texts: How harmless bacteria on skin defence against harmful bacteria?

texts: I have read that there are some harmless bacteria live on skin and they also have role in protecting body against some harmful bacteria but how do they do so? I mean how these bacteria are able to resist other bacteria which are harmful?


texts: Can someone help to identify this insect?

texts:
I found a few of these insects around my house, and I'm curious what insect it is.

Seen mid-August in Singapore
At least several mm but lest than 1 cm long
Seen walking slowly. I can't be sure but don't think it can fly
No sound noticed


texts:
Is it possible to completely realize that I am only dreaming and to completely manage my dream?

Thank you.


texts: Photosynthetic Absorption Spectrum - Pigment vs. Absorption Spectrum

texts:
This is a very confusing question to me that came up while I was studying photosynthesis.

Halobacterium has a photosynthetic membrane that is colored purple. Its photosynthetic action spectrum is exactly complementary (opposite to) the action spectrum for green plants. What wavelengths of light do the Halobacterium photosynthetic pigments absorb?
A) red and yellow
B) blue, green, and red
C) green and yellow
D) red and green
E) blue and red

I don't understand how the answer to this is possibly "blue and red," since the pigment is purple (eliminates violet end of spectrum since purple is transmitted) and the question says the action spectrum (synonymous with the absorption spectrum) is complementary to that of green plants. Green plants absorb best in the blue and red ranges, so naturally I would think the answer is C, green and yellow. What am I missing? Am I confusing the color of the photosynthetic pigment with the absorption spectrum?

Thanks!


texts:
If i want to transform a bacteria (E. coli) with a particular plasmid (in my case pBR322) will the presence of the Rop gene affect the production of it ?
Is it desirable to use a plasmid without that gene to increase plasmid copy number ?

I found some informations about the protein cited on these links:

https://en.wikipedia.org/wiki/Rop_protein

http://www.proteopedia.org/wiki/index.php/Rop_protein


texts:
I saw a bug swimming through my carpet, and promptly squished it. I had never seen this kind of bug before, and wanted to find out what it is, so that I can assess it's danger to my house and family, and know how to responsibly take care of it. However, my dog gobbled it up before I could take a photograph, so all I have to go by is a mental image:

1.5-2.5 inches long (3-6cm)
2-3 segmented body, with a smaller head, and over 3/4 of it's length was the back segment
Mandibles/Pincers at one end of the body (I can't remember which)
I think it only had 6 or so legs.
The dog made a disgruntled face when she ate it, so I think it could have tasted badly, or bit/stung her tongue as she ate it.
I believe it was two colors, with a pale colored section and a reddish-brown section, although I can't remember their locations.

I live in the Northwestern US, and have three trees on my lot: two maples and a boxelder. The house was built in 1954 and has a crawlspace foundation.


texts: How are isopotential maps computed from EEG channel data

texts:
I have some EEG recordings of $1$ minutes, with $500$ samples per seconds and $63$ channels. For each recordings, this effectively yields a $30,000\times 63$ matrix $M$.

How do I extract isopotential maps from the data?

My first try was to simply take each row $m_i\in M_{i,j}$ such that $m$ has length $63$ and plot them with respect to the $x,y$ coordinates given by the location of each of the $63$ channels... However, I seem to get bad plots...

I also tried to bandpass the data first. For alpha waves, my Mathematica code looks like this:

BANDPASSALPHA[x_] :=
 BandpassFilter[x, {8 Pi, 13 Pi}, SampleRate -> 500]
bpalpha = Map[BANDPASSALPHA, dataz];

I bandpassed the columns of the matrix $M$. That is the signal $x$ that is used in BANDPASSALPHA[x] is one of the columns of $c_j\in M_{i,j}$ and are of length $30,000$

According to Wikiepdia: http://en.wikipedia.org/wiki/Isopotential_map, the spatial derivative needs to be computed first...

Does anyone know how isopotential maps from EEG recordings?


texts: How does the structure of tendons change as they become stronger?

texts: I understand the basic structure of tendons, but I wonder how a tendon becomes stronger via exercise. Do the collagen fibers become more aligned/numerous/dense/etc.? Is the tendon expected to become thicker as it gets stronger? Does the cellular content of the tendons somehow change (e.g., more tenocytes, or higher quality tenocytes)? What other factors have a role in tendon strengthening?


texts: What is this fossilized claw found in a Belgian forest? It is 14.5 cm long and 2.5 cm in diameter.


texts:
It's the first time I use this website and I really need help
because I'm totally stuck

Now I'm in school, but I'm trying to prepare for the Olympics
During the preparation, I found the issue on the anatomy of the animals, but it's something new for me - I can't even determine what it is!

What kind of animal is it? Could you determine some, the most vital and major of highlighted points? If you can help me to determine the kind of it, i will be able to use more specific books to find out.

I will be very grateful for any help!


texts: What is the difference between the usages of bis-tris methane and bis-tris propane?

texts: I came across "bis-tris" buffer in Rodney Boyer's Biochemistry Laboratory book and tried looking it up. Then I found that there's bis-tris methane and bis-tris propane that are both buffers. What exactly are they used for and are the usages different?


texts:
I'm new to this site but had a question on evolution, apologies if some of these questions seem basic but they are from a book i am reading challenging the role of chance in evolution.

Taking the example of Polar bears in the Arctic, how does evolution determine that it was white fur that was a beneficial trait rather than any other colour of fur? Is this a random change in cellular chemistry?

The book argues that there should be more evidence of polar bears of all shapes and sizes but with no evidence, asking "why should the creative factors provide only single options in the polar habitat and let natural selection sit idly by?"


texts: What factors limit a shape and size of an organ

texts:
We all know that anatomy deals with structure of human system. I am interested in knowing the factors that determine the shape and size of each organs in the body. For example, we know that kidneys are bean shaped, stomach is a C- shaped organ.

During the developmental stage, like mitosis, and other cellular pathways, what factors sets a boundary for cell division, so that an organ takes its respective size and shape.


texts: What causes change of sex in certain monoecious plants such as Papaya?

texts: certain male flowering plants can be converted to female flowering and fruiting such as Papaya plants by just insertion of an iron nail in their/it's stem near it's roots? How can iron nail alter it genetically from male to female? Biochemically  what causes change in sex of plants from male to female?


texts: Properties of berries that are not shared by strawberries

texts:
What are examples of properties that (all) berries (from a botanical point of view) have and that strawberries do not have? This does not need to be the exact reason, why strawberries are not counted as berries. I'm more looking for properties that emphasize the difference.

Since I'm not a biologist, I'd be happy about simple examples. Thanks a lot!


texts: What is the meaning of the word "Ligandable" in "ligandable proteome"?

texts:
I see "ligandable proteome", "ligandable proteins" and "ligandable targets" an awful lot.

But really I don't know what exactly the word "ligandable" means?

Is that it means, for example, "ligandable proteins" means proteins have ligands?

Thank for your help.


texts: Role of auxin and cytokinins in vascular cambium or callus formation

texts: Usually, auxins promote cell growth and cytokinins promote cell division. But, I got an information from my teacher that, in case of vascular cambium or callus formation, auxins promote cell division and cytokinins promote cell growth. Is this 'information' true? If true, why?


texts: Which came first: The Chicken or the Egg?

texts: Has there been any serious scientific inquiries into answering this age old question?


texts: Do human visual functions degenerate due to genetic factors or by external factors?

texts:
Does eyesight primarily deteriorate 'naturally' due to genetics (genomic/epigenomic factors), or due to external factors such as normal wear and tear, or disease?

By normal wear and tear I include things like repetitive straining of the eyes by reading small text in a dim room night after night.

As a background to my question: By dissecting the causes of visual deterioration into genetic factors versus external factors I hope to relate those causes to the age of onset, and rate of decay of visual acuity.


texts: Downloading specific yeast genes in an automated manner?

texts:
I have 6 genes of Candida albicans yeast namely orf19.723, orf19.5908, orf19.610, orf19.2119, orf19.4998 and orf19.4056. And I have found the corresponding ortholog genes from Broad Institute website of other 16 species of yeast. So I have all gene names. Now how would I specifically download these genes and from where can I do this, preferably in an automated manner?

Also is there any standard naming convention? Because the ORF names given have other names too like BCR1, EFG1 and NDT80.

The list of gene names I have :

The orthologs of C. Albicans with S. cerevisiae
orf19.2119  YHR124W
orf19.4998  YBR033W YKL034W
orf19.5908  YBR083W
orf19.610   YMR016C YKL043W
orf19.723   NONE
orf19.4056  YMR136W

The orthologs of C. Albicans with S. paradoxus
orf19.2119  spar33-g1.1
orf19.4998  spar197-g23.1   spar324-g3.1
orf19.5908  spar200-g4.1
orf19.610   spar184-g1.1    spar324-g10.1
orf19.723   NONE
orf19.4056  spar165-g2.1

The orthologs of C. Albicans with S. mikatae
orf19.2119  NONE
orf19.4998  smik146-g12.1   smik109-g17.1
orf19.5908  smik83-g2.1
orf19.610   smik571-g2.1    smik109-g10.1
orf19.723   NONE
orf19.4056  smik1535-g1.1

The orthologs of C. Albicans with S. bayanus
orf19.2119  sbayc514-g9.1
orf19.4998  sbayc611-g22.1  sbayc652-g20.1
orf19.5908  sbayc678-g131.1
orf19.610   sbayc638-g23.1  sbayc652-g27.1
orf19.723   NONE
orf19.4056  sbayc657-g41.1

The orthologs of C. Albicans with S. castellii
orf19.2119  Scas697.24
orf19.4998  Scas625.4
orf19.5908  Scas718.27  Scas635.12
orf19.610   Scas106.1   Scas709.52  Scas625.8
orf19.723   NONE
orf19.4056  Scas680.22d

The orthologs of C. Albicans with C. glabrata
orf19.2119  CAGL0L13090g
orf19.4998  CAGL0L01947g
orf19.5908  CAGL0M01716g    CAGL0F04081g
orf19.610   CAGL0M07634g    CAGL0L01771g
orf19.723   NONE
orf19.4056  CAGL0I00902g    CAGL0L06776g

The orthologs of C. Albicans with S. kluyveri
orf19.2119  SAKL0E11330g
orf19.4998  SAKL0A09812g
orf19.5908  SAKL0B06578g
orf19.610   SAKL0D13442g
orf19.723   SAKL0A03476g
orf19.4056  SAKL0E04862g

The orthologs of C. Albicans with K. lactis
orf19.2119  KLLA0F24420g
orf19.4998  KLLA0F25674g
orf19.5908  KLLA0E12507g
orf19.610   KLLA0F04840g
orf19.723   NONE
orf19.4056  KLLA0F17116g

The orthologs of C. Albicans with A. gossypii
orf19.2119  AGR347W
orf19.4998  AFR275W
orf19.5908  AER177W
orf19.610   ABR055C
orf19.723   NONE
orf19.4056  ADR249W

The orthologs of C. Albicans with K. waltii
orf19.2119  Kwal33.14699
orf19.4998  Kwal26.8099
orf19.5908  Kwal27.12423
orf19.610   Kwal26.8176
orf19.723   NONE
orf19.4056  Kwal47.17849

The orthologs of C. Albicans with C. tropicalis
orf19.2119  CTRG01097.3
orf19.4998  CTRG03636.3
orf19.5908  CTRG02294.3
orf19.610   NONE
orf19.723   CTRG00608.3
orf19.4056  CTRG04523.3

The orthologs of C. Albicans with L. elongosporus
orf19.2119  LELG01178
orf19.4998  NONE
orf19.5908  LELG02666
orf19.610   LELG05390
orf19.723   LELG03123
orf19.4056  LELG01761

The orthologs of C. Albicans with C. parapsilosis
orf19.2119  CPAG04608
orf19.4998  NONE
orf19.5908  CPAG01691
orf19.610   CPAG00178
orf19.723   CPAG00564
orf19.4056  CPAG05034

The orthologs of C. Albicans with D. hansenii
orf19.2119  DEHA2A07282g
orf19.4998  NONE
orf19.5908  DEHA2G13794g
orf19.610   DEHA2E10978g
orf19.723   DEHA2E05984g
orf19.4056  DEHA2E07172g    DEHA2F25916g

The orthologs of C. Albicans with C. guilliermondii
orf19.2119  PGUG02096.1
orf19.4998  NONE
orf19.5908  PGUG04378.1
orf19.610   PGUG03651.1
orf19.723   PGUG05571.1
orf19.4056  PGUG05533.1

The orthologs of C. Albicans with C. lusitaniae
orf19.2119  CLUG00404
orf19.4998  NONE
orf19.5908  CLUG04694
orf19.610   CLUG02047
orf19.723   CLUG00627
orf19.4056  CLUG05535


texts: What is the percentage of true bugs compared to all animal species on the plant?

texts:
Also, what is the percentage of True Bugs compared to the insect population?

I’m writing a children’s book on bugs and I’m comparing the true bug to the insect. All population info seems to combine the two. Please list sources.


texts: Have scientists ever produce a new species in laboratory by means of natural selection?

texts:
I was wondering, if scientists ever produce a more complex species from a less complex species by means of natural selection? I imagine something like, bacteria which can't photosynthesis and oxygen (chemoautotrophs) to bacteria that can photosynthesis and oxygen like cyanobacteria.

If scientists have never done this, is this theoretically possible to be done in lab by means of natural selection?


texts: Does H. pylori have paracellular activity?

texts:
I know that it has transcellular activity i.e. it can pass through neighbouring cells.
However, I am not completely sure if it does not have paracellular activity, see this:

  H. pylori did not induce any modification of the paracellular pathway
  (R = 148 ± 10 versus 174 ± 16 Ω · cm2; JNa = 4.16 ± 0.44 versus 3.51 ±
  0.41 μEq/h · cm2; JMan = 0.081 ± 0.01 versus 0.058 ± 0.009 μmol/h · cm2), nor did it modify J3H-HRP (2,201 ± 255 versus 2,110 ± 210 ng/h ·
  cm2 for H. pylori-infected and control cells, respectively). However,
  in the presence of H. pylori, we observed a significant increase in
  JHRPi (520 ± 146 versus 171 ± 88 ng/h · cm2). This effect was not
  dependent of the cag status of the strain and was not reproduced by
  the sonicates or the culture supernatants.

Is there any evidence that Helicobacter pylori has paracellular activity?


texts: I'm currently writing a piece of work about telomeres and aging, and wondered if you could share some good papers you've either read or know of.


texts: Is it known how human sweat glands evolved?

texts: If human descends from apes than probably we lost our hair. Perhaps in the age of homo erectus we lost our hairs and began transpiring through our skin with sweat glands. But how did these glands evolve? Is it from another kind of cell which is similar?


texts: Does the body have specific mechanisms for healing burns, or is it general purpose stuff?

texts: I burned my thumb lighting sparklers (fireworks) a few nights ago. I've been pleased with how it's healing, and have been especially impressed because it's not a scenario that really could have come up in our evolutionary history. Then I started thinking that fires are not that common in nature. This prompts the question: do our bodies heal from burns using burn-specific techniques, or do they just follow general “procedures” for repairing damaged skin?


texts:
If there is no immune system,it  seems like vaccines wouldn't do much since there is no adaptive immune system to develop antibodies and memory cells. But can people with AIDS/HIV still be vaccinated? It is expected that a normal person will have antibodies to attack the minimal infection produced by the vaccine and generate memory cells, but without an immune system I expect vaccines to be deadly.

Is that right?


texts: Why can't bacteriophages survive inside the human body thus negating the possibility of using them against bacteria?

texts: I read about the therapeutic uses of bacteriophages in Pelczar's Microbiology. It was written that it is reasonable to think that bacteriophages could be used to kill pathogenic bacteria. However, the book also clearly stated that after a lot of research it was found that bacteriophages can't be used to kill bacteria in the human body because they can't survive inside the human body. But no reason was given why.


texts: How does Yeast-two-hybrid detect interactions between several proteins in one experiment?

texts:
I am trying to understand the Y2H screening method. I can understand how we can check if two specific proteins interact with each other. For example, if we want to check whether protein A and protein B interact, we fuse A with the Activation Domain (AD) of a transcription factor and B with the Binding Domain (BD) of another transcription factor. When the two fusion proteins are transfected into a yeast cell, the reporter gene is expressed only if the AD and the BD get together and form a complete transcription factor and that happens only if proteins A and B interact with each other.

However, I have seen claims that Y2H is a high throughput system, i.e., it can be used to detect several interactions at once. But most articles online that attempt to describe it, seem vague to me.

For example, suppose I fuse the "bait" protein to the BD and several different cDNA's to the AD and let the yeast grow. Next, I observe that the reporter gene is expressed. Doesn't this observation only imply that there exists some protein from the cDNA library that interacts with our bait protein? How do we know exactly which of the target proteins have interacted with the bait and resulted in the expression of the reporter gene?


texts: How can I download a gene sequence from GenBank (NCBI)?

texts:
Could you tell me the steps to find and download a gene sequence from GeneBank?

I would appreciate your help.


texts: Why insects are attracted towards light?

texts: Many insects like bees, dragonflies, wasps and other small insects are attracted towards light. Sometimes they are in groups, sometimes they are in solitude. When the light source source is switched off, they do not fly, rather stay still. What causes them to be so attracted towards light?


texts: Does the brain always enter alpha/beta waves upon brief awakenings during the night?

texts: If you realize you are awake briefly before falling back asleep, have you necessarily exited REM sleep or another stage? That is, is the experience of waking briefly (tossing and turning, etc.) always tied to conscious beta wave patterns?


texts: Can intron become exon in alternative splicing?

texts:
From this image

We can see several exons that are actually introns in other genes. It's not a really a different gene, it's an alternative splicing of a gene. My background is not biology so is it possible for alternative splicing to behave like this? I only know that alternative splicing is just exon skipping and introns will just stay introns and not become exons. Can someone explain this to me and give any suggestions on which part of biology (or genetics) I need to learn. Thank you.


texts: Does increasing the value of k in k-fold coverage requires more memory?

texts:
Study:
Here is what is k-fold coverage which is know as sequence coverage.
According to this, 2-fold coverage means the whole DNA is sequenced more twice in average.
Question:
If I have a genome sequence of length x with 30-fold coverage, then which of the following is correct?

I have to occupy 30x memory for the genome sequence, it means I would be given the genome sequence of length 30x.
It means I would be given the genome sequence of length x, but the sequence is more purified according to the calculation.


texts: Measuring transgenic gene expression with a microplate reader

texts:
I have been working on genetically engineering an E. coli strain to autotrophically oxidize arsenite into arsenate for bioremediation of arsenic contamination in groundwater. For my research, I have been finding ways to quantitatively measure how much arsenite the bacteria oxidizes over time.
After researching ways to quantitatively measure arsenite being oxidized, I have concluded to use the method of Johnson and Pilson (https://www.sciencedirect.com/science/article/pii/S0003267072800059?via%3Dihub).

The arsenate that is formed from arsenite oxidation forms a molybdenum-blue complex with phosphate in the water. As the concentration of arsenate increases, the absorbance value of the water should increase proportionally.

Here was my plan: First, after growing my transgenic bacteria on an amp-plate, I would pipette out various concentrations of cells and arsenite in wells of a 96-well spot plate. I currently plan to use the Fisher Scientific Multiskan FC microplate photometer. I planned on incubating the cells while shaking at 37 C. The main problem I have come across is that my experiment would not be controlled. Over time, the growth of cells will change the absorbance value, not just the molybdenum-blue complex. I need to isolate the variable of just arsenite oxidation.

I have thought of a few possible solutions, but I feel as if I may be missing something crucial. When learning about microplate readers, I know that researchers can use them to measure gene expression. How do these researchers eliminate the variable of cell growth effects on absorbance values?

For one, I have thought of finding a way to filter the cells to one side of the well where they will not affect the absorbance values. Would it be possible for me to cut out a dialysis bag to where it is dipping into the well? In that case, the cells could be suspended in the well, oxidizing arsenite (if my hypothesis is correct).

Anyway, I really want to find a simple method for quantitatively measuring arsenite concentrations over time using a microplate reader without having cell growth affecting absorbance values.


texts: What are reasons we know insects evolved on land rather than water

texts: I am reading up on the evolution of insects, and insects supposedly evolved on land rather than water. How do people know?What evidence is there that insects evolved on land and not water?


texts:
My book says "alleles of the same gene always occur at the same locus, but on a pair of homologous chromosome"
Please how is it possible since genes of particular character always occur on the same chromosome? When we know that alleles combine to form a gene, how comes then do they occur on homologous chromosome?


texts: Does body mass have a bearing on reflex speed?

texts:
A reflex is an unconscious action in response to some specific stimulus, e.g., blinking an eye, or pulling the hand away from a hot pin

I know from school biology, and reading online that withdrawal reflexes are quick because

CNS is involved
Danger receptors send impulses to prevent inhibition of flexion

When a person is extremely obese, do these flexion impulses take longer?

Is a withdrawal reflex in an obese person noticeably slower than in case of a reasonably fit person?


texts: Do any RNAs directly inhibit transcription

texts:
In eukaryotes, microRNAs and small interfering RNAs, as part of protein complexes, can attack specific messenger RNAs with complementary sequences, thereby inhibiting translation. However, RNA can also complement DNA. So, do any regulatory RNAs directly bind to DNA (with a protein complex or alone)?

I am only interested in regulation, not modifying DNA (like CRISPR does). I assume that means I am asking if any regulatory RNAs persistently bind to DNA, blocking RNA polymerases?

This question is for either or both eukaryote and prokaryotes.


texts: Which fish did modern tetrapods descend from?

texts: Did modern tetrapods descend from Tiktaalik or Ichthyostega? While I understand that in terms of all tetrapods, the lineages of Tiktaalik and Ichthyostega both would be included, but I want to know if their lineages have continued to the modern day. Since they also have 10 million years between them, it's possible that both of their lineages have not continued to the modern day. It's also possible that neither of them have continued to the modern day and it was a later fish species altogether whose lineage has continued to this day in the form of currently living tetrapods even though Tiktaalik and Ichthyostega were the first vertebrates on land. I'm especially interested in knowing which fish pecies have humans descended from. I'd be grateful if anyone is able to shed any sorta light on this.


texts: When we laugh or run for sport which autonomic system works?

texts:
When we laugh or run for sport which autonomic system takes place in this time?

While I am not sure what happens in heart while laughing (tachycardia or bradycardia), but for sport running I'm sure that the heart has tachycardia. Does it mean that the sympathetic system works there (or there isn't relation between them)? If it does, then I really don't understand why being anger cause damage to the cardiovascular while sport running said to be healthy for the cardiovascular system, here are both activate the sympathetic system. Isn't it?


texts:
This is another image I found on Google+

All lines are absolutely straight, parallel and perpendicular but why does it appear to have a curvature?

  Related: How does this illusion work?


texts: Why is the protein ubiquitin so ubiquitous?

texts: Ubiquitin is a protein tag that is attached to proteins in order to mark them for destruction/proteolysis by the cell. This system is sometimes used for clearing out harmful viral proteins that infect the cell, but is used in concert with the 26S proteasome to degrade proteins in many cells throughout the body. I just want to know why is ubiquitin so ubiquitous?


texts: Is it impossible for a retrovirus to be lysogenic?

texts:
Is it impossible for retroviruses to be lysogenic? In the lysogenic cycle, the viral genetic material is incorporated into the host cell's DNA. Because retroviruses have RNA, it would be impossible for their genetic material to be incorporated into the host cell's DNA, unless the RNA is reverse-transcribed or something.

Is this the case? How does this work?

Thanks!

evamvid


texts: When are population dynamics models useful? There seems to have been a lot of research about it, but how does it help? If I need data about how a population will evolve under what conditions, I need it because I need data for a decision (such as "can we kill 50% of population X without doing too much damage?"), right? But for that, the model needs to be aware of what causes what. And for that, I have to do experiments, right? Like "let's kill a significant amount of population X and see what happens in the next ten years". I really don't get it.


texts:
I am looking into Glycolysis and TCA cycle.
I have learnt that oxygen is the final electron acceptor.

So, let's say we know the amount of NADH and FADH2 produced under some circumstance related to the Glycolysis and TCA cycle.

How would we calculate the amount of oxygen consumption level?


texts: Why does ammonium oxalate cause swelling of RBCs?

texts:
From Pre examination procedures in laboratory diagnosis by Walter Guder :

  ...It consists of three parts by weight of ammonium oxalate which
  causes swelling of erythrocytes balanced by two parts of potassium
  oxalate which causes shrinkage...

This is regarding use of oxalates as anticoagulants.
To me, it makes sense that potassium oxalate causes shrinkage of erythrocytes but i don't understand why Ammonium oxalate causes swelling. Is it because it converts to Ammonia in alkaline pH of blood, diffuses into the RBC and converts back to ammonium.


texts: Are there any arboreal mammals which eat leeches?

texts:
Are there any tree-dwelling mammals which might be found taking a living leech and eating it?

(And do any hollow-dwelling birds of prey eat leeches?)


texts: Find Mutations Frequencies by Cancer Type

texts:
Is there somewhere that has mutation frequencies by cancer type? So if I were looking at CML, AML, or even more generally at something like leukemia. Is there some database that would contain mutation frequencies? So that I could find that in leukemia 50% of cancers contained a T100G mutation.

I have looked through COSMIC but haven't had much luck.


texts: Is there a way to remove hemoglobin from pig kidney homogenate without deactivating enzymes?

texts: I would like to measure different enzyme activities in centrifuged pig kidney homogenate. I get out of range errors at 450 nm. The samples are still reddish after centrifugation. Is there a way to remove hemoglobin without deactivating / removing enzymes? Thanks!


texts: How does a seed determine when to start germination?

texts: I'm sure there are many different ways for seeds of different species, but what is a general rule? Is it some kind of ideal temperature & wetness that triggers a chemical reaction? What factors stimulate seeds to germinate?


texts: What chemical or biochemical agents do plants use to inhibit each other's growth?

texts:
As I just learned, allelopathy is the action by which plants regulate the growth of other nearby plants.

I have hear of ethylene is a general signal for growth and fruit ripening in particular, but I would like to hear about more specific compounds or proteins that are known to be allelopathic agents and how specific can they be - lots of plants ignore each other and just grow over each other.

@AlanBoyd has pointed me to a journal, but as its not open content, I'm hoping for a next level review of the mechanisms and actors in this topic...

thanks in advance!


texts: Do bacteria develop a resistance to antimicrobial peptides at the same rate as against "regular" antibiotics?

texts:
From what I understand, antimicrobial peptides are roughly grouped into three structural sets, with large variations present between different groups as well as within the groups. Their anti-microbial properties tend to be through slightly different avenues than traditional antibiotics as well, since they can effect cell wall structure and some intracellular targets.

I have been told that antimicrobial peptides are thus able to be effective against as larger spectrum of organisms and that said organisms develop a resistance more slowly.

I do not understand why either of these cases is true, since any antibiotic sharing the same target should have the same effectiveness. Also, evolutionary pressure is what drives resistance, so why should that be reduced against antimicrobial peptides?


texts:
I'm being taught that: a muscle fibre spans the entire length of the muscle, from the originating tendon to the inserting tendon.

The question is, can a muscle fibre contract only partially? Say, if the fibre is 1m long, can only the first 10cm contract without the rest contracting?

Additonally, to help me understand better:
When a neuron innervates a muscle fibre, does it do it only at one spot, or can a muscle fibre be innervated in several spots? Can several neurons innervate the same muscle fibre?


texts:
Is there a database of organisms which would contain their queriable geographic location?

I would need to perform a rather simple query, such as Animals of <Location>, where Location is some well defined geographic area such as Czech Republic or Europe.

So far I have found multiple lists on Wikipedia and other webpages, however they seem to be quite incomplete as their intersect is quite small. Moreover, I have found EOL (Encyclopedia of Life) collections but they appear to struggle the same way.


texts: A simple question about amoeba (Naegleria fowleri)

texts: I have a very simple question about Naegleria fowleri amoeba. Some experts claim that boiling the water for 15 minutes kills Naegleria. However, I have studied somewhere that Naegleria can turn into cyst forms when the environment or the atmosphere becomes harsh to protect itself. So the question is that is it possible for Naegleria to survive boiling temperature if the water is boiled for 15 minutes at 100 degree celcius by converting into cyst form and enter the nose of human and kill the human?


texts:
I first thought this question in the case of

the cause of dry throat after 3-day recovery of dry cough?

but then I realised that the cause of dry cough can be a general thing.

Assume the person had three days recovery of dry cough under Montelukast and codeine (tablet).
He visited gym with little cardiotraining just after the catarrhal inflammation ended (no yellow mucose from throat during mornings anymore.
Just after the training, he felt dry throat after very weak coughs (no codeine medication when doing sport).

I am not sure if the dry throat is caused by

atrophy of the membranes in the throat
or dry cough by Acute respiratory viral infection (possibly through reflex arch; cannot be sure this because no codeine medication).

Let's assume that the dry throat is caused by dry cough (although weak) because virus particle can pass easily the scarring of the mucose membrane in the throat.

I think the atrophy of the membranes in the throat are NOT felt as dry.
Dry cough of the infection is felt shortly as dry.
The sympaticus activity clears the mucose membrane from the throat which alleviated the pain and also irritated the scarring.
Acute virus infection stimulates serous inflammation (as described here) which in the scarred tissue is felt once again as catarrhal inflammation.

So I think the cause of dry cough is catarrhal inflammation.
The localisation of the inflammation is essential to determine the type of inflammation, I think.

What is the cause of dry cough?


texts: Where do I find microsatellite instability annotation for TCGA data

texts:
I have searched through the TCGA data portal but I was unable to find MSI annotation for TCGA Colon Adenocarcinoma (COAD) and Rectum Adenocarcinoma (READ) datasets.

I am searching for the annotation on samples, i.e. if a specific sample is annotated as MSI (microsatellite unstable) or MSS (microsatellite stable). In particular, I found this page, and followed the path:

  Data Matrix & Bulk Download: Select 'Fragment Analysis Results' for Data Type

but with no results.


texts: Why is there no solid evidence (histological, fMRI) that the vestibular hair cells of the inner ear contribute to 53% of the respiratory drive?

texts:
There are these papers which strongly imply that the inner ear hair cells, and not the medulla, is primarily the driving factor in the CO2 drive reflex

https://www.ncbi.nlm.nih.gov/pubmed/21130842

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3988803/

But every fMRI study done on chemoreceptors has shown only areas of the brain and carotid bodies light up in response to CO2. I could not find any fMRI study papers showing that the inner ears light up in response to CO2 or any histological evidence that the hair cells of the inner ear are chemosensitive and play a larger role in chemosensation than the brain like these studies are trying to imply. It is said the central chemoreceptors in the brain contribute to 85% of the CO2 drive reflex and the peripheral chemoreceptors contribute 15%, which seems to leave little room for the inner ear hair cells to play such a vital and significant part.


texts:
We always think of natural selection as occurring at the level of populations not individuals. how about century old trees where germline is being produced from constantly dividing cells. Are all meristems in an old tree sharing the same genetic material, or enough mutations occur that different meristems have a different genetic background and are being selected differentially? Do different cells in a tree behave evolutionary more like different populations?

Added Note: The point I was trying to make is that for multicellular organisms in which the germline/somatic separation does not occur early in life, maybe Lamarck was not that wrong. In school we always learn to ridicule Lamarck with the giraffe story. But maybe in some instances Lamarckism makes at least as much sense as Darwinism.


texts:
is the vascular cambium equivalent to interfascular cambium or intrafascular cambium?

isn't the vascular cambium similar to the intrafascular cambium because both occur inside the vascular bundle


texts: What is the brain's preferred energy source? Glucose or ketones?

texts: As with all cells in our body, I know that the brain can get fed from both glucose and ketones, so my question is, given both of them, which one would the brain prefer to utilize first?


texts: Changes of permeability and driving force during voltage clamp

texts:
An action potential can be understood in terms of voltage changes, and these are fundamentally a function of relative permeability changes, mostly for Sodium and Potassium ions. If for instance the relative permeability of a cell strongly changes in favor of Sodium, the membrane potential approaches the equilibrium potential of this ion, leading to the depolarization of the membrane.

I understand that voltage clamp methods allow us to assess these permeability changes by "clamping" the membrane potential, and equivalently keeping the driving force constant:

$I = g * (V_m - E_{eq})$

with $V_m - E_{eq}$ being the driving force.

Related to that, I have two questions:

(1) Say we are approaching the Na+ equilibrium during an action potential peak, being closer to the Na+-equilibrium means a smaller driving force, hence the ion flux is an interaction driving force x permeability. Hence why the strong emphasis on permeability if the driving force is as relevant?

(2) When we clamp the voltage, say below the Na+ equilibrium at -20mV, we will have a constant influx of Na+. While I understand that this influx consists of only few ions entering the cell, doesn't clamping over a longer period of time change the concentration because the pumps can not keep up with the constant influx of cations, adding up over time?


texts: What is the concentration/molecules per cell of iodothyronine deiodinase in a cell?

texts: I'm trying to parameterize an in silico model and need the approximate concentration (M), or molecules per cell, of iodothyronine deiodinase type II (D2) enzyme in a human cell, ideally a glial cell.  I can only find specific activity values in the literature. Could anyone point me in the right direction, please?


texts: Units of parameters in epidemiological model

texts:
The simplest malaria model is given by $$\frac{dI}{dt} = \frac{\alpha \beta I}{\alpha I + r} (1-I) - \mu I$$
where $\mu$ is the death rate of humans, $\alpha$ is the transmission rate from humans to mosquitoes, $\beta$ is the transmission rate from infected mosquitoes to susceptible humans, and $r$ is the natural death rate of mosquitoes.

Assuming the units are given in $d^{-1}$, or per day, we can assume $r$ to be rather large, given that it isn't part of a larger product (and thus isn't a proportion). We can thus assume $r$ to be anywhere from a few dozen to a few hundred, depending on the size of the population. Recall that this is the amount of mosquitoes killed per day.

$\alpha$ is the transmission rate from humans to mosquitoes, and does appear to be a proportion, so $0 < \alpha < 1$. Thus, $\alpha$ is the probability a mosquito not carrying malaria bites a human $\textit{with}$ malaria. Assuming nothing more than 15% of a population of humans has malaria, and that 95% of a mosquito population do not carry malaria, this is $0.15*0.95 = \alpha = 0.143,$ or a 14% probability.

$\beta$ is also a proportion, and is the transmission rate from infected mosquitoes to susceptible humans. Rather, $\beta$ is the probability an infected mosquito will bite a human. Assuming a generous mosquito population (a few thousand at the least), we assume that about 5% carry malaria and (based on our previous assumptions) they have a 85% chance of biting a susceptible human (given that 15% are already infected). So $\beta = 0.05*0.85 = 0.0425$.

$\mu$ is given as the death rate of humans. Neglecting deaths by reasons other than malaria itself, we assume this value to be about $0.3\%$, given 627,000 deaths in 2012 out out of an estimated 207 million cases that year.

Is this analysis correct? If not, where can I find values for the above parameters? Are there any case studies where I can calculate the above values?

Thank you in advance.


texts: Have proteins been observed to come into existence through mutations and natural selection?

texts: A protein that catalyzes one reaction can theoretically be modified by mutations and natural selection and eventually catalyze another reaction completely unrelated to the original. Has this been observed, documented, or at least postulated to be where a certain protein(s) came from?


texts: Why do cherries sometimes grow as triplets?

texts:
Usually when I think of cherries, I think of them as pairs. I think most of us imagine them that way, but recently, I stumbled on a picture of a triple cherry:

Which I found interesting, but I couldn't find any more info on this, so I hoped to find some answers here. Why do they sometimes grow like that and how often does it happen compared to their regular twin counterparts?


texts: What is the name of this tree with yellow flowers?

texts:
Location is South India,

Tree is very large, but leaves are very small.

Image: http://imgur.com/fgtFzVD


texts: Is there a type of amnesia that separately affects long-term memory?

texts: Is there a medical condition that affects the long term memory, but leaves the short-term and working memories totally or fairly intact?


texts:
Many commonly known animals' limbs usually number between 0 and 10. For example, a non-exhaustive list:

snakes have 0
Members of Bipedidae have 2 legs. Birds and humans have 2 legs (but 4 limbs)
Most mammals, reptiles, amphibians have 4 legs
Echinoderms (e.g., sea stars) typically have 5 legs.
Insects typically have 6 legs
Octopi and arachnids have 8 legs
decapods (e.g., crabs) have 10 legs

....But I can't really think of many examples of animals containing more legs until you reach 30+ legs in centipedes and millipedes. Some millipedes even have as many as 750 legs! The lone example I am aware of, the sunflower sea star, typically has 16-24 (though up to 40) limbs.

So my question is: what are some examples of animals with 12-28 legs?


texts: What happens to fecal matter if it's continually re-eaten?

texts:
After class today, the topic of eating one's one fecal matter came up. There was a sharp divide as to how people thought the defecations would change. I realize this is a bit of an odd question but understanding it would help me understand how our body handles waste.

One theory was that the body would continually reuse some elements of the fecal matter such that, eventually and with no other input, nothing would be defecated.

Another theory was that there are elements in the fecal matter that the body would never make any use of, so it would continually get excreted (up until the person died, of course).

Could someone please explain the likely outcome of continually and only eating your own poop (assuming you could stay alive long enough)?


texts: I found this spider at the edge of a park in Hawaii. ~1cm in length. The area I found it was very dry and had thick tall grasses just a few feet away.


texts: Is it possible to deduce facts about a person's parents just by studying his/her genome?

texts: As an example, suppose Anne had abusive parents. Is it theoretically possible to deduce this from her genome even if she didn't inherit this quality (of being an abusive parent)?


texts: is it theoretically possible to take two fertilized mammalian eggs and push them together to make conjoined twins? How about forming non-identical conjoined twins?


texts: Unsure why Synechococcus moves at angle in cuvette

texts:
I'd really appreciate your help. I'm working with Synechococcus. In my experiment, I have Synechococcus in a solution of milli-Q water. I illuminated it with a focused white light through a pinhole and observed it using a CCD camera. The Synechococcus flows downward, which I think is due to gravity. But, in time, the Synechococcus flows downwards at an angle. Is this due to heat convection? If it is heat convection, it's strange that it sometimes stops flowing. The only visible motion seems to be Brownian motion.

Thank you your help!


texts: What happens to the excess immune cells or WBC in our body?

texts: When we have an infection our immune system produces a large amount of white blood cells (WBCs) in our body to fight against the pathogen or parasite. My question is after the immune response has finished fighting the pathogens, what happens to the excess cells and antibodies that presumably are no longer needed? Will they disintegrate themselves, is there a final step in the immune response to dispose of these cells, or are excess of these cells and proteins present as if they are not in excess (they are filtered no more so than when at normal levels)?


texts:
Considering the paper:

A single amino acid in E-cadherin responsible for
host specificity towards the human pathogen
Listeria monocytogenes

in the abstract portion, what does Pro→Glu mean? Does it mean that, in place of Glu(glucose), pro-16 is placed?


texts:
I  read (from Nature Volume507, S4–S7 (06 March 2014) :

  For reasons that are poorly understood, BCG protects only infants; it
  is ineffective in older children and adults. Its efficacy also depends
  on latitude. BCG works better, and protects people at later ages,
  farther from the equator. Both effects may result from interfering
  exposure to noninfectious mycobacteria that are closely related to
  both BCG and TB. These bacteria are more abundant closer to the
  equator, and while infants are unlikely to have encountered them,
  children and adults have more exposure over time.

I am unable to understand the relation between exposure to noninfectious mycobacteria and lessening of efficacy of BCG vacccine. What exactly is the "interference" caused by the noninfectious mycobacteria ?


texts: If evolution is a gradual and continuous process, how can we say humans came about 200k years ago? What is so special about that point in time?

texts: It just seems arbitrary to me to say "ok, now THIS is officially a human" when you could look at its parents and find no noticeable differences. At no point in the line of my ancestral history is there ever a hard cutoff between one generation and the next. It's a gradual progression. So how can you possibly pick a certain point in time when humans "first came around"? What criteria is used to say what exactly differentiates humans from whatever our ancestors were before 200k years ago? Did we "branch off" from something else at this point?


texts: If higher levels of atmospheric oxygen can lead to larger animals, can it also lead to larger plants?

texts:
According to some information, in the ancient past (at least some) animals grew larger due to a higher levels of oxygen in the atmosphere. So for example there is this study regarding dragonflies.

Can higher levels of atmospheric oxygen also lead to larger plants? For example, would it be possible to grow gigantic strawberries in a hermetically sealed greenhouse that maintains a higher atmospheric oxygen concentration?


texts: Is mammalian vision processed as a sequence of frames?

texts:
I often read that people believe that human vision has an inherent frames-per-second rate (FPS) that causes stroboscopic effects - such as seeing the spokes of a rotating wheel apparently rotating at a different speed or appearing stationary when moving.
For example: in a Physics.SE answer to Can a “superhuman” move so fast that an average person cannot see them?

The human eye-brain visual refresh rate has an "effective frame rate" of around 30fps.
Have you never watched the rims of the wheel in a car next to yours? I can clearly recall many times watching as the wheels sped up how it appears to stand still then move backwards.

This surprises me as I would expect there is no synchronisation of neuron firing in the retina, that neuron firing rates would vary widely depending on light levels and that the brain has no need to process the continuous signals in fixed cycles or in cycles whose length is invariant.
I believe this question, or a good answer to it, would differ from What is the equivalent of shutter-speed in Human eye?
Is human vision in any way subject to a fixed frame rate of 30 FPS?


texts: Identify this indoor plant with strange stem-like leaves

texts:
It appears that this plant branches multiple times from the base of its stem; however, I'm not sure if the base stems are from one organism. It becomes yellowish in color at the tip each stem-like leaves; one node can branch 3-4 leaves at a time.

Additional information:
As for the specimen location- I am currently living in Japan and this plant was bought as a gift for me. It probably is imported from other countries since it doesn't seem to be native here. For maintenance; I was told to just cut the tip of the leaves if it began to fade in color and die; and water the plant at least once a week.


texts: Biosafety Level 1 (BSL-1) surrogate viruses that show greatest similarity to SARS-CoV-2

texts:
I would like to know if there are any viruses that show high similarity to SARS-CoV-2 (particularly in terms of structure) that are very safe to use (i.e., classified as BSL-1).
For example, an avian coronavirus would be good to use but it is BSL-2. Ideally, I would need BSL-1.
Ideally if there were any corona type viruses that were BSL-1 or those which have distinguishing features with proteins emanating from an outer lipid membrane similar to SARS-CoV-2 .
I am particularly interested in finding a virus with similarity to the protruding S1 spike in SARS-CoV-2 (see image).


texts:
I am working on mathematical model for healing of dermal wounds. For anyone who's a bit familiar with Physics and Math, for the model I use the Cauchy Momentum Equation as a basis, and from there I use already established literature to expand to a so-called morphoelastic model.

From a physical perspective, if a force is exerted, you would expect a material to start moving, upon which stresses arise, until a new balance is found. This all usually happens on a timescale of second. Now when wound healing is regarded, the contraction force is exerted by fibroblasts. I have read that wound contraction happens at a speed of up to 0.75/mm per day. On the one hand this is impressive, yet on the other hand it is very slow when viewed from the mechanical perspective.

So my question is: Is there a biological effect or phenomenon that slows down? Could it be that the migration speed of fibroblasts is the bottle neck? Or maybe skin is in some way tethered to underlying tissue? I know very little about biology, so any help would be appreciated!

Thanks in advance


texts:
I began reading this paper (http://www.biomedcentral.com/1471-2105/14/56) and had a few questions about mass spectrometry terminology that I couldn't find answers to elsewhere.  Consider the following line:

"The resulting peptide signals in the LC-MS map are referred to as features while the selection of features for fragmentation with MS/MS is called precursor ion selection."

I'm not sure what an LC-MS map is, so I can't properly understand what features or precursor ion selection are: can someone define these terms for me with examples?


texts:
I met this animal yesterday while walking along a small river in Yokohama, Japan. It came out of the bushes some 5 meters away from me, but while I was launching the camera app on my smartphone, it already went away into a fenced area where I couldn't follow and was quite far, so these are the best pictures I could take. It seemed to have something wrong with it's fur (either molting or sick). Could be a japanese raccoon dog (a.k.a. tanuki), although the images I found on Google don't look much like it to my untrained eye (maybe because of the fur), or some kind of a fox (looked even less likely). Tried asking locals, but they tend not to know anything about animals, unless those animals are either dogs, cats or foods. So, what is this?

EDIT: the size is hard to describe, I would say, it was a bit bigger than a big domestic cat, and also had different proportions - longer body, neck and legs.


texts: Help in identifying an unknown arthropod

texts:
I'm not even sure it's an insect:  the best I can do is identify it as an arthropod.  I captured this slow-moving organism and after a period of observation under high magnification, I concluded that it appears to construct a "shell" from miscellaneous particles or debris.  With a scalpel, I carefully cut this outer casing open to observe the organism, and the pictures show what I found.  It seems to have six legs, like an insect, but is oddly worm-like and wingless.  Total length is approximately 1 cm.  I do not believe that this is a juvenile/larval/instar form.  I've seen several of these where I live, and they always look like this (with maybe a +/- 20% size variation).

Edit:  This specimen was found in San Diego County, California, United States.


texts: Why do sea mammals die on land, and drown on sea?

texts:
It's quite confusing to me, why do sea mammals die on land, but also die from drowning if they couldn't reach the sea surface to breath?

Excuse my ignorance but I am really confused!


texts: Is it safe to feed an adult fire salamander with slime maggots?

texts:
As a reminder, maggots feed of a flesh, while fire salamander consumes his prey alive, without killing it.
Can it happen that the maggot will start eating the salamander from the inside?


texts: What is an on-line measurement? What is an off-line measurement?

texts: See it used here: http://en.wikipedia.org/wiki/Fed-batch. In the table giving the different strategies to control growth in a fed-batch culture, one finds, for example: "on-line measurement of glucose". What does it mean? Is there an off-line meassurement? What does it mean?


texts: Size distribution of all known species in the domain bacteria

texts: I have found the smallest bacteria are around 200nm (e.g Mycoplasma genitalium an ultramicrobacterium) and largest are around 700um (Thiomargarita namibiensis). I am looking for a graph that illustrate the size distribution of all bacteria species. I have googled with no luck.


texts: Does anyone know of a study supporting predictions #2 or #9 of the Extended Evolutionary Synthesis?

texts:
Regarding the 12 predictions made by the Extended Evolutionary Synthesis (http://extendedevolutionarysynthesis.com/about-ees/), does anyone know of a study that supports #2 or #9?

It seems like #1, #3, #5, #8, #10, #11, and #12 do not violate the modern synthesis.  #2 and #9 would though.  Agreed?  But I know of no study that supports them.  Not sure about #4, #6, or #7.


texts: I know what influences the fingerprints to be unique always. But what actually process is taken to make these as we grow?


texts:
I know that conception is a multi-step process. A sperm fuses with an egg. Its contents diffuse into the cytoplasm.
Dad's DNA is transported to the nucleus. Proteins are gradually made from Dad's DNA. Do we know how long that process takes?

I'm most curious about conception in humans, but information about other species is welcome too.

EDIT:  The time I'm interested in is between the fusing of sperm and egg, and the first transcription of the newly incorporated paternal DNA within the zygote's nucleus. However, if conception is better defined by different events, feel free to correct me. I'm far from a specialist in the subject.


texts: A little help understanding DNA supercoiling

texts:
I am studying molecular biology from Lewin's Genes XII and got confused in the supercoiling topic. Since then I read from several other sources and so far understood the following. However, I can't seem to connect the dots. A bit of help in connecting the dots would be greatly appreciated.

So these are the stuff that I understand so far

Supercoiling is coiling of already coiled double helix
Positive supercoiling overwound the DNA (increase the number of turns thus decreasing the number of base pair per turn making it more twisted)
Negative supercoiling underwounds the DNA
Linking number is the sum of twist and writhe, twist is basically number of turns and writhe refers to the number of supercoil. It remains constant as long as phosphodiester bonds are not broken
unwinding DNA at replication fork results in positive supercoil downstream

Now coming to the confusion

In the diagram we can see that negative supercoiling has taken place. Twist value has gone up and to compensate that (to keep the linking number constant as no phosphodiester bond has broken in this case of cccDNA) six negative supercoils have been introduced.

All the books clearly mention that negative supercoil is something that underwounds the DNA resulting in less turns with more base pair per turn. But in this case it is clearly seen that the number of turns have increased (from 36 to 42) and to compensate that -6 supercoil is introduced. So here negative supercoil has resulted in over wounding instead of underwounding

similarly, from the linking number equation > Lk = Tw + Wr, If there is positive supercoiling (i.e., Wr is positive) the Tw (twist value) will go down to keep linking number constant. So, the statement saying positive supercoil wound overwound the DNA is not matching at all. shouldn't positive supercoil increase the Tw as well (I understand mathematically it is not possible because then linking number would change, but all I'm saying is that I fail to connect the concept that says positive supercoil overwounds the DNA (more twisted) with what I see in the equation i.e., twist number drops and only writhe goes up.


texts: Are there examples of PTMs that add different chemical groups (and mass) to different amino acids?

texts:
I'm talking about this type of post-translational modifications. What I'm interested in is not whether some modifications can only occur on specific amino acids (that's clear), but if the nomenclature has examples of addition of slightly different chemical groups to different amino acids known under the same name.
Thanks.


texts: This eggplant fruit is featuring a big scar. What causes such a scratch? Is it a disease or maybe the fruit was hit and then it healed the crack? Is it correct to call it "Eggplant scab"?


texts: How deep does a 0.5mm radius drill need to drill before it start to hurt the brain assuming the drill bit will be pull off without wiggle?

texts:
How deep does a 0.5mm radius drill into the brain need to drill before it start to hurt the brain permanently assuming the drill bit will be pull off without wiggle?

I am assessing how fragile of a brain is.

What are three types of damage that are most likely to happen for 3mm deep, 6mm deep or even deeper


texts: Differentiation of norepinephrine and epinephrine in indications

texts:
Norepinephrine is less beta2 adrenomimetic than epinephrine so more selective so less bronchospasm so may be therofore better in treatment of cardiac failure and different shocks.

However, I am not sure.

I have some intuition that some of them is somehow analog of the other one.

PubMed about norepinephrine in Pharmacology

Sympathomimetics
Adrenergic alpha-Agonists
Vasoconstrictor Agents

PubMed about epinephrine in Pharmacology

Bronchodilator Agents (beta2)
Mydriatics (beta2)
Adrenergic alpha-Agonists
Sympathomimetics
Adrenergic beta-Agonists (this causes those two first indications)
Vasoconstrictor Agents

which is logical because epinephrine is nonselective beta2.
However, I am not sure if those properties include all accepted indications.

This proposes me that norepinephrine can be used better in acute situations.
However, I know that epinephrine injections are more given to allergic people to carry for anaphylactic shock.
Why so?
Probably, because of price.
How does the indications of norepinephrine differ from those in epinephrine?


texts: In one book I read that pteranodons lived in huge colonies. But pteranodon's family in "Dinosaur Train" ( https://en.wikipedia.org/wiki/Dinosaur_Train ) does not seem to be a part of any colony. So, who is right? Did pteranodons live in colonies?


texts: In glycolysis why NAD is positivly charged , why it's not neutral or negative ?


texts: Cell image database for citotoxicity test

texts:
Is there any cell image database for citotoxicity tests? I know that there are several image databases available (like this, this and this one), but none of them have the images for citotoxicity tests.

Thanks in advance,


texts: What are the function(s) of Alu elements in the cell?

texts:
My 2008 biology book (1) states that some 10% of the human genome consists of relatively short (~300 nucleotides long) Alu elements which do not code for proteins but many of which are transcribed into RNA. Do these Alu elements have any function in the cell?

(1) Biology, 8th ed., Campbell & Reece, 2008


texts: What is the evolutionary purpose of the topology of the human ear?

texts: What is the evolutionary purpose of the topology of human ears? I understand why the ears may have a funnel-like shape but if the various "hills and valleys" do not amplify incoming sound, what purpose do they have?


texts: Why will happen if plant phloem does not contain sieve plates?

texts:
What are the primary functions of the sieve plates that make them so crucial? I've done a bit of reading online and found
"Sieve plates are perforated end walls separating the component cells (sieve elements) that make up the phloem sieve tubes in vascular plants. The perforations permit the flow of water and dissolved organic solutes along the tube and are lined with callose."
However, wouldn't the flow of water or organic diluted be faster without the extra sieve plates obstructing the flow? Or is there some other functions of the sieve tubes?


texts: Why are proteins always made in N to C direction?

texts: Why are proteins always synthesized from the N-terminus to the C-terminus? Can there be any “reverse” peptide-bond formation to synthesize proteins in the C-terminal to the N-terminal direction?


texts: I have installed the genomatix software which is a jar file the name is InstallChipInspector21.jar.But now I really don;t know how do I start it ,can any one suggest me a method??


texts: Does mung bean nuclease cleave a phosphate group when it's chewing off 5' or 3' ssDNA ends?

texts:
I'm looking to create blunt ends from sticky ends with mung bean nuclease for subsequent ligation.  Does anyone know full mechanism by which mung bean nuclease will do this?

In particular after the reaction, will the ends of resulting dsDNA have phosphate groups or will I need to phosphorylate the ends with an extra step for successful ligation?


texts: In the Lineweaver-Burk Plot, why does the x-intercept = -1/Km?

texts:
Taking the reciprocal of both sides of the Michaelis-Menten equation yields the Lineweaver-Burk Equation:

$ \dfrac{1}{V} = \dfrac{K_m}{V_{max}}\dfrac{1}{[S]}+ \dfrac{1}{V_{max}} $

Plotting a $ \dfrac{1}{V}$ vs. $\dfrac{1}{[S]}$ graph, I am told that:

y-int $= \dfrac{1}{V_{max}}$ and

x-int $= -\dfrac{1}{K_m}$

How are these relationships derived from the lineweaver-burk plot?  I can see how the y-intercept can be equal to $\dfrac{1}{V_{max}}$ if $\dfrac{1}{[S]} = 0$, but I don't see how x-int $= -\dfrac{1}{K_m}$ by setting $\dfrac{1}{V} = 0$? Can someone demonstrate how these relationships were derived?


texts: Difference between Facultative Aerobes and Facultative anaerobes

texts:
My Prof started off talking about Aerobes, there being obligate aerobes and those that can metabolise compounds such as $\ce{NO3-}$, $\ce{SO4^{2-}}$.
Then he began talking about anaerobes and those that can process $\ce{O2}$, calling them facultative anaerobes.
Are they not the same thing?
Edit:
Prof has responded that yes, they are the same thing, though he didn't say why. My guess is that anaerobes simply refer to organisms that can use things like $\ce{NO3-}$, $\ce{SO4^{2-}}$ to respirate, aerobes simply refer to organisms that can use $\ce{O2}$ to respirate, and facultative refers to how they can tolerate the condition opposite to the one they can use.
ie facultative anaerobe =  anaerobe, but can tolerate oxygen
(facultative aerobe =  aerobe, but can tolerate the lack of oxygen)
Anyone can verify if this is correct?


texts: I have a quantitative morphological data comprising of both growth and yield traits. In my heritability analysis, i discovered that some of the traits have negative variance component and heritability values. Is it fine to report this and what is the explanation for the negative values. Thank you.


texts: Does there exist a reagent that can only be precipitated by Haemoglobin and nothing else?

texts: I recently read Sherlock Holmes and in the book A Study In Scarlet, Holmes says to Watson that he has discovered a reagent that can only be precipitated by Haemoglobin and nothing else. I know about the Guiacum test but is there any other test like I have discussed above as the Sherlock Holmes test.


texts: Where do lost membrane proteins go after exocytosis?

texts:
Exocytotic vesicles take away membrane proteins and glycocalyx on the cell's plasma membrane surface. When those vesicles are released into the interstitial fluid and wherever else, where do they go?

Do they stick to the vesicle everywhere? Or do they get removed from the vesicle? If the vesicle fuses into another cell, do those proteins and carbohydrate attachments stick to the new cell?


texts: Mechanism of Myosin Head Bending in Cross Bridge Cycle Power Stroke Phase

texts:
What is the mechanism of bending of myosin head during the power stroke of the cross-bridge cycle of the muscle contraction? Does this have anything to do with the protein's 3-D structure i.e. folding of protein in space? I would prefer a physics explanation down to either the classical electrical dipole or quantum mechanical interaction amongst the proteins. I want to know what exactly produces the force that powers the bending. I am pretty sure that the force can only be electromagnetic. The question is how the force is manifested in the bending.
Any references for further reading are appreciated.


texts: I've noted that flies in my house have no problem landing on even perfectly clean mirrors. Why don't they fly straight into them? Can they sense that there is a surface there, even though they can't see it?


texts: How does Organ Transplant work well despite having Foreign DNA

texts:
My question is little bit related to this one Why does organ transplant work although it seems organ's motor neuron isn't connected to recipient's CNS but only little bit.
Problem
Suppose the case in which person A got his kidney transplanted (and person B is donor). Now both A and B have different DNAs and how come lung (organ) transplant works well for person A and how does person A's DNA going to "accept" the lung's DNAs and how is replication going to work across the foreign lung?
Question
Will person A's lung contain:

Person A's DNA
Person B's DNA
DNA of both Person A and B (will convert to person A's after some-time having a certain half-life for it)
or
Forever contain both DNAs

Thanks in advance and kindly provide reference for your answer. Thanks


texts:
Has anyone extracted a class of neurons (or a connected set of neurons) and stimulated them electrically to get an understanding of their behavior?

If so, could someone point me to papers along these lines? If not, do people have an idea of why this is not been technically feasible yet? As I would imagine this would be tremendously useful in building neuron models.


texts: How does food preservatives effect salivary digestion?

texts: What effects do common food preservatives have specifically on saliva?


texts: Have Polyphyodonts ever evolved from Diphyodonts?

texts:
The Wikipedia article for polyphyodont says this:

  Although most extant mammals are not polyphyodont, mammalian ancestors were. During the evolution of Therapsida, there was a period during which mammals were so small and short-lived that wear on the teeth yielded no significant selection pressure to constantly replace them.

...which was a bit surprising at first, but makes sense. So I'm wondering - have any species evolved in the opposite direction? In other words, have there been any non-polyphyodont species which have teeth, and evolved into polyphyodonts?


texts: During non-cyclic photophosphorylation, how does NADP+ become NADPH?

texts: I know that NADP+ gets reduced to form NADPH, but what exactly is being donated? Is it two individual electrons (from photolysis or the chlorophyll molecules) and a hydrogen ion (proton)? If this is the case, during the Calvin Cycle, do the NADPH molecules donate the same two individual electrons and hydrogen proton from the light-dependent reactions to become NADP+ again? Thanks.


texts: How does the modern synthesis theory explain the evolution of birds from dinosaurs?

texts:
The theory of evolution claims that birds evolved from dinosaurs only by mutation, genetic drift, migration and natural selection.

However, it seems to me that wings were not selectively advantageous for dinosaurs.

Would you show me a book or a paper which explains this point in detail with academic accuracy?
Level of the book or the paper should have detailed information for an advanced reader.


texts:
I am following M.J. Benton's Vertebrate Palaeontology, which explains how many groups of Synapsida were already extinct in the Mesozoic Era, with one obvious exception being the group of Cynodontia, which includes modern day Mammalia.

Nevertheless, I cannot find when the last non-mammal synapsids got extinct and I would be very grateful to anybody giving more information about the topic.


texts:
I know that microevolution has been experemnted on Lizards

https://www.nationalgeographic.com/animals/2008/04/lizard-evolution-island-darwin/

it is clear that creatures evolve with new environment

for example if you take creatures from warm environment to a cold one there comes the mircoevolution where it help this creatures evolve genetically to adapt with the new environment.

Has any mircoevolution changes (genetically) happened to any of the europian people who moved to south africa centries ago? or to any of the african american who moved from africa to north america?


texts: I am interested in Sociobiology. Which academic field should I study?

texts: I like to study Sociobiology and evolutionary psychology. Which academic fields concentrate on these sciences in bachelor and master degrees?


texts: How is the diploid chromosome number maintained at mitosis?

texts:
A normal human cell is diploid that contains 46 chromosomes in 23 pairs. Thus, when the cell undergoes mitosis, the cells still has the full chromosome with the two sister chromatids. What is it doing in interphase when it produces the other chromosomes?

I thought that the sister chromatids were pulled apart and, in interphase, the single sister chromatid grew another one. How is this possible if a human diploid cell contains 23 pairs of 2 chromosomes each?


texts: What are the major differences between good study habits for biology vs mathematics?

texts:
I'm a math prof. But, I've always loved reading about biology (the paleobiology of microbes and some small animals mostly) it's my hobby but I want to learn more maybe take a course. My longer term goal would be to be able to be of better assistance to my online friends who are biologists who are always asking me to help with the statistics in their papers. (I have been able to help, but I feel like I could do better)

When I study math, I aim to be able to identify and prove all major results from memory, state all definitions, and solve new problems and proofs. I have a process it works.

But with biology I often find that there are multiple definitions or there are big differences between textbook content and studies. It's really upsetting. I understand why this is true, that's just the nature of science, but I don't understand how to best navigate when a topic has multiple interpretations that are all possibly true. I get really hung up on not being able to find one definition for some terms.

Should novices and students stick to textbooks and "widely accepted" definitions? Or should one make and effort to keep up with the most recent research and learn to live with the ambiguity?

I can take one course for free at my university each term. Should I start with 101? Or can I do that through self-study and start with something more specialized?

What is a good self-study book?

My only science background is a few newtonian physics courses.
I'm kind of scared to go to the biology department and ask. Biologists are really intimidating when you teach something simple and clear like math.


texts: Do larger unicellular eukaryotic organisms have larger organelles?

texts: It seems that many of the giant unicellular eukaryotic organisms (size 1mm and above) are multinucleate but there are some with a single nucleus as well (the genus of Acetabularia). My question is: do they have proportially larger organelles (mitochondria etc.)? If so, can they be seen by a person with sharp eyesight when removed from the cell?


texts:
Hiking in some hills near Taipei after a rain, I saw lots of large snails out and about. Here "large" means the shells are say 8 cm long, and the snail itself fully stretched out 10 to 15 cm perhaps.

At one point I saw a cluster of four snails stuck together in a confusing way. The one on the right was slowly climbing uphill, pulling the other three along.

What is going on here? I see some connections between some of the snails, but I can't really understand most of what I'm looking at here, nor why four snails would be stuck together sideways like this.


texts:
I'm wondering about the minimal set of parameters necessary to define a protein's structure.  My understanding is that the backbone geometry is defined by the phi and psi angles (torsion angles), and then from this template the side-chain rotamers are defined.  Is this sufficient to yield a geometric structure, or are there other factors involved?

On a related note, how exactly are two protein structures compared? I often see references to percent similarity, but what does this really mean?  In the Protein Data Bank, atomic coordinates are given, but my intuition is that coordinates are only important relative to all the other amino acids in the chain.  In other words, absolute coordinate comparison would seem to be uninformative.


texts: Can fermentation and aerobic respiration occur at the same time?

texts:
In muscle cells during exercise, does lactic acid fermentation and aeorobic respiration occur at the same time, and does this mean the cell makes more or less ATP during this time?
The cell can't completely lack oxygen, which means that some of pyruvate will move into the mitochondrion, however, lactic acid is also produced which means that anaerobic respiration occurs. Is this reasoning correct or is there some other mechanism that I am skipping that doesn't allow these processes to simultaneously occur?
Also, the NAD+ used for glycolysis is regenerated and net 2 ATP is releaseD in glycolysis, but the NADH doesn't move into the mitochondrion, so if pyruvate moves into the mitochondrion at the end of glycolysis, then there will be less NADH in the mitochondrion, which makes sense because there is too little oxygen and too many electrons in the ETC.


texts: found in garden in wiltshire, england. about 15mm-20mm long. Resting at 6pm on raspberry plant.


texts:
Does the entire surface of the earth contain organisms?
My teacher mentioned that in some parts of the earth, there aren't any organism. Is this true?

Thanks in advance.


texts: CD4+ as Monocytes cell surface receptors

texts:
Today in class,  our teacher was discussing about the pathogenecity of the HIV virus.

He said that the binding between HIV virus and macrophages is done by the interaction between the GP120 of the virus and CD4 receptors,chemokine receptors(CCR-5 and CXCR-4) and fusin receptor present on Macrophages.

My doubt is
I think CD4 receptors are present on T-helper cells only. Are they present on Macrophages too? Do i have a wrong notion about CD4 receptors?
If not, then are there some other receptors responsible for the transfer of viral particles inside monocytes and dendritic cells?

Any extra information is appreciated.


texts: There is not much to explain, I'm wondering if pulled hair, for example of the head, normally does grow back again or not. In reddit, It says this may depend on the follicle integrity, if the follicle is  not hurt then it will grow back and viceversa. It is the case?


texts: What is the difference between the mitotic spindle and microtubules?

texts:
In mitosis, I understand that the centromeres line up on the spindle. I also know that the centrioles form microtubles between the centromeres during mitosis in the metaphase.

But, are microtubles and spindles the same thing? Or do microtubles make up spindles?


texts: Does galactose occur before or after galactose transferase?

texts:
The follow shows a protein pathway pathway.

The question is "where does galactose (GAL) first occur" i.e. which block above is galactose first contained in?

A transferase is defined as (wikipedia):

  any one of a class of enzymes that enact the transfer of specific functional groups (e.g. a methyl or glycosyl group) from one molecule (called the donor) to another (called the acceptor)

This definition of transferase is confusing as:

The question doesn't show any functional groups does it?
From it, I can't figure out whether the galactose transferase is the molecule that is the donor or acceptor

I can't decide if galactose first occurs in S (as a donor) and is transfered into an acceptor upon reaching T, or if another donor forms galactose (as an acceptor) after S, causing T to contain galactose.


texts:
Most trees I know that have their flowers in groups hang these groups down. I noticed, however, that conker flowers grow upwards!
I guess that growing against gravity requires special effort, so conker may benefit somehow from growing the flowers upwards. Is this true? What's the benefit?


texts: If you took a newborn animal and completely isolated it from its species, would it be capable of assuming a fight or flight distance preset by its species, due to their being no basis for what could harm the animal?


texts: How does permanently modifying human DNA work? And how does it impact procreation?

texts:
So I read an article about a metabolic disease being treated with gene therapy, where they inserted corrective dna into the patient.
https://www.independent.co.uk/news/science/dna-permanent-change-cure-disease-experiment-california-brain-madeux-iv-hunter-syndrome-a8055696.html
How can this be permanent though? Wouldn't the other cells "take over" these modified cells when they reproduce, and eventually have back the same old dna?
Furthermore, will this affect offspring in any way? Will they inherit the new dna changes (if that part of the dna is passed on from the parent with the changed dna)?


texts: Can stress-induced cortisol reduce diabetes type I?

texts:
Let us consider a patient with type 1 diabetes.

I think it would be safe to say that diabetes is an autoimmune disease. Now let us suppose this patient comes under stress. As far as I know, cortisol is a stress hormone and is released when a human is under stress. Now cortisol, as far as I know, increases the amount of blood sugar and at the same time is an immunosuppressant.

I would like to know whether this stress-induced cortisol can suppress the immune system, which has gone haywire, and help against diabetes - thereby rendering a suitable amount of stress useful.


texts: Understanding genetic similarity in humans

texts:
I was reading "Blueprint" by Robert Plomin (online preview on webpage) and got stuck when I got to these two sentences in the prologue:

"We are the same as every other human being for more than 99 per cent of these 3 billion DNA steps, which is the blueprint for human nature." (page X)

"familiy members differ a lot genetically - you are 50 per cent similar genetically to your parents and siblings, but this means that you are also 50 per cent different." (page XI)

How does it fit together? Is he talking about different measures of similarity here?


texts: Why would things self-organize in such a manner? I'm a mathematician and I have no baggage in ecology or biology. If the question is too broad maybe someone can point me to formal sources where this type of issues are tackled.


texts: Can any foreign molecule be non- antigenic ? Can any foreign peptide be non-antigenic ? What is the difference between an antigenic and a non-antigenic peptide ?


texts: Why does our body absorb toxic substances or toxic concentrations of a substance if it is capable of regulating gastrointestinal absorption?

texts: Our gastrointestinal system is filled with regulatory molecules that place brakes in the absorption process. For instance, the food that we consume daily is filled with harmful substances that our body does not absorb, and these substances are later excreted. However, when ingesting poison or a potentially poisonous substance at high quantities our gastrointestinal system ends up absorbing these poisonous substances in sufficient quantities (if present) to kill us. Why can't these regulatory mechanisms not entirely prevent the absorption of toxic/poisonous substances that can cause us harm or death?


texts: How long the homologous arms of the "repair" sequence must be to do homologous recombination?

texts:
I am trying to figure out the details of the homolougous recombination in order to be able to insert a certain piece of DNA in the host genome after double strand break.. Does anybody know how long the homology arms of the repair template must be ? Can the left arm be longer than the right one? I have read several papers which have different sizes 90 bp vs kb..
In my case, i am not so much preoccupied by off target but the insertion should occur also on the desired site possibly at high frequency and as fast as possible.
Thank you,
Paola


texts: A question regarding trichomes in plants

texts:
Trichomes in general are features of xerophytic leaves, which reduce water loss by evaporation by trapping water vapor and increasing humidity (as a result lowering the water potential gradient).
BUT I wanted to know whether trichomes also reduce water loss by decreasing "surface area" of the leaf, so that less water loss occurs (considering they occur as finger-like projected structures that occur in large numbers)?


texts: McFarland or O.D of culture what to use and what is the difference?

texts:
I am working on gram positive bacteria for which OD was reported and some reported mcfarland value. I am new to microbiology. i want to confirm the only thing that matters is cfu. please reply for what shoul I prefer
thank you.


texts: Is B27 necessary to culture neural stem cells?

texts: I've seen many papers using B27 (e.g. https://pubmed.ncbi.nlm.nih.gov/24694094/ & https://www.sciencedirect.com/science/article/pii/S0167488919300242) but it is really expensive and I was wondering if it is really necessary to culture neural stem cells? More generally what is the simplest medium that is still used for this purpose?


texts: Meaning of "pure" in "pure plant DNA" (horizontally transferred to bacteria in soil conditions)

texts:
The abstract of Transformation of Acinetobacter baylyi in non-sterile soil using recombinant plant nuclear DNA, by Simpson et al., 2007:

  To provide estimates of horizontal gene transfer from transgenic crops to indigenous soil bacteria, transformation frequencies were obtained for naturally transformable Acinetobacter baylyi BD413 using a chromosomally integrated plant transgene. The transgene comprised sequences for two phenotypic markers: kanamycin resistance (npt II) and green fluorescent protein (gfp), expressed from their own bacterial promoters. Recipient bacteria carried a copy of these two genes, with deletions in their 3'-termini abolishing the marker activity, these genes were integrated into a 16S rRNA gene in the bacterial chromosomal genome or carried on a broad host range plasmid. Successful recombination between the plant transgene and the bacterial genome resulted in restoration of the markers, allowing detection through antibiotic selection and fluorescence. Transformation parameters of increasing complexity, without any enrichment steps, were used to approach the field conditions, while still obtaining measurable transformation frequencies. In pure culture filter experiments, transformation was detected using ground, chopped and whole leaves, as well as whole sterile seedlings, and ground roots. In sterile soil microcosms, transformation was detected using pure plant DNA (3.6 × 10-8 transformants per recipient) and ground leaves (2.5 × 10-11). Transformation was also detected for the first time in non-sterile soil using pure plant DNA (5.5 × 10-11). Since the same constructs were used throughout, these data allow predictions of even more complex environmental systems where measurable frequencies are not easily obtainable.

What is the meaning of pure plant DNA? That the transferred DNA was in the form of purified DNA solution dripped onto soil, as opposed to some ground leaves whose cells included donor DNA (and some of these cells were crushed while being grounded and thus shed some DNA material onto soil)?

Was it done in order to promote transformation?


texts: Why does plasma protein saturation of a drug increase its volume of distribution and clearance rate?

texts:
I need help understanding this statement from Goodman and Gilman's "The Pharmacological Basis of Therapeutics:"

  For a drug that is metabolized
  by the liver with a low intrinsic clearance-extraction ratio, saturation
  of plasma-protein binding will cause both V (distribution volume) and CL (clearance rate) to increase as drug concentrations increase.

This is how the textbook defines distribution volume and clearance.
$$\text {distribution}\ \text{volume} = \frac{\text{amount of drug in the body}}{\text{concentration in plasma or blood}}$$

$$\text{clearance rate} = \text{bioavailability} \ \cdot \frac{\text{dosing rate}}{\text{concentration at steady state}}$$

I think I get the grasp of it somewhat, but I would like to verify if my reasoning is correct.

The reason why volume of distribution increases is because the drug is distributed to tissues other than blood once the plasma proteins are saturated with the drug. As a result, the amount of drug in the body increases while the concentration in plasma or blood stays the same.  Hence, the increase in distribution volume.

As for clearance rate, it increases because the zeroth order reaction is always faster than the first order reaction in Michaelis-Menten kinetics.
However, I am not sure why the fact that plasma proteins are saturated matters.

For the distribution volume to increase, unbound drug concentration in plasma should stay constant while tissue drug concentration has to increase when more drug is administered. For clearance rate to increase, however, unbound drug in plasma needs to be able to increase when more drug is administered. What am I understanding wrong?


texts: If molecular chaperone proteins assist in the folding process of other proteins and misfolded proteins, can chaperone themselves misfold since they are also proteins? What would happen if chaperones misfolded? Can they misfold at all? Why or why not?


texts: How many (taxonomic) families are there?

texts:
Approximately, how many families have been identified?

I've often often come across figures for the total number of species on Earth. Recently, I found myself wondering about the encompassing ranks above them, specifically family, but I can't recall any figures on family and it's a little difficult finding what I want by typing "family" into a Google search. ;)


texts: I am about to simulate a neuron activity with the "Leaky Integrate and Fire" neuron model. But for that I need the membrane resistance. I was really looking a lot online, but I just cant find a value. Does anybody know the measured resistance value, or the value usually used in this model?


texts: Do you produce more sperm after 1 week of abstinence vs 1 year of abstinence

texts:
Question: I was wondering if the amount of sperm increase with the amount of abstinence?

Side questions:

Is their a max amount of sperm?
What happens with the excess amount?


texts: High levels of estrogens and progesterone antagonize prolactin’s effect on the mammary glands, and it’s only after the placenta has been removed and the levels of estrogens and progesterone has decreased that prolactin effectively stimulates milk production in the alveoli. However, I’m also aware that many hormones cause the maturation of the breasts and mammary glands during pregnancy—is anything produced then? When does lactation really occur—before birth or after birth? I ask this because I’ve heard things about milk leaking out of breasts during pregnancy, and there’s also the fact that the breasts seem very heavy and laden with milk during parturition.


texts: Comparative effectiveness of antibiotics against colonies and growing bacteria

texts: Appropriate antibiotics usually eliminate bacteria. However are the same antibiotics as effective against bacteria that have grown to form a colony?


texts: Help me identify this spider from my garden

texts: Found this in my garden today in Sydney, Australia (specifically Lane Cove). Can you tell me what it is?


texts: Why are bugs attracted to light bulbs but not flames?

texts:
Just now, a housefly was bugging me a lot and I wanted to get rid of it. My mother suggested me to turn off the lightbulb and off it went. However a small flame was burning in my room. Why didn't the housefly get attracted to the flame (although it was a luminous flame)?

My first guess is because of the high temperature a flame produces. This Wikipedia article states that:

  A 300 watt tubular halogen bulb operated at full power quickly reaches a temperature of about 540 °C (1,004 °F)

And a charcoal fire can produce temperatures between 750–1,200 °C (1382-2192 °F). Source.

I've seen small bugs getting attracted to large halogen lights in sports complexes. Although these two temperature ranges are a sizable difference apart, 540 °C doesn't seem cool at all. Is it really due to temperature, or is there some other reason?


texts: Why is ATP hydrolysis to ADP, rather than ADP hydrolysis to AMP, used to drive biochemical reactions?

texts:
ADP has two phosphate groups, and can be hydrolysed to AMP in a reaction which involves a similar free energy change to that of hydrolysing ATP to ADP.

Why is the latter reaction, rather than the former reaction, coupled to energetically unfavourable reactions to provide an overall reaction with a negative change in Gibbs Free Energy?


texts: The move from RNA to DNA and the necessity of reverse transcriptase

texts:
In this piece about giant viruses and the origin of life, in the context of the move from RNA world to DNA world, virologist Valerian Dolja states:

  In order to move from RNA to DNA, you need an enzyme called reverse transcriptase

Is this true though? Don't many DNA polymerases work with both, ssDNA and ssRNA templates, i.e. they function as reverse transcriptases although they're not "true" reverse transcriptases. So, in order to move from RNA to DNA, a reverse transcriptase was not a necessity like ribonucleotide reductase was for RNA to Uracil-DNA and thymidylate synthase was for Uracil-DNA to DNA?


texts: How to filter out the antibody light chains into kappa and lambda types on the PDB website?

texts: The antibody light chains can either be kappa or lambda types. I am searching homologous sequences on the RCSB PDB website. Is there a way to filter out these two types?


texts: Why do antidepressants have a delayed onset of action?

texts:
Why do antidepressants take so long to reach efficacy? I've read of theories about it perhaps being due to the strength of negative feedback via serotonergic and adrenergic autoreceptors during the first few weeks of treatment. What I'm looking for in an answer is the following:

The current theories regarding why currently-in-practise antidepressant regimens have a delayed onset of action.
The evidence for these theories.
How these theories fit in with the monoamine hypothesis or whether it is inconsistent with the monoamine hypothesis and how.
Possible solutions to this problem of delayed responses to antidepressant therapy.

All of this is strictly theoretical, there are no actual people involved here, this is simply a scientific inquiry.


texts:
This is a cross-cutting question but I think its core is about biology. Our society's need for energy is dramatically growing and we are messing up with our environment to answer them. Maybe another way to proceed would be to use the primary energy source that is the sun in the same way as it has been used throughout the ages: photosynthesis.

I know the energy effiency is not as good as a solar panel's but it could clearly be compensated by volume. I found surprisingly little information about harvesting energy from photosynthesis which is why I began to wonder where we are at today.

Thanks!

Edit
I meant transforming the chemical energy generated by photosynthesis into electrical energy. For instance, the first algae powered building was unveiled at the International Building Exhibition hosted in Hamburg. This is a whole different approach.
The most basic example of what I would like to talk about seems to be the algae powered lamp that has (apparently) been developped. In other words, it seems that some sort of plant solar panels are under development and I don't understand how it's done.


texts: Would non-human carnivores be able to survive on farmed foods?

texts: Certain creatures that are considered carnivores are non-obligate carnivores and are technically omnivores (such as wolves/dogs).  How different is the potential digestive ability of these species compared to humans?  If they theoretically developed sapience and the intelligence for agriculture, would they be able to survive on the same wide variety of plant foods that we do (i.e. could wolves survive on wheat, rice, etc)


texts: Molecular animations of, say, protein synthesis, are simplified, but how exactly?

texts:
In several animations of biological processes (eg protein synthesis (go to frame 1.20mins), DNA replication, etc), molecules such as amino acids are shown heading straight to the replicating protein as if drawn by a magnet. As far as I know they move randomly. But still, translation occurs at a rate of about 15 amino acids/second and 75 ATP/second, so the rate of gobbling shown in the video clip is not off the mark.

I can think of two explanations:

1) The microscopic world is counter-intuitive. It is so frenetic that normal diffusion is enough to supply the hungry protein. The video simply doesn't show all the input molecules in order not to clutter the picture but essentially it is correct. However, amino acids are not small, and they are attached to the much larger tRNA, so they must be moving relatively slowly by Brownian motion.

2) There are additional helper proteins that concentrate or channel amino acids and ATPs in the vicinity of the ribosome or replicator. Never heard of these.

What is the real explanation?

Edit: To clarify, the question is not about the simulation side of things as such, such as how hard it is to actually make a true simulation. Most simulations, including weather prediction, involve a certain degree of approximations and simplifications. But in this case, there is something definitely untrue in the video clip, namely the molecules being attracted to the ribosome. As explained by a moderator, this means that it is not a true simulation but a "cartoon". So the question is: what would an ideal "non-cartoon" true simulation look like? Would the tRNA be diffusing in at a very fast rate, or are there helper proteins that, for example, tether tRNA in the vicinity of the ribosome? The moderators seem to indicate that diffusion is enough, but I would like to see a reasoned out answer with numbers that show this is the case.


texts: Can you tell the sex of a white willow when it's not flowering?

texts: Can you tell whether a salix alba tree will produce male flowers or female flowers by looking at it, touching it or generally using your unaided senses? If not, is there any way to do that without specialized equipment or lots of expertise?


texts: How can tooth enamel feel pain when drilled by a dentist?

texts:
Enamel has no nerves, so theoretically a tooth should not feel any pain when a dentist bores into it. Yet still we use anesthetics...
Maybe it’s dentin's fault? It apparently has some tubes filled with liquid and the tooth's nerves can feel this liquid's movement. So, maybe, the closer the dentist gets to dentin (especially if he/she touches it), the more pain is felt? By the way of vibrations from the boring tool?


texts: What is this species of asphodel from Morocco?

texts: It grew about 2 metres high. Photographed in spring. It has 6 tepals and 6 stamens.


texts: Can a ladybug be determined just by its number of points?

texts:
I saw a ladybug on my balcony one day and I just counted the dots.

There was 18 black dots on a red/orange elytra.

The location is in Europe (Geneva, Switzerland) and usually we have quite different endemic ladybugs and also the invasive asian ladybug Harmonia axyridis.

I did not found any local ladybugs with such dot counting except articles saying the Harmonia axyridis can be found with a lot of variations (elytra  color, points or stripes, etc...).

The question is: Can I be sure that a ladybugs with 18-points (found in Europe area) is of the genus Harmonia axyridis?

Note that I have a picture of the animal but I want to focus my question on the number of dots exclusively.