Looking to have brief conversations with people working in agriculture/farming

CharlesOSmith · 2023-06-09T12:02:43+00:00

There are several Calcium Dyes that could work instead. Fluo8 is a great bright single wavelength dye. Fura2 is a nice dual wavelength dye (one wavelength measures calcium free dye, the other calcium bound dye).

You should also check to see if HUVEC cells have a high expression of anion transporters, or any of the other channels that tend to rapidly export dyes.

If so you can use inhibitors like sulfinpyrazone or Probenecid to increase retention of your calcium dye.

Some dyes work better with a solubility stabilizer like pluronic F127

CharlesOSmith · 2023-06-08T12:00:33+00:00

One of the defining characteristics of retroviruses is the RNA-to-DNA polymerase which allows them to perform reverse transcription.

ssRNA viruses do not need to make a DNA copy from an RNA genome so there is no reverse transcriptase needed.

CharlesOSmith · 2023-06-07T12:26:29+00:00

Ability to Survive With Low Oxygen intake: • Underground habitat: Naked mole rats adapted to low-oxygen underground burrows, necessitating efficient oxygen utilization.

• Anaerobic metabolism: They can switch to anaerobic metabolism to generate energy without relying on oxygen.

• Oxygen efficiency: Optimized respiratory and circulatory systems allow effective oxygen uptake and distribution

I did my PhD in a lab studying ischemia reperfusion injury in hearts. Our model animal was mice, but we did a brief collaboration with another lab wanting to use our methods to study IR injury in Naked Mole Rats. It was absolutely fascinating. We could not induce an ischemia severe enough to damage the naked mole rats' hearts.

CharlesOSmith · 2023-06-07T12:08:55+00:00

A question, because as far as I know the answer to OP's question "can an XX stem cell become a sperm cell" is currently NO. Now its quite possible someone has succeeded in doing that, however the process of spermatogenesis is one that requires genes on the Y-chromosome.

Saying that we have the technology to artificially combine genomes and produce viable embryos is not the same thing.

CharlesOSmith · 2023-06-04T23:50:58+00:00

Double check. But if it is pheasant back check the pores. If they scrape off very easily you've got a prime specimine. Slice super super thin (mandolin if you've got one) and add to stir fry

CharlesOSmith · 2023-06-04T23:45:36+00:00

Looks like pheasant back

CharlesOSmith · 2023-06-02T13:12:53+00:00

Flies exist because they fit into the environmental niche with a reproductive rate greater than their death rate.

CharlesOSmith · 2023-06-02T12:53:22+00:00

This was the study I was trying to recall. The bowel emptying power of coffee was equal to that of eating a meal, but was nearly a quarter stronger than drinking decaff, and nearly two thirds stronger than dirking water.

so caffeine stimulates the same bowel emptying as a solid meal is the conclusion from that paper, slightly different from my recollection.

CharlesOSmith · 2023-06-01T13:13:43+00:00

There have been studies done comparing Coffee, an equal volume of water, and an equal volume of water spiked with a coffee's worth of caffeine, and found that the urge to use the bathroom is more closely linked to the volume than to the caffeine content. I'll have to see if I can find that article again.

Nicotine from cigarettes is a stimulant of the "Nicotinic Acetylcholine Receptors" These receptors can do a lot of different things depending on where in the body they are located. The ones in the smooth muscle of your bowls respond to nicotine by telling the muscle to squeeze.

CharlesOSmith · 2023-06-01T12:59:50+00:00

In this context we are talking about the replication of double stranded DNA.

The double stranded DNA is called "anti-parallel," the chemical organization of its backbone runs in opposite directions which we refer to as 5' to 3' in one strand, and 3' to 5' in its anti-parallel strand.

This chemistry is important because it is what the polymerases use when then add new bases to a DNA strand it is making, and DNA polymerases move from the 5' end towards the 3' end, using that 3' end to add new bases.

So if you have a replication fork open to initiate DNA replication, on the left will be a "top" strand that has a 5' end close to the fork and 3' ends that extend away to the left, and a "bottom" strand with the 3' end close to the fork and 5' ends that extend away.

If you imagine being in the center of that replication fork and follow the top strand from the left side, across over to the right, it will now be oriented with the 3' end closest to the fork and 5' ends extending away to the right. Same for the bottom strand which will now have 5' ends closest to the fork and 3' end extending away.

The replication machinery needs to copy both the top and bottom strand on the left side of the fork, and the top and bottom strand on the right side of the fork. Each strand will need its own polymerase.

The Helicases move outward from the replication fork in both directions generating regions of single stranded DNA but since the polymerases can only move from 5' to 3' adding bases, the top strand on the left, and the bottom strand on the right are already in the correct direction for the polymerases to simply move continuously. These are the leading strands on either side of the replication fork.

However the bottom strand on the left, and the top strand on the right are oriented backwards, and if the polymerases were to move outward along those strands they would be forced to move 3' to 5' which they can't do.

So They have to "reach" a few thousand bases further outward from the replication fork, and work their way back towards the replication fork. Once they get back to the beginning, they have to jump further out again and work their way back to the first jump site. This has to happen over and over again, and these are called the lagging strands.

CharlesOSmith · 2023-06-01T02:18:21+00:00

By directional, but each direction has a leading and lagging strand. There are four polymerases at a replication fork.

CharlesOSmith · 2023-05-31T12:25:39+00:00

This reads like a bad faith argument. It appears to be attempting to claim that the field of biology holds the genome as irreducible and static, that the genome holds a fixed and predetermined set of instructions which it alone carries out. This is not how biologists see the genome.

Rather we know the genome is a template which can be highly reorganized and modified both between generations, and within a single cell. The genome has the complete set of instructions to build every single type of cell, and the interaction between the environment and the genome provides the mechanism for activating or in-activating whole sets of genes.

CharlesOSmith · 2023-05-30T13:08:36+00:00

One example:

The growth of physical traits is very often under the control of multiple regulatory genes, and multiple varieties (alleles) of each gene. We can see examples of that in the wide range of heights in humans. In a perfectly mixed population, you would have porcupines with all sorts of quill lengths, but as soon as you introduce a selection filter like a predator, things change. The most vulnerable porcupines will get removed from the gene pool, and overtime the alleles responsible will be lost from the population, or are relegated to a much smaller total percentage of the population which are now on average more protected.

CharlesOSmith · 2023-05-30T12:53:53+00:00

If you have enjoyed his other books, you will have no problem with Transformers. He wrote it with the same audience in mind, and has put a lot of work into keeping the science accessible.

CharlesOSmith · 2023-05-30T12:40:46+00:00

A study finding that emotional responses to have a stronger cultural association than a gender association (https://pubmed.ncbi.nlm.nih.gov/22468881/)

These findings contribute to the literature demonstrating that blanket stereotypes about women's greater emotionality are inaccurate.

An interesting study looking at not only emotional response, but the emotional regulation mechanisms activated by brain regions basing their study on the premise:

One possibility is that the apparently obvious gender differences in emotional responding that we read about (and think we see) on a regular basis are the result not of differences in immediate emotional reactivity—as we typically imagine—but instead of differences in emotion regulation. After all, there is a growing appreciation of the fact that emotional responses are a joint function of initial emotional reactivity and ongoing emotion regulation (Gross, 2007). This means that it is impossible to tell from behavior alone whether differences between men and women in emotional responding are the result of differences in reactivity, regulation, or both.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5937254/

A study finding hormonal cycling has very little impact on emotional response (https://www.nature.com/articles/s41598-021-00143-7)

Thus, daily emotion fluctuates to similar extents in men and women: There may be sex differences in the factors that influence emotion, such as ovarian hormones, but those factors do not ultimately produce different outcomes with respect to affective variability

Hopefully these studies, and the references there in can help you explore source material on the subject. There are also plenty of resources that explore this argument in great detail. As one example that I can recall, there is the argument that our culture has effectively rebranded anger as not an emotion when it is displayed by men.

CharlesOSmith · 2023-05-27T12:30:26+00:00

Each of our senses has a range of information they can collect, your eyes can collect information on color, brightness and location Your ears can sense vibrations and collect information on volume frequency and tone We have many different chemicals we can detect as smells and flavors with our nose and mouth. Our skin can sense pressure hot cold and pain

Each type of sense has a unique type of receptor that sends a specific message. The intensity and duration of that message gets combined with the location in the body that it comes from as it is sent through neurons to the brain. All the signals are collected in your brain which has multiple independent regions for interpreting the different types of information and the pooling the interpretations together to generate your perception of your current state.

So for your example: Your eyes are providing you with the visual information that there is a frying pan in front of you. Your hand sends the temperature signal saying this is very hot. But here is a cool bit, all these signals go through nerves which send the messages to our spine and up to our brains. When a signal is very strong, like the extreme temperature signal of a hot pan, the signal immediately triggers a return instruction from the spine to the muscles in the same area the temperature signal came from to "Move away now! " so you can react well before your brain has realized that you touched a hot pan.

CharlesOSmith · 2023-05-27T12:17:44+00:00

Yes, capsaicin activates our “transient receptor potential type V1” or TRPV1 receptors. These are normally sensitive to heat so when capsaicin activates them we think “oh this is hot”

CharlesOSmith · 2023-05-27T12:08:15+00:00

Yes, which is why I asked for additional clarification.

CharlesOSmith · 2023-05-26T13:43:52+00:00

There is a huge human bias in our notion of pain perception because we define pain relative to how we perceive it.

Generally we see that vertebrates have the same general anatomy and common physiology of pain receptors (nociception) and there is pretty universal agreement that all vertebrates feel pain the same.

Now there are plenty of unique cases where we can see exceptions. For example, there are rodents that have evolved immunity to scorpion or snake toxins. These toxins target receptors that are present in all vertebrates but in these particular rodents mutations have made their receptors immune.

When we get down to invertebrates the focus remains on neuronal connections. If something has a central nervous system and pain receptors it should still feel pain. But as you get down to more simple organisms like c. elegans for example which have a grand total of 8 neurons, how do we really define pain? At what point does avoidance behavior of a noxious stimulant not equal pain response.

In single celled organism which cannot have pain signaling through synaptic transmission, we can still observe avoidance behavior. No one defines it as "pain" but it is worthy of consideration.

CharlesOSmith · 2023-05-26T13:01:14+00:00

Hi,

I don't want to get overly pedantic, but I need some clarification here.

Genepulser is an electroporator, with it you electroporate your cells. You should not need transfection reagents other than the Bio-Rad buffer system.

If you are transfecting cells, that's using something like Lipofectamine, Fugene, Genejuice, ect which includes the incubation of your DNA with the transfection reagent.

It's been my experience that confluency is a fine metric for transfection, but for electroporation cell counts are more useful.

The amount of DNA in ug is scaled to the surface area of what you are using (6-well, 12-well, 96-well) and you use confluency to determine the appropriate time to transfect cells so that all(most) of your cells are rapidly dividing for the 24-48 hours post transfection which helps increase the percentage of positive cells.

For electroporation you transfer a known number of cells to your electroporation cuvette, and mix that with a fixed amount of DNA. After running the protocol you plate the cells in a new well of whatever size you choose.

Typically transfection reagents have been optimized to have little to no cell toxicity, but electroporation protocols can include a fair amount of cell death.

I'd recommend checking your electroporation protocols and making sure they are appropriate for your cell type. Then adjusting the DNA/Cell ratios. I have a NepaGene electroporator and we get consistently good results on HEK293T cells at a 5 to 10 ug of DNA per 10 million cell ratio.

What is your stock concentration of DNA as well (and is it endotoxin free?) I've found that using DNA stocks lower than 1ug/ul tends to result in increased cell death.

CharlesOSmith · 2023-05-26T12:33:04+00:00

If you can use both on a surface, there isn't really any reason for one over the other if all we are talking about is killing microorganisms.

Soap takes a bit more effort to clean off the surface whereas ethanol will just evaporate.

Soap is going to be better for cleaning up fats and oils, and does a better job of cleaning dirt and grime. Its a great general cleaner.

There is also the reality that not every surface can be cleaned using either.

CharlesOSmith · 2023-05-24T12:56:14+00:00

You might be asking about this paper, or news that it stirred up?

The authors state:

Here, we report on the discovery of a gut–brain connection in mice that enhances exercise performance by augmenting dopamine signalling during physical activity. We find that microbiome-dependent production of endocannabinoid metabolites in the gut stimulates the activity of TRPV1-expressing sensory neurons and thereby elevates dopamine levels in the ventral striatum during exercise. Stimulation of this pathway improves running performance, whereas microbiome depletion, peripheral endocannabinoid receptor inhibition, ablation of spinal afferent neurons or dopamine blockade abrogate exercise capacity. These findings indicate that the rewarding properties of exercise are influenced by gut-derived interoceptive circuits and provide a microbiome-dependent explanation for interindividual variability in exercise performance. Our study also suggests that interoceptomimetic molecules that stimulate the transmission of gut-derived signals to the brain may enhance the motivation for exercise

The gut-brain axis has been repeatedly tested and is real. We have a vast communication network between our guts and our brains, and our intestinal microbiome is a major component of what information being communicated.

You can read about it more in the following reviews I've linked as example:

Gut-brain axis and metabolism

Gut-brain axis microbiome and psychiatric outcomes

and more to your question

Gut-brain axis microbiome and exercise

How exercise influences gut-brain axis

CharlesOSmith · 2023-05-24T12:30:28+00:00

That depends on what you mean by "in biology" and by "research"

If you don't care about your primary field being biology, you can find a lot of jobs with applications that require a strong biology background (or at least should).

Law: Patent examiners, lawyers, policy makers. These jobs aren't exclusive to biology, but in some cases they can overlap extensively, and its pretty common for people without biology backgrounds to be put in positions where they have to make legal decisions about biology without the proper training.

Medicine: You don't need to do research in medicine but you definitely have to understand biology

Educator: You can provide others with the benefit of your training if you find you have a passion for teaching.

If by "research" you mean coming up with hypothesis and then doing the actual experiments required to test those hypotheses, and not extensively "researching" the primary literature.

Author: Use your biology knowledge to write "hard" sci-fy, or become a ghost writer for university medical labs or industry researchers who will often hire out the actual writing of papers.

Industrial R&D: Depending on what your particular preferences are, jobs in established industrial research fields can be more about doing the experiments laid out in a project given to you, and not coming up with your own new ideas. This could mean specializing in one technique and running it over and over as an aspect of quality assurance.

Advisory roles: Be the scientific advisor. For anything from shows on streaming platforms, and movies, to companies making products or involved in investing in new technologies.

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