + Drospirenone in OCP pills like (Yaz, Yasminelle etc.) while using isotretinoin (Axotret, Roaccutane etc.) is changed? Does isotretinoin weakens the OCP pill by any means in any situation?

I know about interaction towards incrase of lipids. The only info I have found is this: https://www.ncbi.nlm.nih.gov/pubmed/15116059 and results could be translated: we discovered nothing.


texts: How good are the hematologic parameters (e,g, IL6 or others) in predicting which patients will develop a severe COVID-19 disease?

texts:
Clinical implications of the hematologic profile of COVID-19 patients including cytokine storm, coagulation profile and thrombophilic complications are starting to be recognized. Hypercoagulability could be the potential cause of death due to COVID-19:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7585459/
How good is the hematologic profile, including hematologic markers (such as interleukins and others) in predicting if COVID-19 is severe, has mild manifestations or it is asymptomatic?


texts: Can I purify polyhydroxyalkanoates by heating the cells extensively?

texts:
Traditional methods of purifying polyhydroxyalkanoates (PHAs) and other bioplastics made by bacteria involve washing the cells with harsh chemicals or strong bases.I'm interested in maintaining the spatial position of the PHA globules relative to one another. Therefore, I'm hypothesizing that by heating these cells extensively, I can lyse/degrade the cellular matter and be left with only PHAs, especially given that some PHAs have melting points up to 180 degrees.

Is this approach to purifying PHAs plausible? Has it ever been done?


texts: Humans have approximately 25000 genes. Why are these genes on 46 chromosomes? Why not 40 or 50?


texts: What is the lifetime of the vasopressin receptor V2?

texts:
I was looking at the production of vasopressin receptor 2, also known as V2R or ADH-R. What I found is that it is coded by the AVPR2 gene and degraded by the Alix protein (source).

But I did not get a sense of the timescale. After a receptor protein has been produced and embedded itself in the cell membrane, how long does it live? Is it days, weeks, months? Does it live until the cell dies or is it degraded before that?

Does the lifetime differ between each receptor, or on the cell type, or is it roughly the same for all G coupled receptors?


texts:
Am I correct in thinking that in a standard probe synthesis reaction where primer/template are heated up and then cooled down for Klenow to extend, the theoretical maximum amplification is doubling of the template?

Given that there is essentially only one melting/primer hybridization step, there can't be further amplification after doubling?

I understand that there could be edge cases. IE. random hexamers are used where initial amplification product is displaced by a further upstream hexamer. But given an idea situation where we have just one specific primer and one specific dsDNA template that primers can bind to, the maximum yield will be double?


texts: Why our arms stop growing if mitosis never stops?

texts: I wonder if there's a balance between cell death a new mitosis .


texts: Which functional annotations could be useful?

texts:
Analyzing a genome, for a generic gene, which functional annotations (e.g from Gene Ontology) can help understanding its meaning/function or, at least, provide helpful informations?

Annotations of that gene
Annotations of orthologous genes (?)
Annotations of paralogous genes (?)
Co-expressed genes (given a biological condition) (?)
What else?

Thank you.


texts: Why do vaccines sometimes induce a fever?

texts: How does a vaccine cause an immune response such as fever? Why do only some people experience these reactions? Why might those reactions change upon subsequent doses of the same or similar vaccines?


texts: What's the highest glucose concentration (in mM) anywhere in the human body (tissue, capillaries, tumor microenvironment, etc.)?

texts: Glucose blood levels are around 5mM, or 10mM after meals. In capillaries these levels can rise by about 40 %. I haven't found measurements of glucose concentration in tissues, or in extracellular spaces. I'm wondering what's the highest glucose concentration, anywhere in the human body?


texts: Allosteric regulation: why involve extra molecules

texts: Why are molecules such as allolactose (for lac repressor) or 2,3-BPG (for haemoglobin) used for allosteric regulation rather than the actual molecules involved in biochemical pathways, such as lactose and 1,3-BPG? The formation of such "extra" regulators requires energy – what is the advantage of such organisation?


texts: What species is this mosquito-like insect?

texts: I found this in my room in Serbia. It's not a local type of mosquito that I'm familiar with, so I'm very interested. It flies like a fly but it looks like some kind of mosquito. I am looking forward to seeing what this could be.


texts: Why don’t different organisms have nucleic acid genomes containing different bases and sugar?

texts:
All organisms contain genetic material. Be it DNA or RNA, both of them have a fixed pentose group (deoxyribose and ribose). Also they contain the same types of nitrogenous bases, Adenine, Thymine(or Uracil), Guanine, Cytosine.
What makes ribose and these notrogenous bases so good that among all the molecules in our pre-historic chemical pool, these selective compounds made our genetic material.

Why don't different organisms have different bases/sugars? I understand that we all have a common evolutionary ancestor so the the genetic material will be similar. But mutation is possible, so why is that there are no nucleic acids found naturally that are made of different bases or sugars? Just for example, if we had a hexose like glucose for the sugar instead of pentose..


texts: Are ectopic beats considered sinus rhythm for pNN50 purposes?

texts: One quantification of the heart rate variability of an ECG is pNNx, i.e. the proportion of consecutive NN distances that differ by at least 50 ms. When a premature beat occurs, the preceding and following RR intervals are much shorter and longer than the mean. Are these intervals considered NN for the purpose of calculating the pNN50?


texts:
I'd like to block a percentage of PGC-1β or Sod2 expression. According to the following paper's figure beta-blockers inhibit some expression of PGC-1α. Are there any medicines/chemicals which safely and temporarily block 50%-60% expression of PGC-1β or Sod2 in fully developed mice or humans?
Thank you

http://jap.physiology.org/content/107/1/8.full

Fig. 1.
Interactions of β-blockers and mitochondrial biogenesis. Aerobic exercise activates β2-adrenergic receptors (β-AR) on skeletal muscle and induces peroxisome proliferator-activated receptor-γ coactivator-1α (PGC-1α) transcription, a regulator of mitochondrial biogenesis. Selective and nonselective β-blockers can blunt β2-AR signaling, which restricts the expected PGC-1α response following exercise and can impair adaptations to mitochondria and aerobic capacity. V̇O2max, maximum oxygen consumption.


texts: Chlamydomanas are present in Kingdom Protista or Plantae?

texts:
Chlamydomonas, Chlorella are present in Kingdom Protista as well as  Plantae under division algae.

In which kingdom they correctly belong to?


texts: What is the evolutionary advantage of telescopic generations vs normal pregnancy with more young?

texts:
There are a small number of organisms, so far I'm aware only of mites and aphids, which practice telescopic generations, where the a female is pregnant with a daughter that is, itself, already pregnant, meaning the adult is carrying two generations within itself.

I'm trying to better understand the evolutionary advantage of this, specifically when compared to the 'normal' evolutionary strategy of non-telescopic generations but giving birth to more young.

In both cases, telescopic generations vs increased young, the mother invests the same amount of resources towards the pregnancy, be it through multiple daughters or fewer daughters but a head start on granddaughters.  At first glance it would seem this would make both strategies about equal in reproductive success.

In the case of mites which reproduce sexually, by mating in the womb, I can see one potential advantage of increased genetic diversity...presuming there is any noticeable difference between phenotype of grandchildren in a species that practices serial obligatory incest.  Since I'm not certain how large a difference in phenotype children can be expected to have after genes have mostly homogenized I'm not certain how large an advantage this may actually offer, if any.  It also doesn't explain the advantage in the case of aphids which are clonal when practicing telescopic generations

So, there any other reasons I'm missing for why telescopic generations would be preferable to birthing more daughters?


texts: What is the name of this whorled-leaf tree in India?

texts:
Location: South India

Month: June

Season: Rainy

Branch Distribution:

Leaf of the tree:


texts: What proportion of proteins require chaperone-assisted folding?

texts:
I am new to the field of biochemistry (I am a chemist, actually).

I have long known the process of folding as the process that leads to the minimum energy conformation of a protein.

Now, I am introduced to the chaperones, that I didn't know before.

What I am wondering is: my previous view of folding, as a proces of "self-assembly" (the protein folds without external assistance as it is assembled by the ribosome) is real, or any folding process is assisted by chaperones?

If both processes exist, how frequent is the "assisted" folding, compared to the spontaneous process?


texts: Can the sleep/wake cycle be influenced by non-visible spectrum electro-magnetic radiation?

texts:
I've been reading a few papers on Melanopsin and Suprachiasmatic Nucleus (SCN), and see that the sleep/wake transition is influenced and entrained by visible light, particularly in the blue spectrum that is registered by special cones in the eye and is transmitted to the SCN.

I've seen a fleeting hypothesis/mention in two of these articles, that electromagnetic radiation may also play a part in the sleep/wake transition and melatonin release, on top of the blue light. It was some time after I read those articles that it dawned on me to ask this question, and I'm unable to find the exact lines where the mention was made.

Has there been any modern studies on the connection between electro-magnetic radiation (non-visible spectrum) and the human's circadian rhythm entrainment?

Can humans be affected or feel the influence of electro magnetic radiation at all?

If there is a connection, what is the name of a process/organ/gland by which humans can be affected with electromagnetic radiation?

Thank you for your clarification!


texts: Yeast absorption of different spectra of light

texts:
I'd like to monitor the growth of a yeast population by shining light through it and monitoring the change in light that gets through as it grows. I'm not sure if I should use IR, or any particular colour of light.

Are there any charts that show the light absorption of brewers yeast to different spectra of light?


texts: Why is there smooth muscle in our bronchioles?

texts: Having muscle tissue in our bronchioles that can constrict seems like a poor choice for tissue. Why would our airway want to ever close up? Wouldn't it be more beneficial for our bronchioles to just remain open?


texts: Why cancer mutations do accumulate sequentially?

texts:
According to Knudson hypothesis, cancer mutations accumulate in order. Statistics says, that cancer probability increases as sixth order of age, which may mean six consequential steps to cancer.

But, mutations are random in nature. There is no apparent cause, why mutations ABCDEF can't occur in reverse order, i.e. FEDCBA and any other possible orders.

If unordered, any number of required mutations should cause flat age dependency.

Hence, something is ordering these mutations, i.e. making mutation B impossible until A occurs and so on.

What is it?

UPDATE

Cancer incidence dependency on age:

The graph is not linear, which means that mutations are not independent.

UPDATE 2

Let's regard some cancer, which requires 6 mutations. It's incidence distribution should be like shown above.

Now suppose we knew the distribution of all precancer stages, i.e. the distribution of people with 1, 2, 3 and so on mutations. These distributions should look similar to final distribution

Now let's regard only one (first) mutation.

Why is it's incidence age dependent?

Mutations are random. They should not depend on age. If they do depend on age, then they are not random. If "they" are not random, then "they" are not mutations.

Or, in other words, the cause of progression is not a mutation itself.

Isn't it true?


texts:
The creature appears to have a green body with 5 legs of the same size, and one longer than the rest. It moved this long leg around, and it looked like it was using it to sense it’s surroundings.

Location: Manchester, United Kingdom


texts:
The title does, prima facie, appear absurd.

Performing a swallowing action whilst pinching the nostrils shut gives the impression of listening through a bucket filled with water around the head; audible sound levels are perceptibly reduced. Some humans may encounter a similar sensation blowing their nose - hard.

This makes sense give the ears connect to the mouth/nose through the eustachian tubes. Can an odour make its way to the olfactory sensors through the ears?


texts: Are wasps attracted to UV light emissions?

texts:
I remember seeing a documentary where it was shown that bees and wasps are attracted to UV components of a flower colour (please correct me if I am wrong).

Does this mean that they could be attracted by neon lights (that I suspect are emitting also in the UV part of the spectrum)?

I am asking because I have neon lights in my office and if I have the lights on I can't open the window, or a wasp will almost immediately enter the office. I've experimented a bit, and turning off the light makes the wasp go out rather quickly, hence my hypothesis.

I am located in Europe, if that makes a difference for the species involved. Outside the window we have some tall trees, so we keep some lights on even when the sun is out.


texts: I found this larva in Sweden in July. It was about 15 mm long. It reminded me of Orgyia antiqua that I've seen before, but smaller and with a somewhat different colouration.


texts: I was wondering: What is the protein with the highest affinity to lactose? Are there some databases with values for affinity?


texts: Why are insects unafraid when you tap at them from the other side of glass?

texts:
In the summer months we frequently try and kill mosquitos in our home. They are tremendously skittish and get airborne pretty quickly as you approach them. However, if they land on a piece of glass (a window for example) they don't seem at all bothered at you approaching from the other side and tapping the glass where they have landed.

Is this some strange physiology of insects (or at least mosquitos) that they cannot look down? Is it that their eyes function differently to our eyes and cannot see through the glass? For sure, their brains cannot be  developed enough to understand the safety afforded by the glass.


texts: Recently I was playing a quiz and a question was asked about the color of the fur coat of a polar bear. To my surprise the answer was black. I thought it was yellowish white or creamy. Why so ?


texts: Medical term for "holding urine for a long time"

texts: Sometimes I get/feel pain in my stomach because of holding urine for long time. Is there any medical terminology describing: "holding urine for a long time", or pain associated with this activity?


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

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

What species is it?


texts:
Is is well known fact that marine mammals and some birds can sleep with one brain hemisphere at a time, since it's essential for their survival.

However, at least in my opinion, such mechanism would give significant advantage to many other species (e.g. to antelops) because it helps avoiding predators.

While answers to this question explain why sleep is necessary, animals with unihemispheric sleep mode does not seem to suffer from any of mentioned drawbacks of non-sleeping (except maybe increased energy consumption).

Are there any particular disadvantages of unihemispheric sleep versus "normal" sleep?

EDIT: I've stumbled upon the following paper:  Rattenborg N., Amlaner C., Lima S.. 2000. Behavioral, neurophysiological and evolutionary perspectives on unihemispheric sleep. Neuroscience & Biobehavioral Reviews 24: 817–842, which discusses several possible reasons for absense of unihemispheric sleep in most mammals, but does not present any evidence to support their hypothesis. The main reason (from authors' point of view, at least) is the need for very loose coupling of both hemispheres to allow them sleep independently, which might negatively affect overall brain effectiveness.

  Along these lines, sleep may play a role in integrating the
  functions of different brain regions. Thus, BSWS1 in terrestrial
  mammals may be superior to the BSWS in animals with USWS2
  because it allows integration within and between hemispheres, rather than
  just within a particular hemisphere.

  ...

  Specifically, the reorganization of the central nervous system
  required for USWS may interfere with other adaptive brain functions,
  such as integrating the functions of both hemispheres.

  1 Bihemispheric Slow Wave Sleep; 2 Unihemispheric Slow Wave Sleep

They also argue that the unihemispheric sleep might have been present in first mammals, but wasn't giving any advantages on first stages of evolution.

However, this paper was published more that 10 years ago, so there might have been some advances in the field since then.


texts: Is perceived time compressed or expanded while dreaming? (or does it match reality)

texts:
I often dream long extended dreams.  Sometimes I wonder if the timeline of the story of my dream occurs compressed, in a moment, or other times extended slowly over a long duration.

Is there any way to scientifically detect this, and how would it be accomplished?
Are there any prior examples of this study being performed?


texts:
My textbook says,

  In general, the formation of a [chemical] bond releases energy

and continues to state,

  Anabolic reactions (collectively called anabolism) link simple molecules to form more complex molecules. Anabolic reactions require an input of energy because strong bonds within the smaller molecules must be broken to form the more complex molecules.

Do these two statements contradict each other? The first statement says that when two chemicals combine to form a bond, energy is released; the second statement says that when simple molecules are linked, presumably through a bond, an input of energy is required.

Any help is appreciated.


texts: What is the effect of a pure-oxygen environment on a plant?

texts:
Just read What's the effect of oxygen deficit on plants? ; and wondered whether the opposite would have any effect on a plant.

That is to say, if a potted plant were placed under a bell-jar and the air within replaced by pure oxygen would the plant starve? If the environment/soil were loosely radioactive, would it make a difference?


texts: How to preserve leaves between sampling (collection) and analysis?

texts: Suppose I spend a day in a forest, collecting different kinds of leaves, which I would like to analyze under a compound microscope. Now, obviously, measures should be taken to preserve the leaves some how. What would be the appropriate procedure? It seems (based on browsing the web..) that refrigeration could be one option. Is it scientific (used in published papers)?


texts: When was the last common ancestor of pig and human?

texts: Some religions regard pigs as unclean on the grounds that pig flesh is closest in composition to human flesh. I don't believe this for one instant, but it got me thinking, just how close is pig and human on the evolutionary tree?


texts: Do mitochondria use ATP in order make another ATP from glucose?

texts: Do mitochondria use ATP in order make another ATP from glucose, or does it use another source of energy to convert glucose to ATP?


texts: Do all kind of unicellular asexual reproductions let mutations happen, resulting in evolution?

texts: I know about fission, an unicellular asexual reproduction method, where the mother cell splits into two daughter cells. Does this kind of asexual reproductions let mutations happen, leading to much needed evolutionary process? Is it same for all unicellular asexual reproductions?


texts: Why do human females have permanently prominent breasts?

texts:
Humans seem to be the only animal whose females have breasts that permanently have a "full" appearance, ie a prominent amount of tissue even when not lactating, whereas other species' breasts seem to almost totally "deflate" when not longer lactating.

Why is that?

This feature has costs to the organism; significant biomass is dedicated and perhaps mobility is impacted. Given there are costs, for the feature to have come into existence, evolution/adaptation principles suggest there must have been some advantage.

Is there some biological advantage?
Are they vestiges of an adaptation that gave a significant advantage to some prior species or in some specific (presumably cold) prior environmental conditions?
Is there any credible research to support certain reasons?

My suspicion is that although genders can be distinguished easily enough, even from a distance, using other secondary characteristics, the answer may have an anthropological/social answer, rather than a biological one.


texts:
Regading penis Dixson showed that it is not really unique and complex. This argument (and there were some others) was used against the idea of human polygynandry.

But what about vaginal shape? I know it is wider as deeper it goes and cervix is convex shaped, which could  give an advantage for storing semen. However, I am actually wondering if other primates have similar vaginal shapes (because it can shed light on the question of mating system). Are there any studies on the topic?


texts: Can a broken thumb/finger bone not require realignment of the bone?

texts: Is it possible that a finger/thumb bone fracture is so superficial, that the doctor does not need to realign (re-set) the bone before applying the cast? Or does it always require for even a finger/thumb broken bone to be put back in place before applying the cast?


texts: Are the alleles that code for the same phenotype all the same exact sequence?

texts:
The idea that you can be homozygous for a gene means that there are limited options or alleles , correct ?

My question is, if the mom has the allele b which codes for a blue eye, and the dad has an allele which codes for a blue eye too, are these alleles the exact same ? Do they have the same nucleotide sequence ?

This is probably a basic question but no matter how I phrase it, I can't seem to get an answer off of google.


texts: What sort of assay could be used to identify mutants with mutator phenotype?

texts:
By mutator phenotype, I mean being more prone to mutations, for example due to mutations in genes involved in DNA repair.
I was thinking about exposing the cells to agents that damage DNA (uv light, for example). Compared to normal cells, mutators would be less likely to survive, because they lack the ability to repair damages in the genetic material. To a certain extent, that's the principle of radiotherapy (cancer cells are more suscetible towards radiation).
Are there other options? Moreover, is it possible to select the mutators (instead of killing them)?


texts: Why is Capsaicin injection not used instead of nerve surgeries for pain?

texts:
High concentration capsaicin kills c & a-delta nerve fibers permanently or at least long term.
This has been known for 30 years.

But capsaicin is only used in creams and patches, and not for injecting direcly into nerves, and people resort to nerve surgeries like nerve blocks, razor-damaging nerves, or rhizotomy to cut the nerve partially or fully. All of these options affect not just pain functions, but overall sensory functions.

On the other hand, capsaicin destroying c & a-delta fibers just affects pain.
So why is no one interested in capsaicin injection as an option before cutting nerves?


texts: Is there a meaningful difference between direct and indirect light

texts:
I don't see a basis for a distinction, but I've heard several people distinguish between direct and indirect light for people, claiming that indirect light would be better in many cases. "Direct" means that the light goes from the source to your eye without intermediary, and "indirect" means that the light bounces one or more times off other objects before entering your eye.

An example of indirect light, for the purposes of this discussion, is sunlight or indoor artificial light, reading an old-fashioned print book or a non-backlit Kindle. An example of direct light would be any modern computer screen, or a backlit Kindle. The one context I've heard of direct light being preferred is a light alarm clock, where it was stated to be an advantage that light from the alarm clock goes directly to your eyes and is not exclusively bounced off objects in a room.

Now I can see one or two obvious differences; direct light tends to come from a small source (we don't tend to cover walls with LED's), while indirect light is more likely to bounce off everything or at least much more of what you can see. Furthermore, all other things being equal, direct light should be brighter as I am not aware of anything that reflects fully 100% of the photons that strike it (maybe some odd variant on superconductors)? However, I see only superficial distinctions between the two, and not a reason why, if all other things are forced to be equal (e.g. an indirect source being made brighter to compensate for the photons that physical surroundings absorb instead of being reflected), there should be the fundamental difference between direct and indirect light that I have repeatedly heard from people I trust.

Is there such a basic difference, or not, and if there is a difference, what does that difference consist of?

TIA,


texts: Is there more biomass on earth today than there was in the past?

texts:
Is there more, (or less) matter on earth sequestered as a part of biological systems than there was at any(arbitrary) time in the past?

Edit:

I realise I don't have a specific question, and was looking for a lesson of sorts on what is the footprint of life and will the new not come if the old doesn't die and dissolve(biologically atleast).

If you could suggest me good sources to study this, that would be great.


texts: If Helper T-Cells express CD4+ proteins on their surface to bind to MHC Class ll proteins on antigen presenting cells, why do antigen presenting cells also have CD4+ Proteins?


texts: What is the mass or range of weights of individual microbial spores and or cysts?

texts: Also looking for the overall physical dimensions of spores/cysts.  I am trying to estimate how much static charge a spore/cyst would require to overcome the pull of gravity.


texts:
Do penguins have a way to test the ice that they stand on to ensure that the ice will not break? In other words, do penguins make sure that they will not fall into the ice before stepping onto it?
I have conducted research but have come up short, which made me assume that penguins don't test the ice. However, I wanted to make sure before I just made an assumption.


texts: How can I obtain a uniform bacterial sample?

texts:
I'm currently doing a research project wherein I will be testing the antibiotic resistance of a bacterial sample. Due to a risk of contamination during transport, I'm not allowed to request a uniform bacterial sample form a clinical laboratory. So, I have to produce my own sample. Then, I'm planning to identify the morphology of the bacteria to confirm the species or type.
The ideal scenario is obtaining a sample which is entirely one species of bacteria. However, taking a swab, either from somewhere in the lab or from the body will produce a sample with multiple bacterial species. What source of bacteria can provide the most uniform sample, i.e. a sample with a majority of one species of bacteria? Or, is there another way to obtain a uniform sample? Also, note: I will be conducting the experiment in a school laboratory, so I must be able to safely contain the pathogen.
Edit: I have recently updated my project to be specified towards testing on bacteria present in the throat. So, a bacteria present in this area or similar areas would be preferable.


texts: Is it more likely that the very first living organisms had a linear genome?

texts:
Is it right to assume that the first living organisms on earth had a linear genome? I base this on the fact that linear macromolecules are clearly much more common in nature that circular ones. To be honest, I can't even think of any naturally-occurring circular macromolecules that aren't already a part of current living organisms.

Were the very first living organisms more likely to have linear genomes? If so, when during evolutionary time did circular chromosomes originate?


texts: How did plaques form in Salvador Luria's Bacteriophage experiment (discovery of restriction enzymes)?

texts:
I was watching Eric Lander's lecture online describing Luria's experiment (see below for link), and I couldn't understand how plaques form. From my understanding,

Bacteriophage infect strain B
Viral DNA is incorporated
Restriction enzymes cut out viral DNA (mostly)
Some viral DNA is methylated before step 3 occurs.

At this point, to replicate, we would need the infected bacteria to produce more bacteriophage to infect nearby virus. However, due to step 3, the newly incorporated viral DNA will be cut out through restriction enzymes. So in my mind, we only have one bacteria with viral DNA (along with its descendants).

So how does the plaque form?

https://youtu.be/_TdJBLu6hPc?t=890


texts: How to measure quality and quantity of DNA?

texts: I would like to mesure DNA. I quantify the concentration with Qubit fluorometer, but I would like to know also quality of DNA. I try BioAnalyzer (Agilent),but without success. Bioanalyzer measure DNA samples from 100 to 7 000 bp (12 000 bp). Problem is that my DNA is not sheared, I would like to quantify whole mouse DNA. Have you any idea? Thanks!


texts: What is this large brown bug with pincers?

texts: What is this large, brown insect with pincers? Seen in Waltham, Massachusetts.


texts: Recommended reading to quickly get up to speed on infectious diseases

texts:
I am in the beginning stages of a capstone project for my master's in Data Science. For various reasons, I have landed on the subject of Clostridium difficile infection. My background is in Computer Science, Mathematics, and Statistics, but biology is way outside of my wheelhouse. While most of my project will focus on the statistical modelling aspect, I would like to be able to speak intelligently on the subject itself and be able to read through journal articles without getting tripped up on some of the terminology.

I'm not trying to cut corners, but I'm on a tight timeline (about 4 months). What resources - books, references, online courses - would you recommend to bootstrap me into the field of infectious diseases?


texts: Can the mutability of DNA be selected for in a population? I don’t mean selection for the phenotype that is the result of a mutation. Rather, can the rate of mutations in a population be increased by natural selection?


texts: Can anyone give me the common name of this flower/vine?


texts: What is the evolutionary advantage of having pubic hair?

texts: Only humans have pubic hair. What is the evolutionary advantage in having it?


texts: gene transformation from plant to plant - transgenic plant

texts:
I want to know if the expression of a transfered gene depends on source of the gene, if e.g.:

1] I isolate a gene from plant and transfered it to the same plant?

2] I isolate a gene that is highly expressed in plant, and transfer it to another plant ?

3] I isolate a gene that is lowly expressed in plant and transfered it to another plant

Is there a difference between the expression of the transferred gene in these three cases? What does the expression of the transfered gene depend on?


texts: How do I clean and calibrate pipettes, and how often should I do it?

texts:
I work in a lab where all the pipettes are shared. We often have visiting students who come and use the pipettes for a short project. So when I work with them, they might have been handled by other people several times since I last used them. This leads me to worry that they might have been mishandled, or become less accurate somehow.

How do I clean and calibrate pipettes? And how often do I need to do it?


texts: Is there random assortment in metaphase II?

texts:
First, a little notation. Call a the first chromosome from my mother and A its homologous partner from my father. b and B would be the second pair, c and C the third, and so on, down to w and W (the 23rd).

The tetrads in interphase would be expressed as aa AA...ww WW (so, for example, AA are sister chromatids). Finally, use the notation a' and A' to express that those two chromatids have crossed over via recombination.

Ok: I understand that in Metaphase I, there's a random assortment of chromosomes at the equator, so that we might end up with a division like so:

aA'    Aa'
bB'    b'B
CC'    c'C
...
wW'    Ww'

Which pair ends up on the right or left is random, and there are therefore $2^{23}$  possible arrangements.

My question is whether an analogous shuffle happens during metaphase II? I visualize metaphase II as taking one of the columns above and turning it on its side, so that for instance taking the right column you have:

a' B  C  ... w'
A  b' c'     W

These "rows" are then split to become 2 of the 4 gametes.

The question is whether at this stage, before this final split, there is an analogous shuffling possible whereby, say, the A and a' could switch sides?

My intuition is yes, of course, but in all the accounts of meiosis I can find online, the "random assortment" and shuffling is all described as happening in metaphase I.

(I think whether the shuffling between this particular A and a' happens in metaphase I or metaphase II is inconsequential in terms of which one ends up in which daughter cell... but I'd still like to have a sense for what's literally physically happening.)


texts: Which organism can point us to the evolution of sight?

texts:
I'm trying to identify the basic biological mechanisms for sight.

Could you help me with identifying any organism that has the most basic ability to see objects?

Most importantly, creatures like dogs, cats, insects are able to not just see light, but are also able to identify objects and other living beings. I feel that an organism could be classified as "being able to see" if it can identify objects and movement and use its "visual sensory organ" to help it move around, locate food, identify species of animals, differentiate between living and non-living and escape predators if any.

Even if an organism can see just black and white or the most basic perception of sight, it would qualify for what I'm searching for. Is there any such known organism that has such a basic visual perception and has the way its eye+brain perceives images, been studied?

I'm not referring to the kind of "photosensitivity" that plants have. Detecting the presence and direction of light is not sufficient.


texts: Why is beta thalassemia major not lethal while alpha thalassemia with loss of all 4 genes lethal?

texts: So why is beta thalassemia major with two B0 alleles not fatal in utero (despite the hemoglobin not having any B chains), while alpha thalassemia with deletion of all 4 genes encoding for the alpha chain fatal? Is the alpha chain more important than the beta chain?


texts: How is membrane capacitance related to the increased speed of saltatory conduction?

texts:
Here is the original question which inspired my question. As explained by the answers there, the reason saltatory conduction in myelinated neurons is faster than non-myelinated conduction is because the capacitance of the membrane is lowered by reducing the number of channels (Channel density) or equivalently, increasing the spacing between channels. I also did a preliminary study of membrane electrodynamic modelling here and here.

From what I gathered from the linked question, the decreased capacitance overcompensates the effect of absence of channels reinforcing the sodium current, and on the whole, increases the speed of conduction by allowing the depolarizing potential to travel to the adjacent node faster than in case of an unmyelinated fibre. In view of this, I have a question:-

  Why does lower capacitance increase "the effectiveness of nearby
  nodes" or allow the depolarizing voltage to "travel not by ion
  diffusion, but as an electric field"? I am comfortable with capacitors
  and related physics, but why would lower capacitance allow propagation
  of the changing voltage as an electric field, is still unclear to me?
  (The links I have placed also help quantify the problem
  mathematically. This allows us to say that $\lambda$, or the rate of spatial
  decay of potential, increases, decreasing the effective
  length of the neuron. Why should its decrease help faster conduction?)

  And another question is, how would reduced density of sodium voltage
  gated channels cause a decreased capacitance?


texts: Is there a formal definition of signature of natural selection?

texts:
I’ve searched for a definition of signature of natural selection. Unfortunately, I haven’t found any formal definition of it.

The signature of positive selection on standing genetic variation. I found this post that links to an article measuring the signature with an Fst and a Linkage Disequilibrium test.

Are we looking at only some frequency of alleles in different populations? Is the signature only a fixation of alleles in a population where this allele was positively selected?

Another article says:

  A single beneficial substitution can be detected in polymorphism
  data, so long as it occurred recently. The fixation of a favorable
  allele in a population distorts patterns of variation at linked
  sites, thereby leaving a distinguishing signature that lasts up to
  about 104 generations in humans or about 106 in Drosophila
  melanogaster (Przeworski 2002). In principle, targets of positive
  selection can therefore be identified by searching polymorphism data
  for regions that harbor this signature (Nair et al. 2003; Wright et
  al. 2005).

Is it always in linkage disequilibrium?


texts: Which mass spectrometry database search algorithms include the fragment mass accuracy in the calculation of protein scores?

texts:
E.g. in a MASCOT search, the accuracy of the fragment ions in a ms/ms spectrum does not have any influence on the scores of identified proteins (unless the fragment ions are out of the set ms/ms tolerance of course).

I want to know other search algorithms that do include the fragment mass accuracy in the protein identification scores.
Also, if the protein scores are not influenced, i would like to know in which way other evaluation values of MASCOT or SEQUEST results are influenced.

Thanks for your time.


texts: How do you call "pocoya" bird in English?

texts:
I am translating a Spanish book and I have here a bird named in Spanish "pocoya", about which I know the following:

1) it flies at night

2) it makes sounds that allow to confuse it with an injured animal

3) it lives in Nicaragua or at least lived several centuries ago.

My own research brought me here: https://en.wikipedia.org/wiki/Pauraque and here: https://en.wikipedia.org/wiki/Ocellated_poorwill.

I don't know which one of them it could be, nor how it could be in English (the first article doesn't have an English version) when spoken (my indigenous people can't use Latin names, for sure...)

Thank you in advance for your  quick response!


texts: Does eating beans of a mother cause flatulence on babies?

texts:
Is it true that if you eat beans it could cause flatulence on babies (when breastfeeding them)?

I can't find any research or scientific facts about that topic.
I thought the body of the mother would filter "bad" ingedients.


texts: How to calculate percentage of DNA that ancestors contributed?

texts:
In David Reich's book "Who we are and how we got here" there is a graph explaining that more we go back in our ancestors generations, the least we have chances to have any DNA inherited from one of these ancestors because the number of ancestors is doubling every generation while the number of stretches of DNA is only increasing by 71.

In the left side of the graph, there is a percentage indicating how many ancestors contributed to our current DNA. For example : 50% of 1024 ancestors after 10 generations.
I don't understand how this percentage is calculated and it is not explained in the book.
Could someone help me understand it please?


texts:
Henna contain lawsone pigment that attaches to the proteins of the skin,hair,etc.But after a few weeks the color fades?

How does the color fade?

Is the pigment volatile or it is degraded by the body?


texts: I know that the D-loop is  a DNA complex in which the strands of double helix DNA molecule are separated for a stretch and held apart by a third strand of DNA. Usually, this third strand has a base sequence, which is complementary to one of the main strands and pairs in accordance with it. The third strand then sub sequentially displaces the complementary main strand in the region. Im also aware that D-loops occur in many DNA systems, such as in DNA repair, telomere activity, and in mitochondrial circular DNA molecules.  However, my question is why does the D loop only provide information about maternal DNA ancestry?


texts: Can a gene be inactivated using CRISPR if it is not in the interspace of short palindromic repeats?

texts: I have recently studied how CRISPR works but there is something that I do not understand at all. I have heard a lot of people claiming that with this method it is possible to modify any genome by inactivating, activating, removing or adding genes. However, as far as I have understood, DNA regions can only be modified if they are in the interspaces of short palindromic repeats. So, my question is whether a gene that is not in the interspace of short palindromic repeats can be modified or removed? And if it is possible to do so, how?


texts:
Everyone talks about how DNA is the "molecule of life" and "the set of instructions for building you." How complete are the instructions, really, though? To make the question concrete, say I were to remove all of the DNA from a bacterium and replace it with the nuclear DNA from a eukaryote, would the cell (and it's daughters) be able to transition into the same sort of eukaryote as the DNA source? Granted, the lack of mitochondria would be a huge hindrance, but assume we could add some when the bacteria swelled up to a large enough size to accomodate them inside of it. Are there other barriers to this process?

I know that adding any single gene for producing a protein would function as expected when added to a bacterium, but would the lack of a nucleus and organelles prove fatal, or does the nuclear DNA have the information needed to build them up using only the machinery available in a bacterium?

What about an archaea? Or going the other direction - remove the nucleus from a eukaryote, add bacterial DNA, does the cell and its daughters survive to become bacteria?


texts: Energy consumption of the human brain: thinking vs not thinking

texts:
I'm wondering about the human brain's energy consumption at different "uses".

If you use a muscle it uses more energy than if you hold it still. Is the brain like this, or is it "always on" like a kidney or heart? Does it use more energy when you're actively learning or solving a problem? Do intelligent people have more energy hungry brains?

If I'm to sum into a single question, is the brain's energy consumption largely static (individually and over the population), or does it vary?

This question covers only the sleeping aspect and the top answer doesn't source is conclusion of static energy use. I'm still largely interested in differences while learning or problem solving and differences between intelligent and average people.


texts: C-myc/anti-myc Ab Interaction with Fusion Proteins

texts:
I am going to prepare a c-myc fusion protein with the following configuration:

(28-residue signal sequence)-(c-myc)-(GGSGGGSG Linker)-(Protein of Interest (POI))

POI is a transmembrane protein and the 28-residue signal sequence is needed for membrane incorporation in ER.

My concern is the disruption of the c-myc/anti-myc Ab interaction due to the fact that c-myc being fused on both ends. Does anyone have any experience or reference with a similar construct?


texts:
I found this black slug-shaped thing on a leaf by my pond in western Sweden. It's about 15 mm long, positioned on a vertical leaf (I bent it to take the picture).

And I don't even know where to start looking. I was thinking it might be an egg cluster, but can't find anything useful without knowing at least what kind of organism made it.


texts: What is this animal? Reminds me of a crab because of the way it crawls but it looks like a plant.

texts: Crablike animal however it looks like a plant. Doesn't seem that fast when it comes to speed.


texts: Was Darwin aware of the difficulties behind the concept of species?

texts:
Introduction

The concept of species is a very old concept that suffers from not being a natural category. There exists no single definition that would categorize living beings into groups and that would fit our intuitions of what a species should be.

Many of such problems in definitions are revealed in the field of evolutionary biology. For more information about the difficulties behind the definition of the concept of species, have a look at

How could humans have interbred with neanderthals if were a different species?
This post on ring species.

Question

Did Charles Darwin comment on this problem?
If yes, did Charles Darwin comment on the reason why he chose to keep using the term "species" instead of simply "lineage"?


texts: Recommend good conversational books to learn about cell and developmental biology or biochemisty?

texts:
I'm an engineer by training and teaching myself the basics of cell and developmental biology. I'm using Scott F. Gilbert's Developmental Biology and Alberts' Essential Cell Biology right now, and they are both great resources.

Can you recommend good books on similar topics that are written in a non-textbook format?

EDIT: For example, I found books like The Greatest Show on Earth, Extended Phenotype, and Nature via Nurture really useful to learn about the basics of evolution while I was reading Watson's Molecular Biology of the Gene. Are there similarly well-written books for cell biology, developmental biology, or biochemistry? I know this sounds broad, but I'm not asking for textbook recommendations. I'd like to read something that isn't a textbook alongside my current studies.

SECOND EDIT: I'd be like to extend this question to recommendations of broad review articles in Cell and Developmental Biology too. For example 'How do cells know where they are?' is an excellent article on different strategies cells may use to assess distance in a developing embryo.


texts: I need help identifying this particular palm tree. Unfortunately, I don’t have many details to give, and I’m by no means one to say I’m even an amateur at plant identification. We are unsure of its origin and can only confirm it’s age by how long we’ve resided here in Hockessin, Delaware. The plant is over the age of 14, and it stands a little over 12 feet high. The foliage is composed of single green shoots coming from the head of the plant which descend gracefully and reorganize into what one without knowledge would say is bark. We are looking to purchase another tree of this species or a close relative; there was a recent loss of an identical tree which sat opposed to this one.


texts: Why does fixing of cells with something like formaldehyde disrupt the membrane enough for probes, antibodies, and dyes to get into the cell?


texts: Can defibrillation be done with a car battery?

texts:
Can successful defibrillation be done with a car battery? Is it POSSIBLE for this to work?

Let's say you are stuck on a very remote place and something happens to someone...

Moreover, can you jump start someone's heart using the battery of a car and the jumper cables, keeping in mind that:

in order to start a stopped heart you need electrical current applied in a short period, like 20 ms, and at a relatively high tension (200v) and small intensity?
car battery provides low tension current (12v) at a relative high intensity (70-80A) and the period cannot be 20 ms, but around 200-300 ms giving the fact that humans are not able to react that fast.