text:
What is it about bleach that keeps Pharaoh ants away even after drying?
My apartment high-rise has been afflicted with ants in the past few years.  The pest control technician says that it has become a common problem due to warming weather.  Various things have been tried, and I am leaving this in their expert hands (or rather, the apartment management is).  This question is not asking for further countermeasures.
When I find a place or pathway with many ants, I find that simply wiping with a damp cloth or vinegar doesn't keep them away for long.  Wiping is supposed to disrupt their pheromone trails, but I only find somewhat lasting effects if I wipe with undiluted household bleach.  I am pleasantly surprised that they stay away even after the bleach has dried.  After some internet research, I found that bleach leaves behind a salt residue when dried.  Is it the salt residue that keeps the ants away when wiping otherwise doesn't have lasting effect?
I've had another corroborative experience that leads me to suspect that salt residue has a repulsive effect on pharaoh ants.  I keep a large beer glass of very salty water on hand because of the dental benefits of salt water rinse.  I probably use too strong a solution, which likely has drawbacks (something I have yet to research).  It is kept on top of the fridge.  Around the glass is salt water staining.  I never see ants around it, even though ants like water.  I admit that this corroboration is not very strong, as I generally do not see ants on top of the fridge anyway

Although not familiar with the requirements set by biology SE this strikes me as being a suitable question for this site, since it is more about the sensorial perception and behavioral response of the ants, where the chemistry is important but relatively straightforward (and well addressed by the current answer).

My bleach solution seems ill-advised, both because of the fumes and the adverse effects on laminate countertops.  It looks as if I will have to get comfortable again with ants on my food preparation surface.

It's likely that the bleach (hypochlorite), which is a strong oxidizer, is destroying the trails more effectively than the vinegar. The mechanism of action here is the organic pheromone molecules, known as monomorine-1 and faranal are broken down into smaller organic molecules through oxidation. This chemically disrupts the trail and it takes some time for the ants to re-establish it.
I'm no organic chemist, but the acetic acid in vinegar may be a good smell masker for us, but I don't think it will have any chemical effect on the pheromones.

Thanks!  I upvoted the answer.  I have no idea how I can determine if it is the right answer.  Maybe a biological chemist can weigh in with a more authoritative assessment?

@user2153235 You might get a better response if you request migration to the Chemistry SE, though there are some good biochemists on here too, who might be able to answer authoritatively.

I will try that.  Er....I was just about to cross-post. I then googled how to migrate. From what I read here and here, I suspect that I have to flag the question for closure and specify a migration as the reason. Unfortunately, I can't find a Close link/button.  Maybe because I am the OP?

@user2153235 there should be a "Flag" link at the bottom of the text. I think that'll let you request migration, though I've never tried.

Done.  Thanks, Bob1!

Another answer that is fairly speculative (though quite plausible, in my view) results from the fact that I am using undiluted household bleach.  It leaves such a heavy salt residue.  Information online is mixed as to whether and how much ants dislike salt.  In my case, however, it may be that the salt simply provides a physical barrier against ants travelling up to the countertop from the seam between the sink and the countertop.  I actually see white crustiness forming at the seams after jamming the bleach soaked rag along the seam.


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What is the biological name of this plant?

The plant was observed in a rural area near Digha.

This is Ageratum conyzoides, a flower of Asteraceae family.
The common Bengali name of this plant is Uchunti.
Other than this purple colour a white colour of this flower is also observed.

@Ayandip If the question has been correctly addressed you can accept the answer by clicking on the tick under the downvote arrow.Also you can  upvote it.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

sort: votes


text:
Do ants actually stick better after "licking" their legs?
I found an uncommonly large black ant and put it in a glass cup to observe it. It initially had a lot of trouble climbing vertically by any amount. However, I noticed it paused and when I looked closely, it seemed to run its front legs quickly between its mandibles, and it looked as though it secreted some kind of orange liquid through its mouth. After it did this and climbed again, it climbed a little bit further up the cup, but fell down again.
Then, it repeated the process of pausing and running its front legs between its mandibles. After this, it tried to climb again and I saw it was able to climb a little bit further than it did after the first run before falling down, though I didn't think to measure the exact height on a drinking glass. I saw it repeat this process yet again, and it stuck to the cup even better and climbed even higher before inevitably falling, and I assumed it would continue this process indefinitely until it was able to climb out of the cup, so I threw it back outside.
I would hypothesize that the ant was coating its legs with its own saliva which has evolved to be sticky for situations like this, seeing as how it so quickly exhibited the mental aptitude for recognizing its climbing challenge. But, I'm not biology expert. Perhaps its legs already inherently possess all stickiness ability it needs, and it is only that its legs were dirty or covered with water.

Lots of relevant information at the Wikipedia page for insect adhesion and in this paper. No mention of 'saliva', I suspect that what you saw was grooming to prepare adhesive structures.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


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Are the controls for RT-PCR the same as those for RT-qPCR?
I am searching for negative and positive controls for RT-PCR but all the results seem to point towards RT-qPCR. Are the controls the same for both?
I have found

-RT control
No template control
exogenous control
endogenous control
no amplification control

Do they apply for both or just RT-qPCR?

Those acronyms get slung around a lot with slightly different definitions.  RT = reverse-transcription and q = quantitative?

@Punintended yes, that's what they mean to my knowledge. but since the steps differ in both these methods I was wondering if the same controls applied to both.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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Could you force meiosis in a cell that normally uses mitosis
I've read in the red queen something that suggests the DNA repair mechanisms are better in meiosis than they are in mitosis.
I was wondering if occasionally we could force some of our cells that use mitosis to use meiosis so as to clean up mistakes in our DNA.

It is not clear from your question if you understand the basics of mitosis and meiosis, especially the differences of outcomes of the two processes. Your question will have higher chance of being answered if you explicitly state what effort you have made to answer it yourself.

How would meiosis "clean up mistakes" in DNA?

@forest I would assume he is talking about gene conversion during meiosis and the hypothesis/theory stating that crossing-over has evolved from a DNA repair mechanism.

it isn't going to help somatic cells to undergo meiosis, because at the end they would be haploid and not really capable of doing good somatic cell stuff... ie. if you were heterozygous for something that was a autosomal recessive disease ... half of the cells would end up with it... also if you were male (human) half of your cells would have a Y chromosome and half would have an X... in general in higher animals the gametophyte generation doesn't do a lot of living on its own.

@BagiM, yes I was sort of referring to the hypothesis you refer to. I was just reading "the red queen" and saw reference to the idea that germ cells had a better DNA repair mechanism that regular cells during meiosis and was wondering there might be some way to get somatic cells to occasionally use a better firm of DNA repair. I realize the haploid problem Grady mentioned. I'm not tried to get somatic cells to use meiosis exactly. Was just wondering if we could somehow encourage cells to us a better DNA repair mechanism. I am a physicist. I have cancer and am interested improved DNA repair.

@chemong In normal body cells there already is Homology directed repair. If I remember correctly it is active in G2 phase where sister chromatids can serve as a template for reparation. The gene conversion would not do much good in multicellular organism because it would introduce genetic diversity of individual cells (in some cells allele A gets converted to B, in others B to A). Genetic diversity is a base of natural selection and I fear the whole thing would kickstart cancer instead of preventing it.


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Using spp. for taxa other than Genus
Can spp. be used for taxa other than genus ? For example Noctuidae spp. meaning certain genera in the Noctuidae family.

eric I think this is an interesting question, but I'll suggest you modify a bit: You ask" "...meaning certain genera...". "Spp." would still likely refer to species and not genera in the application you're asking about.


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Toxic Metals and Oxidative Phosphorylation
I was reviewing the toxicity of certain toxic metals, specifically cadmium and their effect on Oxidative Phosphorylation and Cellular Respiration, I have found that metals such as cadmium inhibit certain antioxidant enzymes such as catalase, resulting in oxidative stress as a result of excess of Reactive Oxygen Species or free radicals, I also have come across information that states that toxic metals can bind to the mitochondria and interfere with oxidative phosphorylation, possibly in the electron transfer change or in another way. I was wondering if anyone is aware of the other ways in which cadmium interferes with oxidative phosphorylation as it bonds with the mitochondria, or if attaching to antioxidant enzymes IS actually binding to the mitochondria.


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Cadmium Poisoning and Toxicity Mechanisms
Is anyone aware of the toxic mechanisms of specific instances in which cadmium ions can interfere with cellular functions resulting in acute cadmium poisoning?

What have you found in your own attempts to research the question?


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Electron Transport Chain Proton Pumping into the Intermembrane Space
In regards to the electron transport chain, I know that complex I pumps 4 H+, complex III pumps 4 H+, and complex IV pumps 2 H+, but where do these numbers come from? If someone could explain this, that would be great. For example, I'm confused at how 4 H+ are pumped when only two enter complex I via NADH + H+.


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synthesis of zn nanoparticle
Sir the protocol I followed where it has been written... 1st using lactobacillus in Mrs media (50 ml in 250 ml conical)..we allowed to incubate for 24 hrs then added 0.1M znSO4 (50ml) and 0.4 M NaOH(50ml)...followed by a vigorous mixture heating it for 15 mints at 40°C ...white portion observed at the bottom of conical..(.which I also showed)...followed by centrifugation washing it with deionised water again again ...finally pelleted portion collected which allowed to dry to make it powdery form..then it observed under UV spectroscopy by mixture the powdery with  deionise water...
But sir I don't get any pick in UV spectroscopy.. Is  there any method synthesis Zn Nanoparticles using lactobacillus culture?

Can you provide a link to the protocol you followed? Is it from a published paper?

Also, please format your question properly. Use bullet points to explain the protocol step-wise. Moreover, add some more details on how you analysed it and what you expect is the problem. Did you try repeating the experiment at least once more?


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How do I efficiently develop a plant cultivar?
Or, perhaps: how do I develop a cultivar at all?
First off, my knowledge and experience on the subject is close to nil. I've got a decent enough knowledge of gardening concepts, but have done precious little plant breeding, and nearly everything I know about genetics comes from the reptile hobby and the breeding of various morphs (also haven't done any of that).
But I wanted to try my hand at plant breeding - at least, get started somewhere.
I've decided to go for something simple - a dandelion. Hardy, easy to grow, flowers quick and I know will definitely reproduce for me. Contamination from external sources might be an issue but there's several easy fixes for that. I could probably wait around and inbreed them until some funny traits pop up but for now I want to try some obvious changes - wider leaves, bigger flower, maybe both.
All I (think I) know is that I'll have to keep track of my individuals and their ancestry and select for traits based on their current expression and genetic pedigree. On the surface that sounds pretty simple but I don't know the details of the execution. Is there a specific way plant breeders do it? Software that would make the management easier?
I tried looking this up, but Google isn't very extensive on this subject. Any advice or resources that can get me started would be greatly appreciated.

You have made quite unlucky choice by picking dandelion. Most dandelions reproduce by apomixis. The seeds produced (without polination) are clones of mother plant. It would be hard (if its even possible) to force them to cross, which puts many classical breeding techniques out of your reach.

@BagiM Wow, didn't know that. I know there are already dandelion cultivars which is why I thought it would be possible. Are there any other simple plants you'd recommend?

Creation of cultivars of species that reproduces only vegetatively or through apomixis is possible by accumulation desired mutations (mutagenesis). What you cannot do is cross two plants with desired traits and create homozygots  or double mutants. You would have to start with cultivar closest to what you want and try to mutate it then pick one plant with best properties and try to mutate it further. What you also cannot do is to segregate undesired trait from desirable one.

... It is hard to tell you which plant to choose. It depends on what you want to do. I would recommend to read as much as possible on plant genetics and specific genetics of plant you choose. Breeding is application of the genetics theory and is included in some plant genetics textbooks. Once you are well versed in plant genetics it will be clear to you what you can do, what outcomes to expect and you will be able make this decision for yourself.

@BagiM Thanks. I'll definitely keep trying to study plant genetics. As for dandelions I don't think it's a complete loss - just a matter of making sure I have diploid plants. The cultivars I have came from Europe, which even though they're still T. officinale much of the dandelion population is diploid (except for Northern Europe). I just want something quick and easy to breed so I can easy tell if I'm doing something right or not.


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Why are mammals the only animals with pinnae / outer ears?
Yes, I know owls have feathery "ear tufts", but these are less suited for hearing and more for display.
And I find it hard to believe that animals like dinosaurs or other cursorial archosaurs would not rely on sound as much as a mammal would. It's just too useful of a sense.
One potential clue is the fact that most non-mammal tetrapods appear to use electrical tuning to discern different sounds, whereas mammals use the hair cells of their longer cochlea to mechanically discriminate sound. I feel like this is related but not completely connected to why a fleshy outer ear structure that can collect and focus in on the direction of a sound.
Why did the pinnae evolve in mammals and why are they the only ones with such a structure?

If an organism does not have outer ear, it does not mean it does not rely on sounds. Birds heavily rely on sounds for so many aspect of their life. Owl is a great example,

Which isn't the question. The whole idea of the pinnae is that they aid in the collection and focusing of sound, yet other animals seem to be able to do this relatively well so there must be some reason they don't have pinnae.

I understood (maybe misunderstood) the sentence I find it hard to believe that animals like dinosaurs or other cursorial archosaurs would not rely on sound as much as a mammal would as assuming that absence of pinnea means poor use of the sense of hearing.

Indeed. It was more of a rhetorical doubt.

Do you really think there can be an objective answer to a question of the form “why did this NOT evolve in any other animals? All you end up with is circular arguments of the type that are the very antithesis of science. The one answer you have so far just describes the thing and says how wonderful it is.

@David The question is literally "why did this evolve in only one group of animals", and I just got such an objective answer. It's always puzzled me why StackExchange users try to belittle the OP into thinking their question is stupid/too broad/impossible to answer while it clearly isn't that insurmountable.

I think it is worth noting that not all mammals have pinnae (the external component of the ear) – i.e. Australian monotremes and the marsupial mole. Also, props to T-Rex for calling out the online bullying, which is totally unnecessary.

Ear pinnae in Katydid insects to detect bat ultrasounds: https://doi.org/10.7554/eLife.77628

Short answer Mammalian hearing is unique and amazing.
The mammalian ear is unique and highly sensitive with a built in amplification system that means even minute changes in sound can be detected. The bony amplification is also the reason the mammalian (or at least therian) cochlea is huge, every incremental increase yielded markedly more information, it has to get quite large before you hit the point of diminshing returns. This means mammals can get a lot out of even small investments into improving hearing. The vast majority of other groups just would not get any benefit from an external ear. their ears are not sensitive enough to gain anything the faint echoes external ears collect. The one group that would get some benefit (owls), has something functionally similar to an external ear.

The mammalian ear evolved from the repurposing of vestigial jaw bones no other group had (or more correctly they did not become vestigial in other groups). Mammals are the only group with a single bone in the lower jaw. it is a fascinating story and well worth a look. It kinda makes up for how awful mammalian eyes are.

A Lizard would need ears of 8cm to focus it's upper hearing range.
Lizards and birds can hear as high as 4kHz to 10 kHz, which corresponds to an energy wavelength of 8cm to 3cm, so a frog would need ears of about 8cm to collect and focus the sound, and a bird would need ears of about 3cm. Bird calls are also mostly limited to about 8khz, about 1 octave higher than note 88 on a piano.
Also, the distance in between the two ears of i.e. a bird is less than the wavelength of the sound that they detect, so they have less sense of which direction sounds come from.
Cats and mice can hear sound waves of about 0.5cm, so their ears can augment and focus the sound efficienty and can also shield the ears so they just hear one side each.
Soft materials absorb sound, that's why audio speakers use carbon fiber and other rigid diaphragms to transmit high frequencies, and that's why toast has higher frequencies than bread, so mammals had to use the stiffness of articulated bones to pick up high frequencies of sound. It's a complex adaptation step, a bit like the evolution of the eye.
Here is a vid about mammal ears the wiki.
Early mammals were nocturnal, it may be a contributing factor.

The argument on body size / sound wavelength doesn't stand much with large dinosaures, does it?

Yes, it's more likely that a dinosaur could evolve giant ears to amplify and locate sound, especially if it's a nocturnal avian dinosaur. it's the high-frequency limit of a vertebrate's inner ear relative to it's size that influences if it would benefit from ears. Birds and lizards would have evolved ears if they didn't need giant ears relative to body size because their inner earbones are intrinsically limited to big wavelengths. Say a dinosaur has an upper hearing range for 5cm wavelengths, and it had 5cm ears.


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Can I use a basic compound microscope to analyze the ploidy of plant chromosomes?
So, I'm not really any kind of trained botanist. But I do have two things: some dandelion seeds from France, and, collecting dust in my garage along with related accessories, this thing.
Normally, the dandelions growing in an American yard are apomictic triploids, but in Europe there's both triploids and sexual diploids, the latter getting even more common the further south. I'm assuming that, because these French seeds are a specific common cultivar (Vert de Montmagny), that regular sexual selection was used in breeding it, making it a diploid. But I don't know who to ask to confirm this so I may as well do some testing. If it's a diploid, maybe I can do some breeding of my own?
But I don't even know the first step. Are there some parts of a plant that I'll have an easier time finding chromosomes in? What do I put them in to express their DNA and what do they best stain in? Would I even be able to discern the different chromosome shapes without training? I've heard the standard science project way to extract DNA (dish soap, salt, alcohol) damages the chromosomes so that you wouldn't really find them in a microscope; if true I hope there's another way.

If you want mitotic chromosomes then you want to look at apical meristems — probably the primary root from germinating seedlings will be easiest.  Apical meristems are at the growing tips of roots (and shoots) and contain regions of rapidly dividing cells.  Since you can only see chromosomes as separate bodies when they are condensed for cell division this increases your chances of visualizing chromosomes.
However, you will need to stain the roots to visualize the chromatin (material that makes up chromosomes).
This paper has a protocol for staining dandelion root tips, but I don't know whether you can obtain all the necessary compounds.  However, colchicine and para-dichlorobenzene probably aren't really necessary (they will increase the number of cells in mitosis) and are toxic so best to avoid those steps anyway.
Note, it looks like you would also need a 100x oil immersion lens, which doesn't look like it comes with the microscope you listed.
You may also find this paper useful as a starting point for making "homemade" chromosome stains.
Good luck!


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Database of plant morphology
Wondering if there are any open databases out there that specify the branching and flowering patterns of plant species, similar to algorithmic botany book.


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How to get taxonomic tree data
I am looking for taxonomy data of individual species and their classes something like the following format:
{
  "type": "family",
  "parentType": "order",
  "parentScientificName": "hymenoptera",
  "commonName": "ant",
  "scientificName": "formicidae"
}

{
  "type": "species",
  "parentType": "genus",
  "parentScientificName": "...",
  "commonName": "black ant",
  "scientificName": "lasius niger"
}

Basically, from this, you can construct the full taxonomic tree. When looking at the pubmed taxonomy data I don't see how to reconstruct the tree. Please show me how.

I can't leave a comment at the time of writing this (since I don't have enough reputation right now), so I'll leave this as an answer.
Your question is a bit confusing. It's titled "How to get taxonomic data", but at the end of the post, you mention "Basically, from this, you can construct the full taxonomic tree. When looking at the pubmed taxonomy data I don't see how to reconstruct the tree. Please show me how."
I'll try to address both your questions here.
Acquiring the lineage data:
Are you perhaps looking for something like this?
NCBI taxonomy itself is also accessible programmatically via E-Utilities.
Constructing an evolutionary tree:
You could perhaps use something like the data.tree R package to construct your tree using the lineage data.
Your question is a bit too vague, so I apologize if my answer is of no assistance here.


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Cracking sounds made by glowing plankton
Recently I had opportunity to swim in place with glowing plankton, it was amazing experience and it as well gave birth to few questions in my head.
I manged to google that they can glow thanks to chemical reaction called Bioluminescence.
Once submerged I could hear a cracking sounds, are these sounds as well effect of said chemical reaction?
Few more questions I am wondering:
How often can the plankton light up? Do they need to recharge or something?
Do they light up during the day as well but we can't see them because of daylight or do they act depending on how much light is there around them?


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Is there a link between brain's energy consumption and human experience?
I was read the article (in Scientific American Mind)  about energy consumption of brain. There are:

Say you are learning a new skill—how to juggle or speak Spanish.
  Neuroscientists have made the fascinating observation that when we do
  something completely novel, a broad range of brain areas becomes
  active. As we become more skilled at the task, however, our brain
  becomes more focused: we require only the essential brain regions and
  need increasingly less energy to perform that task. Once we have
  mastered a skill—we become fluent in Spanish—only the brain areas
  directly involved remain active. Thus, learning a new skill requires
  more brainpower than a well-practiced activity.

...

Overall, though, on an individual level, our brain adapts and becomes
  more efficient as we gain mastery. We build new connections among
  neurons to keep pace with the greater demand on our neural resources.
  As our skill level grows in a particular area, our brain will
  inevitably require less energy to perform that task.

I tried to check what was written there. I tried to find experienced facts that refute or support this article. I did not find anything.
Question: are there experimental scientific data that show a decrease in energy consumption by the brain, while doing a certain activity, as professionalism grows? Or maybe there are experimental data that show the opposite? Or is there really no correlation between energy consumption and the growth of professionalism?

@user1136 Your comment could (should) be an answer. Answering in comments is discouraged in the SE model because it's not possible to both up and downvote your comment, it can't be accepted as an answer, and because comments are meant to be temporary and can be deleted at any time.


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Do snails like water?
Simply question, do snail show when it's raining because they like it or/and need hydration and food or are they showing up just to escape somewhere, because they're scared of drowning?

Most types of snails survive droughts (that would kill otherwise through Dehydratation) by producing much mucos around themselves. This mucos will dry out if the sun comes up, so they hide under leaves or in the ground. If it's raining, those rings of mucos hydralise or "melt" and the snail begins to crawl. Like most amphibians snail take their oxygen by their skin furthermore they have lungs. By raninning they start moving for searching food, cause they dry out in sun.


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Why do large, aromatic residues prefer beta-pleated sheets?
I read in many journals that amino acids with branched and large aromatic R-groups have higher beta pleated sheet propensities. However, none really go in depth into the significance or reasoning behind this finding. I have made an educated guess based on my findings on alpha helix propensities:
In alpha helices, branched and aromatic R-groups are not favored as the g+ and g- isomers can extend into the helix and interfere with the hydrogen bonding. In beta pleated sheets, however, the R-groups are pointed perpendicular to the hydrogen bonds, and even large R-groups like that of phenylalanine or tryptophan will not able to reach the site of hydrogen bonding. Coupled with the fact that smaller amino acids will rather be more tightly bound to each other (so they prefer helices, e.g. collagen helix, alpha helix, save space, amide hydrogens and carbonyl oxygens closer together), larger amino acids therefore favor formation of beta pleated sheets.
I need a few key pieces of info to really accept my own explanation (if it is correct) as factual. First, I will need proof that beta pleated sheets are more structurally rigid than alpha helices (or else, smaller R-groups like that of alanine and cysteine will also prefer beta pleated sheets). I also kinda want to see the structure of beta pleated sheets with large R-groups to further ground the thought in my head, as I can't really see how R-groups like valine (heavily branched) will not affect hydrogen bonding. As an example, I attach one that I found for alpha helices.

are you familiar with visualization software such as Pymol or VMD?

I have found this image on Biology LibreTexts, and they have answered my question. Like I suspected, the large residues will mainly project out of the beta pleated sheet and will not interfere much with the backbone hydrogen bonds. In alpha helices, however, the branched and aromatic residues are still able to project into the helix (as they are not pointing completely outwards) and disrupt the bonds.
To better visualize it, imagine a foam cylinder and toothpicks poking out of it at an angle. Now imagine the toothpick branches out in all directions (to simulate rotamers). It will poke the cylinder again. Now imagine a flat foam board with toothpicks sticking out of it up and down at an angle. Even if it branches out, it will not ever poke the board again unless it branches backwards (impossible for residues, I reckon).
In beta pleated sheets, aromatic interactions between two aromatic rings might further stabilize the structure. In alpha helices, the residues are pointing away from the helix and therefore not that close to each other; but in beta pleated sheets, they are close enough to interact.
I have also found a viable reason to why beta pleated sheets are supposedly more "rigid" than most other secondary structures. Alpha pleated sheets are really compact and only involve one peptide chain, whereas beta pleated sheets are less compact and include two or more peptide chains, limiting the movement and decreasing the overall entropy.
If you still have trouble visualizing, visit the Biology LibreTexts page and look at their splendid diagrams modelling the secondary structures. They really helped me in understanding it. It is quite elusive, so I'll link it here

This table is from the Wikipedia page for α-helix:

As you can see aromatics are not the worst offenders. In fact, barring proline (whose backbone torsion angles are unsuited to helices), Gly is the worst offender. A likely reason for this is Gly being too flexible i.e. its small side chain H allows it to adopt backbone torsion angles unsuited for α-helix.
As another example let's look at silk, an extended anti parallel β-sheet structure, from libretexts.

As you can see, the small side chains of Ala and Gly in fact allows the β-strands to come close enough to form backbone hydrogen bonds. In fact, from the same reference I quote - "Unlike the α helix, though, the side chains are squeezed rather close together in a pleated-sheet arrangement. In consequence very bulky side chains make the structure unstable."
So it is not entirely true that aromatic amino acids prefer pleated β-sheets.
So what are we missing? We are missing the chemical environment in which the the amino acid residues are placed. Remember, most of the propensity charts we look at are average propensities across known protein structures. In a specific protein, its specific chemical context can radically change the secondary structure propensities.

I am aware of the effects of proline and glycine on secondary protein structures, but didn't find it relevant to the question, but thanks for further clarifying it anyways. Your example of silk is really insightful as well. However, I am still wondering why the aromatic residues have a higher average propensity (through various chemical contexts,  like you mentioned); at least, relatively higher than smaller residues like on alanine, glutamate etc.

Also, I am confused when you say that alanine and glycine allow the beta-pleated sheets to come close enough to form backbone hydrogen bonds. Aren't backbone hydrogen bonds formed despite the residues (excluding proline)? Do you mean the hydrogen bonds will be stronger as they are closer together? In antiparallel beta sheets the amide hydrogen and carbonyl oxygen are pointing directly at each other, so I doubt they will not form bonds even if there is more space in between.

@chematwork The strength of a hydrogen bond depends on the distance between the bond donor and acceptor, electronegativities of the atoms and the angle donor--H--acceptor. So if you have bulky side chain residues in beta sheets (e.g. a benzene ring is around 4 A in length) you can see that they will weaken  hydrogen bonds as the distances between the bond donor and acceptor will increase.

@chematwork — This answer is far better than yours because it exposes the fundamental fallacy of “the average beta sheet” of your question. The average human being has one ovary and one testicle. Alpha helices do allow certain general principles, but the variety of conformations of beta-sheets in proteins, and the variety of their environments preclude all but the most superficial statements. When few structures were known, this sort of thing was all one could say. Fifty years have passed since then.

@David I checked the beta sheet propensities of aromatic side chains and while they have high average  propensities, I seriously doubt a polypeptide of only aromatic side chains will show a tendency to form a beta sheet. Sadly I don't have enough expertise to run MD simulations to check this.

@chematwork  “A polypeptide of only aromatic residues”.  What relevance does that have to real proteins?


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Confusion regarding the Kir2.1 inward-rectifying potassium channel
I was trying to find out more about gustation and the transduction of sourness when I came across the supposed inward-rectifying potassium channel $\ce{K+_{ir} 2.1}$. Here's the thing, despite being inward rectifying, all the articles I read about it involves it sending potassium ions out of the cell. I thought that maybe there is a special mechanism that makes it outward-rectifying, or just switches off its mechanism for inward rectification but to no avail.
So here's the context: On taste buds that detect $\ce{H+}$ ions, when intracellular pH rises due to intake of protons, potassium channels will be closed which causes accumulation of $\ce{K+}$ and thus depolarisation. The article pinpoints $\ce{K+_{ir} 2.1}$ as one of the potassium channels involved, saying that its inhibition will allow for depolarisation. This doesn't make sense to me, if this channel is supposed to prefer intake of potassium ions and almost entirely prohibit outward flow. If we want to accumulate potassium in the cell, shouldn't this channel be left open?
The only thing I can think of is that this channel remains open at membrane potentials near that of resting potential. So maybe then there is no selectivity over which direction the ions travel, so there is a net outward flow?
I'll link some of the articles I mentioned below:
The K+ channel KIR2.1 functions in tandem with proton influx to mediate sour taste transduction
Inhibition of Kir2.1 channel-induced depolarization promotes cell biological activity and differentiation by modulating autophagy in late endothelial progenitor cells.

Short answer
"Inward rectifying" doesn't mean "only allows inward current". Current through inward-rectifying channels can be (and often is) entirely outward in physiological settings.
Explanation
For a non-rectifying channel, there is a linear current-voltage relationship. If you plot current through the channel at various holding voltages, you get a straight line.
For inward-rectifying potassium channels, you get less current as you depolarize, like this:

(from Wikipedia)
At negative voltages, the channel is pretty linear and strongly inward (negative). However, at more positive voltages, the linear trend is attenuated.
However, this relationship does not upset the equilibrium potential for a given ion. For a potassium channel, if you have a cell with a potassium reversal potential that is more negative than the membrane potential, you'll still get an outward flow of potassium ions (in the figure, note all the lines above 0, representing voltages more positive than the potassium reversal potential; they're positive/outward even if they're small). What is different for the inward-rectifying channel is that as you depolarize the cell, the current does not increase the way you would expect it to increase for a non-rectifying channel.
For example, for a non-rectifying channel, you'd expect with a potassium reversal of -90mV, the current would be the same magnitude but opposite sign at -120 mV and -60 mV (30 mV above and below reversal). For a inward rectifying channel, you will still have the same change in sign, but the magnitude will be less at -60 mV than at -120 mV.

its inhibition will allow for depolarisation

Any channel permeable to some ion (or combination of ions) will tend to move the voltage towards the reversal potential for that ion/ions. So, as long as potassium reversal is more negative than threshold, all potassium-only conductances are inhibitory, whether they rectify or not.


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Why can't C1r cleave C4 proteins?
I am researching the complement system, and have ran into something I'm not really sure about. In the past, the C1r2s2 complex was thought to be an 8-like structure tucked inside C1q's collagenous strands. However, this article says that the serine proteases actually protrude away from the core. Originally, it is said the C1s SP cleaves the C4 and C2 proteins because the C1r proteins are hidden in the core. If this new structure is true, however, then the C1s and C1r proteins are close to each other outside the C1q core. If this is the case, what is preventing C4 from being cleaved by C1r instead of C1s? Their serine protease domains should be largely identical.

I have found an answer. The serine proteases on complement proteins actually have very limited enzyme substrate specificity. C1r only has two natural substrates, zymogen C1r and C1s, whereas C1s can only cleave C4, C2 and a few non-complement proteins. This was proven by superimposing the structure of serpins (serine protease inhibitors) with C1r and C1s. This analysis revealed that the access to these substrate-binding sub-sites is severely restricted, compared with digestive serine proteases such as trypsin. The trypsin or chymotrypsin-like pockets were only the primary specificity pockets. The strong preference displayed for Gln residues at P2 and Ile residues at P1 matched those found in physiological substrates of C1r, zymogen C1r and C1s. An example on how these specificity filters work can be seen when we substitute the Gln at P2 with Asn or Gly. To only allow Gln residues, polar or charged molecules will be placed where Gln’s residue’s polar head will be, and hydrophobic residues where the carbon chain will be.  When Asn is substituted for Gln, the shorter carbon chain will cause the polar head to overlap with the hydrophobic residues of C1r, which is highly detrimental for binding. Substituting this with Gly will eliminate the interaction altogether, so it will not be as detrimental, but the stability resulting from the Gln-C1r interaction will be lost.
More information in this article here.

You mean substrate specificity. And to say that an enzyme cannot cleave a substrate because of substrate specificity is saying nothing at all. Just delete your question.

@David I've tried to, but it is not allowing me. So, I'll just try to make my answer a bit better so it can help others.


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Question about osmosis

The concentration of water outside potatoes B and C is  more than the concentration of water inside the potatoes. So water will flow inside the potato. Now, since the concentration of water in the hollowed portions is less, water will move inside the hollowed portion and hence fill the hollowed portion of potatoes B and C. I think since potato D is boiled and hence it's cells are dead it can't perform Osmosis and water does not fill inside the hollowed portion of potato D. Is my reasoning correct ? And I can't get why there won't be any water in hollowed portion of potato A. Is it that the hollowed portion of potato A does not contain any solution so no water would go there and if this reasoning is correct then it implies that osmosis is only possible when there are two solutions with different concentrations and not in any other case ?

Please do not post text as images. It is not searchable or indexed, and cannot be read with accessibility devices.

I’m voting to close this question because it is: 1) an (unlabeled) homework question with insufficient research (e.g. looking up a definition of osmosis), 2) contains text as image (despite the OP being advised against this), and 3) would have been best posted in [Chemistry.SE].

Osmosis is actually taking place between the sugar/ salt solution and the cytoplasm inside the potato cells. Or if you want to expand more on this, then water is flowing first from the water in the trough to inside the cells, and then from the cells into the solution present in the hollow of the potato
Osmosis occurs in cup b and c because the sugar or salt makes a concentrated solution which is hypertonic to the cytoplasm, hence water flows out through partially permeable cell membrane by osmosis.
Cup a is an experimental control. It contains no sugar/salt so it can be proven that it was the concentration difference between the solutions that was causing osmosis. No sugar means no solution, just nothing over there(no water , no sugar, no salt, no solution) so osmosis can't occur.
As far as D is concerned, you are wrong that osmosis requires being alive. Osmosis is a natural passive/automatic process, it can happen in dead things too. It's hard to say what can be causing the osmosis to stop. The best guess would be that boiling damages the cell membranes of the potatoes so that aquaporins(water channels in the cell membrane through which water flows naturally by osmosis) are destroyed. Thus the water can't flow through the damages cell membrane.

Oh! So there must be two solutions separated by a semi permeable membrane for osmosis to occur.


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What kind of shiny bronze beetle is this?

Lots of these on my rosemary bush
About 7mm long

Please provide your location. Thanks.

The plant helped identifying the beetle: This is a rosemary beetle (Chrysolina americana), which feeds on rosemary,  lavender and thyme. See here and here for some more information.


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Why does bed bugs not carry disease?
Whenever I look up this topic, all I get is articles that say "Bed bugs don't carry disease...", but they never explain why?  Is it something in their saliva that kills microbes?  Something in their gut maybe?  When they are crawling over the floor wouldn't it be logical that they would carry microbes, I mean cockroaches do?

It's not entirely true.
For example, a 2014 study demonstrates bed bugs can transmit Chagas disease. From Penn Medicine News:

The bed bug may be just as dangerous as its sinister cousin, the triatomine, or “kissing” bug. A new study from Penn Medicine researchers in the Center for Clinical Epidemiology and Biostatistics demonstrated that bed bugs, like the triatomines, can transmit Trypanosoma cruzi, the parasite that causes Chagas disease, one of the most prevalent and deadly diseases in the Americas.

(I'll update with more details when I get off the road)

When bed bugs crawl about, presumably they must be coming into contact with microbes and then they crawl on humans.  How is it they don't pass those microbes onto us?  With cockroaches they crawl about and transmit those microbes, what is so different with bed bugs?  Is there something on their legs that make the microbes fall off before they get to us or what?

@Travis I would want to be seconded but my guess is that bedbugs don't live in dirty places or rotting substances therefore don't catch a lot of harmful microbes.


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Species Identification

I found this in my hair this morning! Yucko! Please help me identify it. I have tried and tried to no avail.Thanks in advance.

What size is this? And where in the world are you located?

This appears to be an insect head; without the rest of the animal any identification is going to be suspect.


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Is it better to receive a certain dose of radition gradually or all at once?
Suppose you had to choose between getting exposed to 1000 mSv gradually over the next 5 years, or all at once exactly 5 years from now.
Which one would be the healthiest option? Is the probability of having developed a disease like cancer after those 5 years the same in both cases?
Phrased differently: Are the effects of multiple doses of radiation entirely probabilistic and/or cumulative?
Thanks in advance!

The period of time over which a dosage is given matters critically. You probably have experienced this in your daily life. If you are out in the bright, summer, sun for 8 consecutive hours on a single day, you are likely to get a sunburn. If you are out in the sun for a total of 8 hours spread evenly over a month, you're very unlikely to get sunburned.
You body has mechanisms that can repair radiation damage or limit it's effect, but these processes take time. A particularly important processes is apoptosis. A cell can detect if its DNA has been critically damaged, and self-destruct before something else goes wrong. If the exposure is acute, there my not be time for the apoptosis mechanism to take effect before it is damaged itself, possibly transforming the cell into a cancerous state. There is considerable evidence that lower dose rates do give rise to fewer cancers.


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Do lychees cause encephalitis?
In India, there is a recent outbreak of this disease after many consumed lychees.
Many people link this to lychee's "toxins".
I'm not a biology major hence can't elaborate further on this, but here are some links.
Link 1
Link 2
Here is another that claims that lychees must not be consumed empty stomach .
Link 3

There are many articles on this topic (including many intended for laypersons). Did you even try to read the articles carefully, that you yourself mentioned? I'm voting to put this question on hold because I don't even see a question here.

@WYSIWYG the studies are published by the newspapers, which in general shouldn't be considered reputable . I only asked here to verify if there is an actual scientific evidence for this.

Your second link is an article in Lancet, a highly reputed medical journal.


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What enzyme or bacteria could dissolve plastic?
What enzyme or bacteria could dissolve plastic aside from acetone? Preferably, low-cost and environmentally friendly. Any suggestions would be helpful.
I'm targeting for thin plastic (low-density polyethylene). Environmentally friendly for me is that it follows the EPA standards from the USA. I'm targeting for around 150 USD. I'm okay with solvents that make the plastic swell, but a chemical that could dissolve it is preferable.
I asked this on the ChemStack Exchange and I'm not sure if enzymes and bacteria are allowed there so I'm asking here too. Thank you!

You should wait before the [chemistry.se] people decide that it is off topic there before posting to another SE. Don't simultaneously post on multiple websites. If it is indeed off topic there, they can migrate the question here.

Anyway, did you try searching google scholar on this topic?

Yes, I tried, but I found out that Ideonella sakaiensis works, but it digests plastics in 6 weeks. I'm trying to find a more effective way to digest bacteria. Thanks!

@JosephLopez You should include prior research in your question. It would be kind of rude if someone wrote up a whole answer about Ideonella sakaiensis and then you responded "yeah but that takes a long time I'm looking for something better." However, you should also note it seems you are asking for a bit of a holy grail here: an EPA friendly way to quickly deal with one of the biggest pollution challenges of today? Sounds like a Nobel prize, not a SE answer.

Not an enzyme, but D-limonen does a good job dissolving polystyrene. See here for example. It's cheap, and I assume about as environmentally friendly as dissolving plastic can be.

Thanks! Looking into it now with fresh eyes, my tone sounds kind of rude.... Thanks for correcting me! @BryanKrause

Thanks @theforestecologist for the suggestion!


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Fructose vs glucose
I was watching a video on the dangers of fructose and comparing it to alcohol and all of this stemming from the fact that the liver can not break down fructose like it can glucose.  But then I was reading an in depth depiction of glycolysis the first step in glucose catabolism and one of the steps is converting the glucose to a specific kind of fructose so my question is why would our cells convert the glucose to fructose in order to change it to pyruvate if it’s so dangerous?

Fructose as such is not dangerous, but excessive fructose intake can contribute to the development of fatty liver, for example. There are several articles about fructose on Biology, Medical Sciences and Skeptics SE, so you may want to ckeck those first.

I don't have much time now, so only as a comment, which I can make to a full answer later on. Without having seen this video, this is with high likelihood sensationalism without much reason. The metabolism of fructose from dietary sources is almost entirely done in the liver, which can lead to fatty liver syndrome if permanently too much fructose is contained in your diet.

Related: https://biology.stackexchange.com/questions/82478/detrimental-effects-of-fructose-in-fruit-on-the-liver , https://skeptics.stackexchange.com/questions/34808/is-fructose-the-1-source-of-obesity-in-the-united-states-today , https://medicalsciences.stackexchange.com/questions/8681/eating-fruit-is-not-so-healthy , https://medicalsciences.stackexchange.com/questions/19476/is-consuming-fruits-and-veggies-particularly-high-in-fructose-unhealthy

Fructose will be converted to Fructose 1-Phosphate while glucose will be converted into primarily Fructose 6-Phosphate during metabolism. The position of the phosphate determine the pathway used for metabolism.


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Are 2A cleavage sites functional in bacteria?
In mammalian cell lines, 2A self-cleaving peptides are frequently used to for expression of multiple genes from a single transcript. They've got some issues, e.g., leaving some proteins as fusions, but so do all of the other options, so 2As are a pretty good choice for many situations.
I have found 2As being used in many other organisms as well, including yeast and plants, but they seem to generally not be used for bacteria.  I've found a couple of articles (e.g. [1], [2]) that do claim to have successfully used 2A sequences in bacteria. If this actually worked well, however, I would expect to see it much more widely used.
Are 2A sites in fact functional in bacteria and, if so, are there any issues that inhibit their use there?

2A self cleaving peptides do apparently work in bacteria (as the papers in your question suggest), but it seems that they are not commonly used in these chassis simply because they are not needed.
For context, in prokaryotes, translation is initiated by the ribosome binding to a shine-dalgarno (SD) sequence on the mRNA. These SDs can be placed anywhere along the mRNA strand, and so multiple SDs can be present. This means that translation can begin at multiple points along the mRNA, and hence proteins can be co-expressed by one promoter by including multiple RBSs and stop codons within the expression unit (i.e. promoter-RBS-CDS1-stop-RBS-CDS2-stop-terminator).
However, in many eukaryotes, translation begins at the 5' end of the mRNA where the ribosome is assembled, and scans along the mRNA until it finds the start codon. Once the protein has been synthesised and the stop codon reached, the ribosome falls off of the mRNA. This means that if there was another CDS encoded after the first stop codon, it won't be translated.
It should be noted that it is possible for eukaryotes to generate mRNA encoding multiple proteins, but as it was assumed for a long time that this was unique to prokaryotes, there is less research for this in eukaryotes. This paper has some useful information: https://academic.oup.com/femsyr/article/2/2/215/536601.
Because of these differences, for most applications, if co-expression in bacteria is required it is much simpler to add in multiple RBSs and stop codons than to rely on something like 2A peptides which, as you mentioned, do not always work and can result in fused proteins. However in eukaryotes, techniques such as 2A peptides are important considerations for co-expression as poly-cistronic mRNA (mRNA encoding multiple proteins) seem to be much less common.
This doesn't mean that there aren't applications for 2A peptides in bacteria, but they are much more specific and hence their use doesn't turn up so much in the literature.
These wikipedia pages have some good reading and references:

https://en.wikipedia.org/wiki/Internal_ribosome_entry_site
https://en.wikipedia.org/wiki/Eukaryotic_translation

Disclaimer: I don't work with eukaryotes so most of the information about gene co-expression and how common it is has been gathered from reading for this question.

Very interesting, thank you! This is the opposite of what I was guessing, given my past experience where eukaryotic techniques don't work in bacteria because bacteria have a more constrained toolkit.

A potential advantage of 2A peptides over multiple RBSs is that the former ensures a 1:1 ratio between the resulting proteins.
Also note that 2A peptides are not actually cleaving the peptide chain (i.e., there is not proteolytic activity involved). "Cleavage" is instead the results of ribosome skipping.


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Is there any problem with using a single stop codon with a single CDS in prokaryotes?
All protein coding sequences in the iGEM Registry are supposed to end with a double stop codon. Presumably, this is to decrease the potential for read-through, which could be problematic if one is putting together a polycistronic design.
If the design is intended to have only one CDS, however, and is targeted at a prokaryote (which have "backup" ribosome release mechanisms), then is there any problem with using only a single stop codon?

The impact of any read-through from a leaky stop codon in an expression unit with only one CDS would probably depend on a few things, mainly (i) where is the next in-frame stop codon, (ii) what are you trying to express, and (iii) how leaky is the stop codon?
In cases where the next in-frame stop codon is only a few base pairs away, there would probably be little impact, however in other cases the next stop codon could be far away. In these cases, there are two things which may cause an impact.
The first is that a long peptide sequence could be added to your protein, which depending on what you are expressing, may cause your protein to misfold or lose functionality.
The second is that you could get ribosome stalling, especially if any of the codons between your stop codon and a second stop codon require rare tRNAs. As you mentioned in your question, there are mechanisms for rescue in these scenarios, however if your CDS is expressed under a strong promoter on a high copy number plasmid, this mechanism may need to be mounted much more often than usual and cause burden on the cell. I should note that this is speculation on my part as I can’t find any studies which have shown this.
The actual impact any of these scenarios may have on your system would likely be strongly dependent on how leaky the stop codon actually is. As there are many examples of constructs which use only a singe TAA in their design with no apparent negative affects, presumably under ‘normal’ circumstances there is little risk to using a single stop codon.

I found an estimate of read-through in at least one gene being approximately 4%, which seems pretty high! https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5133446/

If there is only one CDS, presumably there will be a transcriptional termination directly after the CDS (after the stop codon actually), which makes any read-through coming from using a single stop codon almost negligible.

Is there any issue with ribosomes getting stuck on the terminator?

Actually, somethings we tend to forget in prokaryotes are: 1. in general there are many ribosomes translating at the same time, the same mRNA. 2. Ribosomes start to translate directly on the nascent mRNA, as RNAP is transcribing.

What about on the other side? Can they get stuck on the end?

Perhaps I could add for eukaryotic systems which terminate all stop codons by a single protein, eRF1, this study by Schmied et al., showed readthrough of all stop codons to be less than 0.2% by wild-type eRF1, which seems acceptably low! I am unsure how this would transfer to prokaryotic systems which diverges in its use of two release factors - RF1 and RF2. I would of thought termination by UAA which is shared by both factors would be quite stringent.


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Measuring luminescence in a fluorescence plate reader
We're considering organizing some interlaboratory work on calibrating luminescence reporters (e.g., luciferase), and one of the key questions I don't know the answer to is whether most plate readers can measure luminescence or not.
From a first principles perspective, any fluorescence plate reader ought to be able to measure luminescence as well - just don't turn on the excitation light source. Thus, I would expect that a typical fluorescence reader should also be able to measure luminescence.
On the other hand, searching online, I am swamped by manufacturers eager to sell me specialized luminescence readers that emphasize their sensitivity, which leads me to think that maybe typical fluorescence plate readers can't measure luminescence.
My question, then, is this: should I expect that a typical current fluorescence plate reader will also be able to measure luminescence, or is this a much more specialized capability?

As the other answers here say, technically plate readers which are capable of fluorescent measurements can also make luminescent readings, but the sensitivity may be low (https://www.biotek.com/resources/technical-notes/use-of-the-fluorescence-optics-to-measure-luminescent-reactions-in-high-well-density-microplates-measuring-luminescence-in-1536-well-microplates/).
What I haven't seen mentioned is that there is potentially another hardware limitation depending on what type of luminescence you're using. Broadly there are two types: glow and flash luminescence.
Glow luminescence is probably most similar to fluorescence in that it builds gradually and can remain stable over an extended period (think of a lightbulb being turned on and warming up). Flash luminescence, however, is much more transient as the name might suggest. Reactions which cause flash luminescence produce a short burst of light (which could last seconds to minutes) which is typically brighter than that produced by glow luminescence. (https://www.bmglabtech.com/what-is-the-difference-between-flash-and-glow-luminescence-assays/)
As some flash luminescence assays will only produce a signal for a few seconds after the reagent is added, it is important to have immediate measurement, which can be provided by using auto-injectors within the plate reader. (https://www.biotek.com/products/detection-flash-luminescence-technology.html) These may or may not be included in a plate reader dedicated to fluorescent readings.
So to summarise, while luminescence can be measured by plate readers which can measure fluorescence, the sensitivity may be too low. In addition, extra hardware requirements, such as auto-injectors, may be required for certain luminescence assays.

Do you know if luciferase is flash or glow? I'm guessing it's glow, since otherwise it wouldn't be so popular, but I hadn't heard of flash before your answer.

It depends on the type of luciferase and the reagents/conditions used. I know from experience that bacterial luciferase (the lux operon) can produce a stable signal in vivo. There are luciferase assays using firefly luciferase for both flash and glow (https://www.thermofisher.com/order/catalog/product/16174 and https://www.thermofisher.com/order/catalog/product/16176)

Fascinating --- I didn't realize there was so much variety in luciferase.

I am René Inckemann and  I am PhD student at the Max Planck Institute in Marburg, Germany. In my PhD I am using luminescence on a regular basis and I was also responsible to organize some of our Platereaders.
So therefore I can tell you that you need a Platereader which is able to measure luminescence and you can not simply take a fluorescence platereader. The hardware for measuring luminescence and fluorescence is different.
However many Platereader models in these days already come with both options for the hardware, which means that you can measure luminescence and fluorescence in the same device. You just have to check your platereader model if it is capable of measuring luminescence.So you don't need a seperate platereader just for luminescence, but you need one, which has the luminescence addon installed.
Regarding your idea for normalizing luminescence, I also have strong interest in that and we have already started working on that. Maybe we can exchange ideas at some point?

Do you know if the hardware difference is primarily about sensitivity, or something else?

Anecdotally, all of the fluorescence capable plate readers that I have used have also been luminescence capable (BMG and Tecan models).
If access to luminescence capable plate readers is restrictive, we have also been able to measure luminescence using a GelDoc designed for imaging electrophoresis gels. This may be something to explore since I imagine gel imagers are more widespread that plate readers.

A priori what you say about the fluorescence and luminescence readers is correct,  even wikipedia states this directly:
Luminescence detection is simpler optically than fluorescence detection because luminescence
does not require a light source for excitation or optics for selecting discrete excitation
wavelengths.

However, it is worth comparing the fluorescence and the luminescence devices sensitivity and saturation threshold. It might well be that a luminescence device, designed to detect very weak levels of luminescence is blinded (i.e., saturated) by stronger light. What is more relevant to your case, the detectors in a fluorescence device might be insufficiently sensitive for practical purposes of luminescence study.
Still, it is better to consult a real expert before spending money on a new piece of equipment.


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Can I do an MS in biotechnology after a bachelors degree in chemical engineering?
I recently graduated from high school and now have to make a decision about my undergrad major. I am interested in biotechnology but my parents suggested that I should opt for a broad based degree and then specialize in my field of interest in grad school. So I read up about chemical engineering and I think it would be an interesting major, but my real interest probably lies in biotech.Is it possible to transition form chemical engineering to bio-related fields in grad school?

This will probably to a high degree depend on the (exact) curriculum and prerequisites of your chosen bachelor and master.
Also note that I'm not from the US and judging from the terms you are using, it seems that you are, so everything I say is also a bit speculative.
In general biochemistry and to some degrees also biotechnology will have a lot of overlap with many aspects of chemistry (or at least organic chemistry). Depending of the focus of each program this might, make it possible to switch over from one to the other. One thing you will definitely not learn in any chemical mayor is molecular biology, which may well be a requirement for studying in any biotech related field later on.
If both your majors focus more on the technological aspect and less on the biological or chemical you should probably be fine. The equipments used in (modern) biology and chemistry is in many cases similar, though biotech involves more equipment specialised for the handling and analysis of cells. The underlying principles are still the same though.
In your case I would recommend you to check the requirements of different MS or grad schools, that you'd be interested in first, and the see if you can meet these with a chemical engineering mayor (and maybe/probably some added courses like molecular biology).

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


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How atom works and it's different from DNA?
I am studying atoms recently because I am writing a short story and the characters would talk about it for a bit. And I wish it's scientifically accurate.
So I read a lot of articles about the atom and here is something that I saw:

Around three-quarters of a human body is water, made from oxygen and
  hydrogen atoms. These atoms, along with all the others in the world,
  have been around for eons, shifting through any number of organic and
  inorganic processes, or simply hanging about in the atmosphere.
  Anybody could have some oxygen or hydrogen atoms in their constitution
  that had once been part of Einstein, Elvis Presley or Mother Teresa.
  On the other hand, an atom could have once been part of a decomposing
  piece of rat offal.

So, if I really got some atoms of Einstein, it doesn't work like DNA which I might have curly hair right?
Thanks!

If you recycle plastic or metal then does it mean that it will retain the properties of the the object that it had been in the past? Think about it. I don't want to be dismissive but your question is super elementary! You must do some reading on your part before asking others.

you should probably read what is DNA, this should clear things up

DNA is a complex molecule which contains the genetic information. DNA, just like any other molecule, is made of atoms. However, the atoms themselves do not contain any genetic information.
To be more accurate, DNA is made of a double strand (themselves made of atoms) and among those two strands are a succession of elements that we call nucleotides. The 4 four possible nucleotides; Adenine, Thymine, Cytosine and Guanine (usually, just called, A,T,C and G). Nucleotides are simple(-ish) molecules. The genetic information is in the succession of four nucleotides. For an analogy, consider the nucleotides to be letters and the succession of letters make words and sentences. The letters themselves don't hold information but their succession does. For example, the letter "r" in itself does not have much meaning but it is essential for the sentence "The door is red" to make sense.
So, whether one of the atom found in a given nucleotide (or anywhere else) has been in Einstein's body or not, does not change anything in your genetic information.


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what is the name of this fish?
]2
fishes are of length 2 to 3 inches.

Welcome to SE Biology. Tank fish are pets so I suggest you search the Pets SE for an identification. There's little biological interest in pet identifications, if you want to leave this question here adding geographical information may avoid some downvotes.

Looks like Jewel Fish, a cichlid that has been kept for a long time. Hemichromus bimaculatus , native to west Africa a bit different from "African Cichlids" which are from east Africa. Source : Exotic Aquarium Fishes by W. T. Innes ( the guy neon tetras are named after), 1937 ; But I don't think you can find it online .


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How is there no limit to a human lifespan again?
It's probably just misconstrued pop science, but I thought a read an article recently that said there's no known limit on how long humans can live. I could have sworn though that there were a few automatic processes that took place though, like that the chromosomes all shorten in length every time they're copied (is there any limit to that? Also, why does that matter?), the retinas in the eyes harden, the metabolism slows down, the heart muscles wears out, etc.
So, how could it be true?

I'm not sure this is a very informative question without the original offending article.
Specifically I think the key is known limit. We here of people living to increasingly long lengths these days, and with regenerative medicine, this could go on for some time. We don't, and probably can't, know a definitive maximum age currently - even if one exists.

The quote is something akin to "ageing is plastic, and not a natural law". However, without the source material, it's hard to know how to answer this question. This video on ageing from one of my lecturers at undergrad might interest you.

Mm, no, it doesn't matter what the source material is here. It's a typical scenario, so if someone actually is accredited they will have the knowledge to speak to the phenomena either way, the same way a physicists doesn't need reference material if someone asks "are energy and mass really equivalent?"

You're probably reading about the recently-published responses to a publication that argued there is a limit to human lifespan.
The original article is Evidence for a limit to human lifespan, and in the June 29 issue of Nature there are five responses to it:

Contesting the evidence for limited human lifespan
Many possible maximum lifespan trajectories
Is there evidence for a limit to human lifespan?
Questionable evidence for a limit to human lifespan
Maximum human lifespan may increase to 125 years

Each of these responses has, in turn, a reply from the original authors.
The arguments turn on fairly intricate details of statistical analysis and database interpretation, and I think it's fair to say that outside experts remain unconvinced either way -- neither the original article, nor any of the five responses, nor any of the five responses to the responses, presents a slam-dunk case for or against a limit to human lifespan.

"It's therefore pretty pointless to discuss mechanisms how lifespan may or may not be limited, since it's entirely unclear if lifespan is limited and that's not likely to change in the near future." - You might reword this to make clear you are talking about the context of this particular question. Understanding whether lifespan is limited from a research standpoint will almost certainly involve understanding the mechanisms first.

I've removed that paragraph until I think of a better way to phrase it

There will be no "limit" to human lifespan, if for humans the "survival function" $l(x)$- the probability, for all subsequent ages $x$, that a newborn will still be alive at age $x$ - never hits $0$, but only asymptotes towards it. (The survival function is estimated by the fraction $l_x = \frac{N_x}{N_0}$, of a group of newborns, who in a cohort study are seen to still be alive at age $x$. For finite cohorts the fraction surviving of course will eventually hit $0$, when the last member dies, even if the idealized survival function does not.)
This is the case for "Gompertzian" survival functions, where $l(x)$ decreases super-exponentially, rapidly approaching but never hitting $0$.
(Gompertzian survival functions are more usually described in terms of their age-specific, instantaneous relative rate of decrease [the survival function's slope at age $x$, divided by its height at age $x$, times -1], which is also called the hazard rate or force of mortality $\mu_x = - \frac{{N'}_x}{N_x}$. For Gompertzian survival functions, the force of mortality grows exponentially with age.)
Human survival functions are roughly Gompertzian throughout most of adult life, although the force of mortality's growth may decelerate in very late life.

This type of logic doesn't apply to this problem. I agree with the responses in @iayork's answer that the original paper has some flaws, but you can't just say "because this model applies at ages we have observed, therefore this is true."


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Are penguins plantigrade or digigrade?
I'm trying to rig a 3D model of a penguin, but I don't know where to put the bones near the ankle because I can't tell if they're digigrade or plantigrade. Nearly all birds are digigrade, but penguins spend a lot of time walking and don't generally grasp or run with their talons.

Plantigrade.

The penguins are highly specialized for their flightless aquatic
  existence. The feet are located much farther back than those of other
  birds, with the result that the bird carries itself mostly upright;
  its walk can thus be described as plantigrade (i.e., on the soles).
  The sole comprises the whole foot instead of just the toes, as in
  other birds. The most notable characteristic of the group is the
  transformation of the forelimb into a paddle. This is accompanied by a
  body morphology particularly adapted to movement in a liquid medium.
  The thoracic (rib) cage is well developed, and the sternum bears a
  pronounced keel for the attachment of the pectoral muscles, which move
  the flippers. The flipper has the same skeletal base as the wing of
  flying birds but with its elements shortened and flattened, producing
  a relatively rigid limb covered with very short feathers—an ideal
  organ for rapid propulsion. The body plumage likewise consists of very
  short feathers, which minimize friction and turbulence. The density of
  the plumage and the layer of air that it retains provide almost
  complete insulation of the body.

https://www.britannica.com/animal/penguin#ref3467


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How do plants store energy by potassium battery?
Plants have a so-called potassium battery system for energy storage/conversation. Wikipedia only has a reference to a technical article. Can someone explain it in a layman's language (or refer to a non-technical article)?

Oof, I'm not much of a fan of that Wikipedia article's segue to a "biological potassium battery" since the mechanism and purpose is totally different. The cited article is fine but the summary in Wikipedia is taking a statement in the article way too literally.

@BryanKrause I guess that wikipedia page is not properly curated. It also says that Prussian Blue is a potassium compound (it is Fe₄[Fe(CN)₆]₃)

@WYSIWYG Good catch, I hadn't really looked at the quality of the rest of the page. Yet another reminder to be a bit careful with Wikipedia...

I'll give it a layman's attempt in sort of an "ELI5" approach. I hope the analogy isn't too simplistic, and please don't take it too literally.
How do plants use K+?
Plants control K+ concentrations and do work within the plant by pumping K+ between different compartments. Because water tends to follow solute concentrations (osmosis), plants can do things like suck in water simply by moving potassium around.
(note: animal cells do something similar: this is how your nervous system, kidneys, digestive tract, and other cells/organs perform their functions, but using different ions or combinations of ions)
Analogy to some human activities
Moving all this K+ around takes a lot of energy. Creating a concentration gradient is a lot like pumping water uphill: you put some energy in, but you are storing that energy as potential energy for the water flowing back downhill, or the ions flowing back against their concentration gradient (or water flowing the other way). But normally, plants use this as a way to spend energy to do useful things, rather than a way to store it. It's like they are pumping the water up the hill and then floating useful ores or lumber on a boat as it flows back down the hill.
What is actually happening that Wikipedia describes as a plant "K+ battery"
The article cited on Wikipedia, though, Gajdanowicz et al 2011, shows that sometimes plants take advantage of the mobility of potassium ions to assist the H+ ATPase that is another form of energy storage. Plants use H+ (proton) concentration gradients similarly to how they use K+ concentration gradients, but they are used to power different processes in the plant. Sort of like two different types of batteries.
Return to the analogy, and why this is useful to the plant
Normally both H+ gradients and K+ gradients are powered by ATP, which is indirectly produced via photosynthesis: think of it like the plant's coal-fired power plant. Converting K+ concentration gradients to H+ concentration gradients would be like using the water you pumped up the hill to power a hydroelectric plant that is charging a car battery. The benefit for the plant is that, because K+ can be easily moved around, the plant is able to power those hydroelectric plants anywhere around the hill, and that can be advantageous if a particular part of the plant is low on other sources of energy.


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Why is AMR not widespread?
we know that resistant strains (MDR, XDR, PDR) have arisen in single incidents around the globe but why are these bacteria not common and not spreading quickly as humans keep using antibiotics and killing the non-resistant strains which these Amr strains have to compete for resources. One might say that they ARE spreading but my question is why is the increase in population so slow. compare it with malaria parasite 'plasmodium' which despite being a higher organism with slower reproduction cycle kills so many.

@iayork answered your question perfectly. May I suggest you mark it the answer, or clarify your question. See: https://biology.stackexchange.com/help/someone-answers

Natural selection is environment-dependent. A mutation that makes an individual more fit in one context, might make it less fit in a different context.
The mutations that make bacteria more fit in an environment where they're exposed to antibiotics generally make them less fit in a "natural" environment where they don't have to deal with antibiotics. That means that MDR bacteria are often out-competed by their less-resistant competitors, unless they're in the "right" environment for them, such as a hospital or an infected, antibiotic-treated patient.
Some references:

Barnett M, Busby SR, Mitchison DA. Tubercle bacilli resistant to isoniazid: virulence and response to treatment with isoniazid in guinea-pigs and mice. Br J Exp Pathol 1953; 34:568–81.
urgos M, Deriemer K, Small PM, Hopewell PC, Daley CL. Effect of drug resistance on the generation of secondary cases of tuberculosis. J Infect Dis 2003; 118:1878–84.
Davies AP, Billington OJ, Bannister BA, Weir WR, McHugh TD, Gillespie SH. Comparison of fitness of two isolates of Mycobacterium tuberculosis, one of which had developed multi-drug resistance during the course of treatment. J Infect 2000; 41:184–7.
Gagneux S, Long CD, Small PM, Van T, Schoolnik GK, Bohannan BJM. The competitive cost of antibiotic resistance in Mycobacterium tuberculosis. Science 2006; 312:1944–6.
Li Z, Kelley C, Collins F, Rouse D, Morris S. Expression of katG in Mycobacterium tuberculosis is associated with its growth and persistence in mice and guinea pigs. J Infect Dis 1998; 177:1030–5.
Middlebrook G, Cohn M. Some observations on the pathogenicity of isoniazid-resistant variants of tubercle bacilli author. Science 1953; 118:297–9.
van Soolingen D, Borgdorff MW, de Haas PE et al. Molecular epidemiology of tuberculosis in the Netherlands: a nationwide study from 1993 through 1997. J Infect Dis 1999; 180:726–36.

In addition, the M. tuberculosis complex, except for M. canetti, had lost the ability to do horizontal gene transfer. Resistances thus arise by point mutations or indels, a comparatively slower route than in other species of bacteria.


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Why are fungi and algae microbes?
Both fungi and algae have very small cells but so do most animals. Yet both of them are visible to naked eye just like other organisms.
Why do we call them as microorganisms then ?

Not all fungi and algae are considered microbes, just the unicellular ones.

Because both of those produce single-cells able to viably survive and grow on your own. For example, take a fungal spore and it can grow into a full fungus given enough food. I assume algae cells are the same way. In a single-cell form, fungi and algae qualify as self-sufficient microbes.
Animal cells are typically specialized and dependent on a support framework. Usually, a single animal cell left out on its own is largely doomed.

And egg is an animal cell and usually left out in case of reptiles and mammals

*avians ..not mammals /sorry

Most eggs need to be tended to regularly, watched over, kept warm, or placed in a specific environment, which arguably serves as a "support framework"


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How valid is the theory of human's chimp-pig origin?
Edit: I have also asked the question on skeptics.stackexchange.com and it has been answered there. Here is the link.
There is a person called Dr. Eugene McCarthy who has a theory that the origin of humans come from pig-chimp hybridization (online article about his theory). How acceptable is his theory in comparison to the other common theories?

Welcome to Biology.SE. This question would be better on-topic on skeptics.SE.

As an evolutionary geneticist, I have never heard of such hypothesis and it sounds like a non-sense, silly joke! Note that the article you link is NOT a peer-reviewed paper and therefore does not make any contribution to our knowledge (but it is good that you linked it). If you ask your question on skeptics, they will likely trace back the origin of this (a priori) myth and debunk fake evidence (if any).

To further @GerardoFurtado, theory in science means a hypothesis (or a set of hypotheses) that is very highly supported by tons of evidence. In popular language however, theory is often used as a synonyme of hypothesis.

Note that this so-called  Dr. Eugene McCarthy does not seem to have ever published anything on the subject and is not associated to any university or other recognized institution. It is possible that this person does not even exist!

I have read part of the linked article. It really makes no sense whatsoever and as @iayork said, it is unclear what must be debunk as there is so little that make any sense in any way! But again, on Skeptics.SE they will probably do a better job than we want to here on Biology.SE

This guy is so unsure of himself that he feels the need to spread random tweets and quotes from supporters throughout his work, as if science was some sort of popularity contest where the most Facebook "likes" wins.

While the article referenced in this question is patently ridiculous, I don't see how this question is off topic here, even if it is in fact on topic on Skeptics SE. This seems like a perfectly reasonable question here.

The post has been opened (and answered) on here on Skeptics.SE.

@Remi.b Should I remove the question here or it's OK?

It is now on hold anyway. I think the best would be to add the skeptics.se link at the top of the post (saying the question has been answered there) and leave the post as it is. Thanks

Briefly, the "theory" makes no genetic sense. Pig and human genomes have both been sequenced, and their sequences are completely incompatible with this model.
The "theory" is completely idiotic in many other ways -- debunking it almost becomes difficult because there are so many ways it fails to make sense -- but the genetics alone make it impossible.

It is not always easy to say this with full force in natural sciences, but: NO, this theory is NOT true, probably not even by any means. Extraordinary claim require extraordinary evidence. But wow, there is NO evidence AT ALL for this claim.
Before tackling the main point, I give a side note that would actually be sufficient to not be concerned with the argument itself: Extraordinary evidence is rarely (if ever) presented (i) by single people's research (rather then by a really large body of evidence provided by several independet reseearch groups, different lines of arguments, ...) and (ii) outside of peer-review high-quality journals. For example, you do not report major findings on your dubious website relating to a reference like this:

To cite this publication
  McCarthy, E. M. 2013. Mammalian Hybrids. www.macroevolution.net/mammalian-hybrids.html (Add access date).

However, I would also adress one actual issue. For the sake of argument, I consider the claims to be just as valid as any other claim I ever heard based on morphological features (and with that I do not say that anatomical comparsions in general are nonsense. Au contraire, I believe that these comparisons are important to reconstruct evolutionary histories, especially but not only in extinct organisms where DNA comparison is not an option).
In extant animals (like humans), however, anatomical and genetic comparisons tend to converge and/or the anatomical evidence is adjusted to insights gained from genetic comparisons (meaning that anatomical similarities supporting the findings of genetic comparisons are found really often. Do I provide a citation for this? No, there are thousands or even millions. This is SO well-known that any journal probably accepts this as common textbook knowledge and does not even ask for one).
Long story short: There is NO genetic evidence AT ALL that indicates a mixed descendence of humans from chimpanzees and pigs (wow, I would never had thought, I would write a sentence like this, ever in my life). Additionally, there is NO anatomical evidence for that mixed descendence AT ALL apart from McCarthy (2013) - haha.
PS: I posted a corresponding answer to the skeptics.SE question as well.

both Suidae and Primates  like every creature on earth have a common ancestor in history , but they are simply too different to breed together .
Therefore the theory makes no sense , unless it uses pig and chimp in a metaphoric sense .


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Why did we evolve to control our breath?
I had this question in my mind and tried to think of why we would evolve to be able to control our breath. I remembered the Aquatic Ape Hypothesis, which makes a lot of sense and would explain it, though it is not a confirmed scientific theory (but that is another topic).
I also found this question, but it has not been answered properly. A Google search hasn't given me much either.
So my question is, what is the current scientific thinking on this topic (if there is one)?
edit I know that the Aquatic Ape Hypothesis is not a scientific theory. I did not ask anything about it, I only brought it up because it came up a lot when I was looking for an answer to my question. I do not want "maybe this is why it evolved", I was more interested in some creditable scientific paper or something similar.

The aquatic ape theory is a complete conspiracy. Even the link you provided debunks it. I would ask simply "What advantages does holding your breath provide?" and I imagine answers would be along the lines of "stops breathing through smoke or smog, quieter than breathing, allows water crossings of rivers and lakes" (probably others I have missed). I'm not sure whether you're asking for these things, or an tree of life node at which we can pinpoint breath holding with different functions appearing and disappearing.

Speaking is part of the things we do thanks to controlling our breath. Note also that other mammals are also able to vocalize and therefore there are good reasons to think that this is unrelated to recent hominid evolution. In any case, the aquatic ape theory is not a theory but a hypothesis (see here for semantic) that is for the moment supported by very little to no evidence.

@James 'conspiracy' is a bit strong, isn't it? It's popular with some non-scientists but has never been accepted as a credible or useful hypothesis by the scientific mainstream due to fundamental flaws. (For anyone interested in the idea and some of its flaws, the Wikipedia page on it is actually quite good: https://en.wikipedia.org/wiki/Aquatic_ape_hypothesis).

It should also read "hypothesis" and not "theory". A theory in science is a standing theoretical building with the possibility to prove it.

@matthias-schreiber Don't worry, I realised you weren't proposing the AAH and I think you were absolutely right to mention it given the context. If you hadn't someone else would have!

I some time ago read that it has to do with both bipedal movement (allowing the decoupling of step and breath anatomically), endurance running which seemed to be important in our ancestors, and the evolution of language (in which the production of phonemes, in fact, is not possible without controlling breath). I cannot find the source, though, so I will not make this into an answer.

I'd take a look at mammalian dive reflex... humans have a much weaker response than aquatic mammals, so it is quite possible that this is also seen in other apes as well. And that may be a good reason to need to evolve breath control, to do what no longer comes reflexively. It could also be a fact of our consciousness over the biological processes that are occurring inside of us and we have an idea of cause an effect that other animals may not. If I hold my breath I can get the juicy oysters underwater...   master it and you eat better and survive to reproduce and well natural selection.

It is also very difficult to form an evolutionary argument surrounding a behavior, especially if the environmental pressure than led to it occurred hundreds of millennia ago. And if you want credible scientific articles, then learn to use resources like PubMed, Academic Search Complete, not Google. Even Google Scholar can be a bit iffy.

A lot of mammals can control their breathing, dogs for instance can also hold their breath. Basically anything that can vocalize can control its breathing.

From the abstract of MacLarnon & Hewitt, "The evolution of human speech: the role of enhanced breathing control", Am J Phys Anthropol. 1999 Jul;109(3):341-63:

Evidence presented herein shows that modern humans and Neanderthals have an expanded thoracic vertebral canal compared with australopithecines and Homo ergaster, who had canals of the same relative size as extant nonhuman primates. Based on previously published analyses, these results demonstrate that there was an increase in thoracic innervation during human evolution. Possible explanations for this increase include postural control for bipedalism, increased difficulty of parturition, respiration for endurance running, an aquatic phase, and choking avoidance. These can all be ruled out, either because of their evolutionary timing, or because they are insufficiently demanding neurologically. The remaining possible functional cause is increased control of breathing for speech.

It would be nice to see some explanation for any downvote -- I'll try to improve the answer if possible.


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Prevent clumping of bacteria in my media so that I can measure turbidity?
Forgive my naivety, I'm an undergraduate Chemical Engineering student doing research this summer into growth rates of various combinations of bacterial isolates.
I have about 9 isolates from a toxic leachate, and I am looking into finding combinations of these 9 isolates which degrade the leachate the fastest. I have also have the general consortium of what was growing in the leachate.
I am trying to compare the growth rates of my isolates (and combinations) to this growth rate in order to demonstrate some increase in treatment efficiency. (The idea is that a faster growth rate in the leachate demonstrates a faster breakdown of the leachate)
My current way of measuring growth is to fill a 96-well plate with some known volume of leachate and inoculate the appropriate isolates into the appropriate wells. This is my community matrix. Then I run my plate reader (TECAN) for 72-hours in order to measure the turbidity change over time, as an indirect measure of leachate breakdown.
The problem is that many of my isolates and combinations of isolates, including the consortium clump when they grow, meaning that the plate reader I am using does not measure the growth the way I'd like it to.
Here is an example of a good growth curve of Brevundimonas diminuta growing in my leachate, which I consider good:

Here is my "growth curve" of my consortium, the bacteria have a tendency to clump here:

Essentially, I am asking if there is a way for "force" my bacteria to grow in a planktonic fashion?
More information:
These are my isolates:

Brevundimonas diminuta
Streptomyces sp.
Lysinibacillus sp
Alcaligenes sp.
Pseudomonas sp.
Pseudomonas fluorescens
Paenibacillus sp
Pseudomonas fluorescens
Stenotrophomonas chelatiphaga

These and the consortium grow the way I want them to in M9 salts supplemented with acetate, all planktonic, and measuring their growth in that is very easy, but I want to demonstrate a growth curve in my leachate. I don't know a way to do this on a scale which the 96 well plate reader allows me to do. I can get 32 different combinations out in a single plate if I grow them in triplicates.
A post-doc has been trying to measure a decrease in ammonia flourescence in the plate reader, but has had less luck than me.

Have you tried to see if light vortexing of the plate will break up the clumps? Pipetting up and down often will provide enough shear stress as well.
Lastly, you could sacrifice the experiment at different time points, and do a high speed centrifugation to pellet the bacteria, and remove the liquid to another 96 well plate to read on your plate reader.

@akaDrHouse Yes. The plate reader shakes the plate over the 72 hour reading period, but clumps still form over that time. I pipette up and down when inoculating in order to break up whatever clumps there may be too.

Good question. Some bacteria would grow that way in certain media. By preventing that you would essentially be disrupting their growth. You can possibly adopt a different method of growth estimation. Perhaps you can measure glucose consumption but even that would not be very accurate. Growth dynamics is not always straightforward.

@WYSIWYG Thank you for the suggestion, the problem is that glucose is not the carbon source in my leachate. It's likely a bunch of aromatics.

Well, if the idea is that a faster growth rate in the leachate demonstrates a faster breakdown of the leachate, then why not just measure the components of the leachate? If the composition is not fixed or if there are many components then the task would be difficult. Alternatively, you can image the plates at different time points and analyse the images. You may have to develop an algorithm to differentiate between the bacteria as each would behave differently. For example, cell-1's growth may be measured using turbiditty whereas for cell-2 the size of the clump should be measured.

If your carbon source is a bunch of aromatics, then UV fluorescence may be used to measure their concentration but this will require a lot of standardization.

@WYSIWYG yes, I've mentioned that they do not clump in M9 salts and acetate minimal media. Unfortunately because im using an automated plate reader, the measurements can only be absorption/scattering/fluorescence. And also the leachate is not very well defined. Different bacteria will break down different components of the leachate, and so I think measuring the change in concentration of these components (even if I knew what they were) would be very difficult.

Let us continue this discussion in chat.