What kind of beetle is this? I live in Denmark, Europe and I found this insect wandering around in my garden the other day. It's some kind of beetle, but I don't know what kind it is or the species. The beetle could also fly and had red wings beneath its armor.

Help would be much appreciated. Thank you.

As @Ilan wrote, this is a Cantharidae but most probably Cantharis fusca, which is very common species in northern Europe. Cantharis rustica is similar but has reddish femurs and the black spot is more centered on the pronotum. It is not C. lecontei, which is a North American species.

If you go looking at flowers of Anthriscus sylvestris for an hour or two, you will most likely see at least Cantharis fusca, Cantharis rustica and Cantharis obscura - they are all very common in Scandinavia during early spring/summer. The larvae of all these species live on the ground/in plant litter as predators.

Cantharis fusca

Cantharis rustica         .................... Cantharis obscura


Where can I find historical data on world-wide ecology parameters? I hope this is the right StackExchange forum for such a question.

I'm looking for large data sets on world-wide ecology parameters, such as annual temperatures by latitude, annual rainfall, CO₂ and O₂ concentration in the atmosphere and in the oceans, data about the insect population, plants, algae, and so on.

Is there any research institute or NGO collecting such data and making it available to the public?

Adding some additional database sources:

-- Climate --

Prism

The PRISM Climate Group gathers climate observations from a wide range of monitoring networks, applies sophisticated quality control measures, and develops spatial climate datasets to reveal short- and long-term climate patterns.

WorldClim

WorldClim is a set of global climate layers (climate grids) with a spatial resolution of about 1 square kilometer. The data can be used for mapping and spatial modeling in a GIS or with other computer programs.

NOAA's NCEI

NOAA's National Centers for Environmental Information (NCEI) are responsible for hosting and providing public access to one of the most significant archives for environmental data on Earth with over 20 petabytes of comprehensive atmospheric, coastal, oceanic, and geophysical data. See NCDC (climate), NODC (Oceans), NGDC (Geophysics), and NCDDC (Coasts).

NCEI has a HUGE repository of datasets. Sometimes you have to dig (e.g., here).

TROPICAL STORM TRACKS DATABASE

The storm tracks database is derived from the storm data published by the National Hurricane Center (NHC). This web page provides a convenient user interface for casually browsing storm information, including location, category, and wind speed.

-- Traits --

TRY

TRY is a Plant Trait Database. More formally, it's a network of vegetation scientists headed by DIVERSITAS/IGBP, and the Max Planck Institute for Biogeochemistry, providing a global archive of curated plant traits.

BioTraits

This is an online resource for empirical data on how biological traits respond to environmental drivers such as temperature, light, and salinity.

-- Species --

GPDD

The CPB / NCEAS Global Population Dynamics Database largest collection of animal and plant population data in the world, and brings together nearly five thousand time series in one databa

Global Invasive Species Database

The GISD is a free, online searchable source of information about species that negatively impact biodiversity. It focuses on invasive alien species that threaten native biodiversity and covers all taxonomic groups from micro-organisms to animals and plants.

Movebank

Movebank is a free, online database of animal tracking data hosted by the Max Planck Institute for Ornithology. They help animal tracking researchers to manage, share, protect, analyze, and archive their data.

Global Plants

Global Plants is the world’s largest database of digitized plant specimens and a locus for international scientific research and collaboration.

COPEPOD

The Coastal & Oceanic Plankton Ecology, Production & Observation Database (COPEPOD) is an online database of plankton abundance, biomass, and composition data. COPEPOD's online zooplankton and phytoplankton data content ranges from long term ecosystem monitoring surveys to detailed process studies

COMPADRE & COMADRE

COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database site. Contain matrix population models of hundreds of plant and animal species

Catalogue of Life

One of the most comprehensive and authoritative global index of species currently available. It consists of a single integrated species checklist and taxonomic hierarchy. The Catalogue holds essential information on the names, relationships and distributions of over 1.6 million species.

-- Forests --

FAO Forestry Database

The FAO Forestry Department maintains an array of online databases where information covering various aspects of forestry is stored for analysis and further dissemination.

FIA

U.S. forest Service's Forest Inventory and Analysis database contains continuous forest census data for the United States.

European Forest Institute Database

EFI is running a number of online databases with data and information on different aspects of European forests, forestry and forest research.

CTFS-ForestGEO

The Center for Tropical Forest Science - Forest Global Earth Observatory (CTFS-ForestGEO) is a global network of forest research plots and scientists dedicated to the study of tropical and temperate forest function and diversity

-- Other --

NutNet

The Nutrient Network (NutNet) is a grassroots research effort to address pervasive human impacts on ecosystems (via alteration of global nutrient budgets and changes in the abundance and identity of consumers) within a coordinated research network comprised of more than 40 grassland sites worldwide.

...Also see the Ecological Databases page on INNGE Wiki for more resources!!

Ex: Ecological Data Wiki:
The site is a source for finding ecological datasets and quickly figuring out the best ways to use them. Just think of it as the Wikipedia of ecology data.


How can a recessive allele propagate until they manifest? Suppose a specific gene has two possible alleles. In a given population all members have only the dominant one. By a mutation on member receives the first recessive allele of that population. Is it possible that one day the descendants of this population have this allele manifested? I think it's very unlikely that this allele survive until another similar mutation occurs and they get manifested in the phenotype.

The short answer is: Because of genetic drift. If a mutation does not influence the fitness in heterozygote individuals, then its frequency varies only through genetic drift while it reaches some high enough frequency. If by chance, the frequency of this new allele achieve a high enough level so that the homozygous for this allele given by $x^2$ where $x$ is the frequency of the new allele is high enough to have considerable effect, then the selection coefficient $s$ between the recess if homozygote and the two other genotypes matters.

Hope that helps you. Don't hesitate to ask further more accurate question if you need more details. Or let us know if this does not answer your question.


Is an X ml dose of a drug at 50% bioavailability roughly equivalent to a 2X ml dose at 25% bioavailability? For the sake of simplicity, assume:

The two doses are the same drug metabolized in the exact same way, and the only difference is the amount that reaches the bloodstream (and thereafter the brain).
This drug is only meant to influence the brain, so differing concentrations in various organs don't matter.
This drug is short-term and nothing lingers in the body after it has been excreted or broken down.

My understanding is that bioavailability means the proportion of drug that reaches the bloodstream. So, all things being equal, does that mean an administration of a drug will be twice as potent if the bioavailability is doubled?

All things being equal, does that mean an administration of a drug will be twice as potent if the bioavailability is doubled?

Bioavailability is initially taught, and sometimes reported as a proportion, $F$, the concentration in drug in plasma under a test condition (typically oral administration) over the concentration of of the same dose of the drug under a reference condition (typically IV administration).

In the simplest case, under zero order kinetics (the rates of all reactions that cause a change in concentration of the drug are independent of that drug's concentration), you can substitue $F\cdot D$, for a dose, where $F$ is the bioavailability and $D$ is the dose (see equation 2-16 in Goodman and Gilman's The Pharmacological Basis of Therapeutics, Chapter 2).

So, for your question, you can write down the state with equal plasma concentrations, $0.5\cdot D_1 = 0.25 \cdot D_2$, which reduces to $2D_1 = D_2$

Potency is a hairy term, defined in many different ways (some with more hand waving than others), but lets say for the purposes of this question that potency is the oral dose $D$ required to produce a measurable effect, $E$, and relative potency is the oral dose of formulation 1, $D_1$ required for a set effect, $E$, over the oral dose of formulation 2, $D_2$ for the same effect (modified from Goodman and Gilman Chapter 3). So, if the effect of your drug is directly proportional to its concentration in plasma ($E = kC$), then yes, the formulation with twice the bioavailability will be twice as potent.

I was going to write a long treatise on why this is not necessarily going to be the case, but since you were so specific about all things being equal, I'll just say this: bioavailability is often not reducible to a single $F$, which is why the FDA requires a lot of information on Bioavailability. This is for good reason, because kinetics are often not zero order, and even once we get to plasma concentration, the concentration term that drives efficacy can be $AUC$, $C_{max}$, time above a threshold, and sometimes even hard to correlate directly to plasma concentration at all. But, in the simplest case, all things being equal, your answer is yes.


Immunodominant Peptide Can someone please explain me the concept of Immunodominant peptide in simple language?? I did read the wiki article but did not understand it clearly. Please help!
(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)

If you have an antigen (something foreign for the immune system, for example a virus or bacteria) this consists of many different epitopes (immunogenic regions), as shown in the figure below (from the German Wikipedia, Antikörper means antibodies). The antigens are taken up by special cells of the immune system and processed to get small peptides:

To produce highly specific antibodies, the body has to undergo a specific immune reaction against these peptides. In the beginning of this reaction antibodies usually have a rather low affinity (bind only weak) against their antigen. This is changed by the so called affinity maturation in which the antibodies are mutated to make a variety of different new antibodies. These are then again "checked" against the antigen and the ones with a higher affinity are positively selected.

So antibodies with a strong binding to their antigen are favoured against such which have a less strong binding which can lead the selection of only a few antibodies, even if a complex antigen which has many immunogenic peptides is used. This is positive in the way that these antibodies are very effective in directing an immune response against the virus/bacteria but can be critical if the pathogen has a high mutation rate as this leads to a pathogen which does not have this antigen anymore.


How does Bernoulli’s Principle apply to the cardiovascular system? Below are graphs which illustrate the cross-sectional area, velocity, and fluid pressure through each vascular segment of the cardiovascular system.

It makes sense that velocity and cross-sectional area should be inversely related graphically (by the equation of continuity, ($v_1A_1=v_2A_2$). However, Bernoulli’s principle states that where velocity is high, pressure is low, and vice versa. However, in the graph above, clearly pressure is decreasing as you move away from the aorta, regardless of velocity.

I can understand how the pressure in capillaries will be higher than those in venules, since a higher pressure in capillaries would accelerate the blood as it moves into the venules with a lesser total cross-sectional area. This agrees graphically, since, past the purple stripe, the pressure curve decreases as the velocity curve rises. Yet the mean arterial pressure in the aorta and arteries seems to violate the relationship between velocity and pressure stated in Bernoulli’s principle. What is there to make of this?

(Image taken from Campbell Biology, 10th edition)

Bernoulli's principle can be a little tricky when applied to the cardiovascular system, but it still holds true across the entire system. You mention a good point that the relationship doesn't seem quite right at the aorta or arteries, because of the constant fluctuation of pressure between systolic and diastolic without a significant change in diameter of the vessel. Remember that this is due to the pulsatile flow of blood from the heart, and has nothing to do with Bernoulli's principle. If the flow was constant (i.e. not pulsatile) then the pressure would be constant as the diameter of the vessels is constant. As the diameter of the vessels begins to decrease the velocity would increase to maintain a constant value.

As you mention, Bernoulli's principle describes how the product of area and velocity of flow must be constant across a system. When the total surface area of the system increases, the pressure decreases as well as flow. It is important to remember that even though the capillaries are so small and individually high resistance (which you would think according to Bernoulli's principle should increase the velocity), you are effectively adding an innumerable number of these very small resistors in parallel (not in series) and the resistance overall (and subsequently pressure + flow) decreases greatly.

When adding resistance in series the total resistance is additive and it adds up quickly! $$R_{Total} = R_1 + R_2 + R_3$$
While resistance in parallel adds the reciprocal of the resistor, meaning that as more resistors (or capillary pathways) are added the total resistance continues to decrease because of the following relationship: $$\frac{1}{R_{Total}} = \frac{1}{R_1}+\frac{1}{R_2}+\frac{1}{R_3}$$

The parallel resistance stuff was difficult for me to grasp when I was a student, because it never seemed to make sense in my mind that the resistance significantly decreased when you added all these small capillaries. One of my physiology professors described it well when he said, "Think of adding resistance in parallel, in the way that capillary beds and other vessels are in the cardiovascular system, like giving the blood another place to go." If the blood has more places that it can go, then it's easier to see why resistance falls so much when you add a bunch of extra places for the blood to flow.


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

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

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

Klenow seems to lack exonuclease activity ("proof-reading"), but otherwise works like normal DNA polymerase, so I wouldn't expect anything different from PCR. On each step, as long as there is enough template and primers, you'll get doubling of current template.


Can human organs be transplanted indefinitely? I watched this movie, where they rented hearts to people for a year. I wonder if it is possible to transplant a heart indefinitely from person to person, or does the heart have a lifetime? So, do human organs age and eventually die, or is it possible to transplant organs indefinitely? What is the limiting factor for life of human organs?

First of all, it will be practically impossible to make an estimation of how long a transplanted organ will live and how many times it could be transplanted. However, it is relatively safe to say that it will not live forever.

To be able to receive an organ transplantation, the HLA MHC-complexes of donor and receiver need to be matched very carefully, to limit the host-vs-graft reaction. This limits the number of possible donor-receiver patient pars drastically. So to be able to do a "row transplantation" (one receiver to the next and so on), they need to have matching MHC-complexes.

Otherwise the immune system of the receiver turns against the transplanted organ and will eventually destroy it. To avoid this reaction, transplantation patients also receive drugs, which severely suppress their immune system, thus making other infections potentially dangerous. This reaction will still take place, since you cannot shut down the immune system of the receiver completely (for obvious reasons), though it happens at a much slower rate. Transplanted organs will only live for a certain time (see estimates from a number of transplantations below) and it is possible that people need to receive transplants twice in their life.

For this reason, no doctor will put their patient at risk by giving them an organ which might have a reduced lifetime. The risk of the operation itself is also substantial.  Additionally, the original receiver needs to be dead to do this, as he would otherise need another organ in exchange.

What we can do is to take the average number of a lot of transplantations together and calculate some average life-years for a transplant. According to table 2 in this paper ("The Life-Years Saved by a Deceased Organ Donor") the "average benefit by type of transplant (life-years)" is:

Kidney: 7.2 years
Liver: 16.9 years
Lung: 2.1 years
Heart: 14.5 years
Kidney-Pancreas: 12.9 years

These numbers are not definite, since the life style of the donor and the receiver as well as infections of the transplated patient (who has a severely suppressed immune system – this is critical) also play an important role in determining the lifetime of the organ.


What does it mean to clone a gene? When I look up information related to the identification of disease genes, texts will often refer to the gene being "first cloned." What does "clone" mean in this context? Is it simply a synonym for discovery?

Usually this is used in the context of gene analysis and further characterization. What is done, is that a piece of foreign DNA (either generated by digesting genomic DNA (from human or mouse for example) or by PCR amplification) digested at the end of the DNA to have matching open ends with a bacterial vector.

The DNA of interest is then ligated with the vector and can then be replicated in bacteria and isolated easily in great yields. This plasmid can then further analysed (by restriction analysis, sequencing etc.), the gene or its promoter manipulated and mutated, or in case of protein coding genes the gene overexpressed in the cells. All this is useful to analyze the function of unknown genes. See the figure for a schematic overview (from  Campbell AP Biology Book 8th edition, via this website):

Technically making a clone means that you generate multiple genetically identical daughter cells from one precursor.


Why do kefir grains stop growing in soy milk? Kefir is a fermented milk drink made with kefir grains. It usually is prepared by inoculating cow, goat or sheep milk with kefir grains.

I would like to prepare the drink with soy milk, which worked fine for some months. Then the kefir grain stagnated in its growth. I use bottled soy milk from the supermarket. I do not produce the soy milk by myself.

In "real" milk the kefir grains never stop growing (and dividing), but in soy milk they apparently do.

Why do the kefir grains stop growing in soy milk? Are they lacking a specific nutrient that is only contained in milk from animals?

Yes, they are behaving differently because of the lack of nutrients, including lactose, and possibly because of the presence of other chemicals in soy milk that aren't in dairy.

Kefir grains are a complex community of different types of lactic acid bacteria and yeasts which metabolize (eat) various nutrients/chemicals in their environment. Because soy milk is a chemically different environment than dairy milk, these communities function in different ways. Over repeated propagations in soy milk, you probably have cultivated a very different community in regards to species diversity and the chemical products.

As Liu and Lin describe here
, the kefir community members in dairy milk are eating mainly lactose, whereas in soymilk they are eating sucrose, raffinose and stachyose. As a result, the reproduction of the bacteria and the yeasts differs, as did the alcohol and lactic-acid contents of the end-product.

Because your question is a practical one, you might be interested to know that in that paper, the authors found that adding 1% sucrose (table sugar) or 1% glucose to the soymilk produced an end-product that more closely mimicked that of dairy milk. You could give that a try and see if it improves your kefir growth.

 Liu JR, Lin CW. 2000. Production of kefir from soymilk with or without added glucose, lactose, or sucrose. Journal of Food Science 65: 716–719.


the evolution of the human brain size I was thinking, as I know, sometimes the process of producing DNA did not work well(correct me if I'm wrong), so it gives us some changes in the object we gonna have(for example: increasing or decreasing a part, enabling  or disabling  a part), could human brain grow more that it is now?

I assume, you mean by "producing DNA" Neanderthals had larger brains than us. Basically, this is possible and generally, brain size correlates with body size. What you may ask here is: Can our brain size to body size ratio increase? Probably yes... I can't think of a reason, why not?

But please please be aware of that intelligence, does not have to correlate with brain size. e.g. elephants and humans. There may be some limits of the smallest possible brain size for certain mental tasks and skills. But wiring and plasticity is probably more important than the bulk size.


What causes notches in elephants' ears? What causes the elephants' ear to rip like this?

Is it a natural process as they get old, or it's injuries, like consequence of fighting with other elephants?

A natural process is something quite vague: this is a natural process, but it's not related to the elephant's ageing. Neither is it (normally) related to fighting.

Those notches and tears are caused by the daily activities of elephants, feeding in the bushes. The longer the ear, the more prone it is to damage. On the other hand, thicker ears are less prone to damage.

Day by day, the number and pattern of tears/notches/holes changes.

Curiously, this pattern of tears/notches/holes is used by researchers to identify individuals. Not only that, but also the pattern of the veins in the ears (you can see them in the left ear):

Thus, the same way the tail of a humpback whale or a human fingerprint is unique to each individual, so are the elephants' ears.

Sources:

http://voices.nationalgeographic.com/2013/08/16/name-that-elephant-how-to-identify-elephants-in-the-wild/
https://www.elephantvoices.org/support-now/814-how-to-use-ear-notches-and-tears-to-id-african-elephants-.html


Why does it hurt more when you touch a nerve directly? I am not a biologist nor know much about biology (so please explain in layman's terms) however I have always been curious as to why this is.

What causes the difference in pain between touching an open wound and pushing down on your skin? In both circumstances you are applying pressure to the nerves except one is a foreign object touching the nerve and the other is the nerve's natural surroundings in your body.

Why is it that a foreign object causes so much more pain?

I answered the other question and it is similar. However, this one is different enough that I will give a slightly more simple explanation.

Nerves transmit messages using electrical current, more specifically the flow of sodium and potassium. Just remember that it's electricity. When you have any sort of cut or damage, your body recruits white blood cells which protect you from any bacteria that might enter. They also cause inflammation to prevent those bacteria from spreading (and to warn other cells that they may become infected). It is also important that we feel pain, so we know something is wrong (because we have the ability to do something about it). That's why inflammation causes pain. It does this by lowering our threshold so our nerves are more sensitive. In other words, it takes less damage, pressure etc. to cause our nerves to send the pain signal. Normally, it is set higher, so we don't suffer too much pain. Naturally if you want clarification on anything just ask.


Can fever cure Ebola disease? Why is ebola disease does not cured on elevating body temperature by body defense system?
Can we cure it either by elevating or reducing body temperature (in ice bath) and creating hostile environment for virus?

Short Answer: Fever cannot cure Ebola simply because the virus is not temperature-sensitive.

Background: Fever is a defense mechanism of the body which is specific to temperature-sensitive virus and bacteria. It is so because high temperature induces stronger immune response and makes the body hostile for the pathogen1. Ebola virus, on the other hand, is not affected by this mechanism because it can survive over a much broader range of temperature. Ebola virus is moderately temperature-sensitive, and can survive in temperatures as low as 4°C2 and as high as 60°C3 (at least for half an hour). So, in practical sense, it is not possible to cure ebola disease by heating or cooling the body, either naturally or artificially. But, if we ignore practicality, then Yes, you can cure ebola disease if you take an ice bath or a steam bath for hours so that your core body temperature drops to 4°C (in former case) or 60°C (in latter case). However, it wouldn't be a very nice idea as your body would become hostile for yourself before becoming hostile for the virus.

Having cleared the point about making body hostile for the virus, we are now left with another option: inducing stronger immune response. However, this will not work either because of a peculiar, but dangerous, property of such viruses: they use our defense system against us. Ebola virus, coming under the category of Filoviridae4, attacks host's immune cells, specifically monocytes and macrophages, to replicate inside them. This serves dual purpose; first, the virus has its work done, and second, it kills the host's immune cells. Although how ebola enters into immune cells is not understood, but it has been shown that the virus is helped by the host's antibodies in entering into immune cells5 (quite ironic). Ebola virus can also accomplish this through a process known as macropinocytosis6 (a form of endocytosis). You can refer to this page for its life cycle as well as the diagram of the ebola virion which I've used above, or just have a look at the diagram below from here:

References:

What is the benefit of fever during infections? - Biology Stack Exchange
Okware SI, Omaswa FG, Zaramba S, Opio A, Lutwama JJ, Kamugisha J, et al. An outbreak of Ebola in Uganda. Trop Med Int Health. 2002;7:1068–75. doi: 10.1046/j.1365-3156.2002.00944.x
Mitchell SW, McCormick JB. Physicochemical inactivation of Lassa, Ebola, and Marburg viruses and effect on clinical laboratory analyses. J Clin Microbiol. 1984;20:486–9
Wikipedia contributors. "Filoviridae." Wikipedia, The Free Encyclopedia. Wikipedia, The Free Encyclopedia, 24 Sep. 2016. Web. 5 Apr. 2017.
Takada, A. & Kawaoka, Y. Antibody-dependent enhancement of viral infection: molecular mechanisms and in vivo implications. Rev. Med. Virol. 13, 387–398 (2003).
Hunt, C. L., Kolokoltsov, A. A., Davey, R. A. & Maury, W. The Tyro3 receptor kinase Axl enhances macropinocytosis of Zaire ebolavirus. J. Virol. 85, 334–347 (2011).


Why don't vaccines cause bacterial resistance? Since bacteria can evolve to overcome antibiotic use, why wouldn't they be able to evolve to overcome antibody or cell-mediated immunity?

(One possible explanation: antibiotics have only one target while vaccines elicit antibodies against multiple targets and multiple T-cell epitopes. Even more targets arise when comparing sub-unit vs inactivated vaccines, where the number of targets are extremely higher using inactivated vaccines, containing whole bacterial cell.)

Unfortunately, we do see examples of bacteria and viruses evolving vaccine resistance. For instance, vaccine resistant strains of polio and pertussis have recently been identified.

Yet these seem like the exception rather than the rule. One thing that makes it harder for pathogens to evolve resistance is that vaccines usually generate antibodies to multiple antigens, all of which the pathogen would have to alter.

Another reason vaccines tend not to drive vaccine resistance is that the diseases for which we vaccinate are typically those that are not antigenically variable. (Haemophilus influenza is a notable exception; there we use a conjugate vaccine). This may have something to do with how we view vaccine efficacy. For example, we don't say that the influenza virus evolves vaccine resistance--yet we need a new vaccination each year due to antigenic shift.

If you are interested in learning more, Angela McLean has a nice article looking into this question.


How similar do proteins have to be to trigger the same immune response? The title really says it all. How precise or vague is the immunity we get from vaccination or from having encountered a germ before?

Is it about protein parts that are recognised if they are identical? Full proteins? Which kinds of mutations break the recognition and which don't?

Immunoglobulins don't recognize entire proteins, but rather,specific shapes (called epitopes). These epitopes must also be present on the surface of the invading bacteria or virus for the immunoglobulin to have access. The epitope must be exactly the same. Any change in the amino acid sequence would change the shape. But an epitope is a relatively small part of the larger protein. If the shape is the same between different proteins, it would trigger an immune response.


How does protein denaturation work? I was wondering how protein denaturation works.

Are there covalent bonds, such as disulfide bridges involved, or is it based purely on non-covalent bonds such as hydrogen bonds? Why is denaturation irreversible in most cases if only non-covalent bonds are involved?
Is it possible to denature protein by rapid changes in electromagnetic field or pressure? (The articles I have read so far mention only stress factors like sudden pH, osmolarity, temperature changes...)
How can I protect a protein against denaturation? e.g. in PCR we use a heat resistant DNA polymerase, so certain amino acid sequences might protect against heat denaturation, but I need reassurance about this.

Really the question how does protein folding work?  But let me answer your questions...

1) Very few proteins have disulfide bonds (usually secreted proteins) or really any covalent bond stabilizing the amino acid chain beyond the bonds that make up the polypeptide itself.  Denaturation is only reversible in relatively few cases in fact.  A few proteins, usually very small ones can be nursed back into a native folded state from an unfolded one, and then only a percentage of the sample will reattain the folded state.

2) Sure.  In fact pressure changes the hydrogen bonded structure of the water and also therefore the thermodynamics of protein structure and has been used to study protein folding. Generally the electomagnetic field does not affect the state of the protein fold.  I cite the fact that many many proteins have been studied via nuclear magnetic resonance, in which the proteins have been inserted into some of the most powerful magnets that can fit into a reasonably sized room.   That is not to say that the protein function might not be affected by such a field.  I'm sure by the time the field is large enough to ionize water or the peptide change you would see something... so you can always push things too the breaking point.

3) Many proteins from thermophilic organisms are more resistant to denaturation and companies actually engineer proteins to be resistant to all sorts of outrageous conditions and still be folded and functional.  Laundry detergent is full of crystallized enzymes that will sit happily in detergent for a long time.  I don't even know if these products have a shelf life.

Overall proteins are vulnerable to denaturation for a good reason- the cell degrades them when it doesn't need their function and can recycle them for their component amino acids. If they were all this robust the cell would starve to death quickly.  If there is a biological role to a protein that is denatured and then refolds itself it is only for extremely rare situations.  Proteins for the most part don't fall apart once they are folded and if they do, they are done.

Some possible exceptions: some antibiotic peptides which fold into pores that kill their targets and the amyloid plaque which takes on a different fold when in the brain which is associated with - but may not cause - Alzheimer's.


When is the lactase in lactose-free milk active? Recently we have started suspecting that one of our children has hypolactasia (lactose intolerance), and so accordingly I have had my first exposure to lactose-free dairy- and dairy-like products. In addition to soy milk and almond milk, we have recently purchased actual dairy milk that was labeled lactose-free. This gave me the impression that they had used some process to remove the lactose, but looking at the ingredients more closely, it seems that they simply added lactase enzyme to the milk to assist breaking down the sugars.

My question is this: when is the lactase enzyme active? Does the lactase activity begin right as it is added to the milk, or will it not become active until ingested?

Essentially, I'm wondering if this type of milk can/should be used in cooking or baking. High temperatures will certainly denature the lactase enzymes in the milk, but if the lactose has already been broken down, this shouldn't be a problem.

Having done an inordinate number of rather mind-numbing A.S. practicals involving milk and enzymes the year before last, in my experience lactase always began breaking down the lactose immediately and converting a boiling tube worth of milk in less than 50 minutes at below room temperature.

To further allay your concerns, this website suggests that most Lactose Free milk has undergone UHT treatment - therefore cooking shouldn't be a problem as the enzymes have presumably been added before the pasteurisation, and are therefore denatured - I can't see why you'd then go to the extra trouble of adding the lactase aseptically after pasteurisation; and if the lactase shows in the ingredient list it presumably wasn't done with immobilised enzymes in the factory.


How to determine the evolution of a dimension of fitness that has high variability of selection intensity? How can one determine the evolution of a dimension of fitness that has high variability of selection intensity (low in some generations, high in others) compared to other dimensions of fitness?

It's complicated. The classic answer is from Dempster 1955 Cold Spring Harb Symp Quant Biol 1955. 20: 25-32 (doi:10.1101/SQB.1955.020.01.005), which has a whole section on "Selection Intensity Varying With Time".  Summarizing:

An example from Kimura (1954) with a mean selective coefficient of zero: "the variation of selection facilitates the loss or near loss of alleles thus tending, if anything, to decrease rather than maintain genetic heterogeneity".
An example with haploid populations (approximately equal to the diploid case for weak selection) with a time-varying selection coefficient of $s_k$ shows that the behaviour of allele frequencies over time depends on the mean value of $m=\left\langle x_k \right\rangle= \left\langle\ln(1/(1-s_k) \right\rangle$, i.e. the geometric mean of the relative fitness; in general, the geometric mean is smaller than the arithmetic mean (i.e. variation in time would lower the fitness advantage of the more-fit allele). I believe the bottom line here (although it takes quite a bit of work to understand the whole story) is as given in the last sentence of the paper: "Selection pressures variable in space or time could act to maintain genetic variance of fitness ..."

On the other hand, Tănase-Nicola and Nemenman (2011), "Fitness in time-dependent environments includes a geometric phase contribution" (DOI: 10.1098/rsif.2011.0695) say it's still more complex:

  the selection coefficient in infinitely slowly changing environments (we call this the adiabatic limit) is given by a time-average of static selection coefficients corresponding to each environment. This time-average is equivalent to the geometric mean result of Dempster [10]. It is independent of the order or the speed with which different environmental states are visited. However, for environments varying at a slow but finite rate, this time-average is not the whole story ...

All of the above is about the evolutionary dynamics of a single allele, not a comparison of the evolution multiple alleles/traits within the same genome.  Things could get (much) more complicated in that case, even in the absence of explicit pleiotropy, linkage, etc. (e.g the Hill-Robertson effect). I doubt there's a simple answer; I would suggest heuristic guesses based on independent dynamics of alleles based on the single-allele phenomena described above, followed by simulation ...


Anopheles arabiensis lifespan and sporogony duration What is the longest observed lifespan of a mosquito, especially of the species Anopheles arabiensis? How long does it take for Plasmodium parasites to develop and move into the salivary glands of these mosquitoes?

I need this information to calibrate my model on malaria transmission.

What is the longest observed lifespan of a mosquito, especially of the species Anopheles arabiensis?

Mean lifespan calculations for Anopheles arabiensis range from 14 days (Karoki, 2013)* to 21 days (Yamada et al. 2014)**

*This Masters thesis tests efficacy of different drugs against An. arabiensis, 14 days is the mean control lifespan.
**These An. arabiensis are of a specific strain but no indication is given that the life span is different than normal An. arabiensis.

The CDC Anopheles mosquito page is another good source for information on Anopheles life spans:

  The adult females can live up to a month (or more in captivity) but most probably do not live more than 1-2 weeks in nature.

How long does it take for Plasmodium parasites to develop and move into the salivary glands of these mosquitoes?

US National Institutes of Health:

  Growth and division of each oocyst produces thousands of active haploid forms called sporozoites. After 8-15 days, the oocyst bursts, releasing sporozoites into the body cavity of the mosquito, from which they travel to and invade the mosquito salivary glands.

United States Air Force (USAF):

  The length of the developmental stage in the mosquito not only depends on the Plasmodium species but also the mosquito host and the ambient temperature.  This may range from eight days in Plasmodium vivax to as long as 30 days in Plasmodium malariae.

Wikipedia (Plasmodium falciparum) :

  Over the period of a 1–3 weeks, the oocyst grows to a size of tens to hundreds of micrometres... The sporozoites then migrate to the salivary glands and complete their differentiation. Once mature, the sporozoites can proceed to infect a human host during a subsequent mosquito bite.

US Center for Disease Control:

  After 10-18 days, the parasites are found (as "sporozoites") in the mosquito's salivary glands. When the Anopheles mosquito takes a blood meal on another human, the sporozoites are injected with the mosquito's saliva and start another human infection when they parasitize the liver cells.

Overall, it depends who you ask, but especially on the species of Plasmodium you're working with. I'd look for specific papers on the development cycle you're modeling and run with it.


How does the intracellular accumulation of cyclic AMP cause edema in case of anthrax? Edema factor is adenyl cyclase which is activated only inside the target cell. It leads to intracellular accumulation of cyclic AMP resulting in edema. How?

Edema factor is a high efficiency adenylyl cyclase, an enzyme that converts ATP to cyclic AMP (cAMP). cAMP is an important second messenger in many pathways, which you can read about in Albert's Molecular Biology of the Cell. In order to be an effective second messenger, it must be tightly regulated. Several bacterial toxins disrupt this regulation, by creating an excessive amount of cAMP directly (B. anthracis EF), forcing the local activator of adenylyl cyclase to stay on (V. cholerae CT), or preventing the local inactivator of adenylyl cyclase from turning it off (B. pertussis). Some of these pathways are well understood. The pathway between cholera toxin and lethal loss of intestinal fluid, as mediated by elevated cAMP, is particularly well understood. The pathway between edema factor, edema toxin, cAMP, and tissue/organ edema is not well understood, as illustrated by this lovely figure, from this review:

Note the nice question mark between Edema Toxin and Edema

It could be mediated by protein kinase A (PKA), and probably is at least partially. It could also be mediated by EPAC and the small G-proteins Rap-1 and Rap-2 (and probably is, at least partially). It could even be mediated by the loss of ATP, since the anthrax ET is so efficient at catalyzing the conversion of ATP to cAMP.


What is this droplet of liquid that comes out of a mosquito? I have been looking at pictures of different species of mosquito and several times I came across pictures where the mosquito seems to be secreting some kind of fluid.

In the pictures one can clearly see that the mosquito both secretes transparent fluid and blood.

What kind of fluid is the transparent stuff? Could it be plasma from the host's blood?
Why does the mosquito do it?

Short answer
Excretion of blood and urine may prevent overheating by reducing body temperature through evaporative coolong (akin to perspiration). Excretion of blood and urine also concentrates the ingested blood.

Background
Female Anopheles mosquitoes seek blood for nutrients necessary to egg production. The cold-blooded insects may excrete some freshly ingested blood as a way to avoid overheating when consuming blood as warm as 104 degrees Fahrenheit (40°C). It is thought that excretion of a droplet of fluid aids in evaporative cooling, similar to perspiration in humans, to reduce the animal's temperature. The excretion of urine may serve a similar purpose, namely avoiding overheating during blood ingestion. By keeping the urine or blood droplet attached to the abdomen, excessive heat can be eliminated (Lahonde & Lazarri, 2012).

In the malaria mosquito (Anopheles stephens) the excretion of fluids has been investigated in detail. Females ingest blood meals that are equivalent to more than twice their unfed body mass. Engorged animals can fly only with great difficulty, making them more prone to predation. The blood meal serves primarily as a source of protein for egg development, but it also contains considerable amounts of unwanted salts and water that threaten haemolymph homeostasis. To counter this, a rapid natriuresis and diuresis commences even before the blood meal is completed, and ∼40% of the imbibed plasma volume and salt are voided within 1–2 h of feeding (Coast et al., 2005).

References
- Coast et al. Exp Biol (2005); 208: 3281-91
- Lahonde & Lazarri, Curr Biol (2012); 22: 40–5

Further readings
- Do mosquitoes urinate on you when they bite you?


Question about the threshold potential I am a student of Physiology, and I have ended up a bit confused after what I've read today regarding events during a threshold potential. So, while cells are in their resting membrane potential, the inward current of sodium is equal and opposite to the outward current of potassium. The same is true about the threshold potential.

When the threshold potential is reached, the inward sodium current is exactly equal and opposite to the outward potassium current. If this is true, why is there a change in the voltage of the membrane, let's say from -70 mV to -55 mV? I mean, both of the currents are equal and opposite and therefore there shouldn't be any change in the resting potential of the membrane.

Below is a figure showing the sequence of events during an action potential (AP). While the resting potential is characterized by an equilibrium, during an AP this balance is markedly 'disturbed'. The action potential is characterized by a specific timed series of events, namely the opening of Na+ channels in the initial depolarization phase, followed by an opening of K+ channels in the subsequent repolarization phase. During these phases, the Na+ and K+ currents are anything, but balanced.

Fig. 1. Series of events during an AP. source: Brigham Young University-Idaho


What's going on when roots turn green and grow into the air? You're looking at a hibiscus and an orchid growing in the same pot. I'm curious why the hibiscus started growing green roots into the air. Or am I looking at a third plant that somehow made its way into the pot?

July 27th

All it does is branch and get longer.

There are no leaves and the shoot doesn't thicken or turn to bark.

A new sprout appears every few days.

Is the hibiscus so root bound it's trying to escape the pot?

July 9th

I found this article online that does describes hibiscus plants as having a "spreading" type root system that will also form new shoots away from the parent plant ... http://homeguides.sfgate.com/type-root-hibiscus-have-49085.html

I also noticed that you have an attached orchid with aerial roots attached to the hibiscus plant.  If you are misting the orchid roots periodically, you may be dampening the surface soil in the pot and encouraging the growth of shoot forming spreading roots on the hibiscus plant to develop and grow upward.


Why telomere shortening slowing down cancer? I am reading Alternative Lengthening of Telomeres in Mammalian Cells, about how telomeres linked to human cancers.

  Due to the end-replication problem,5,6 the ends of linear chromosomes
  shorten with each round of DNA replication.7 In human somatic cells,
  the progressive telomere shortening that occurs with continued
  proliferation eventually results in the triggering of a replicative
  checkpoint. Telomere shortening and the structural changes that it
  presumably causes, leads to a DNA-damage checkpoint response at the
  telomere and induction of a permanent p53- and Rb-dependent growth
  arrest (i.e., replicative senescence).8-10 Because this limits the
  proliferative capacity of somatic cells, including those that have
  accumulated oncogenic mutations, telomere shortening and replicative
  senescence are a potent tumor suppressor mechanism.

The paragraph states a shorter telomere is a potential suppressor to cancers. Why is that? Why exactly a somatic cell proliferate slower with a shorter telomere DNA sequence?

Conversely, why a longer minority leads to human cancers?

Think about the 24 different linear chromosomes in a diploid human XY cell.  In the absence of active telomerase enzyme to repair the chromosome ends following one round of cell division, then every time that cell divides each end of each chromosome will get a little bit shorter.

If the cell keeps dividing indefinitely, like a tumor cell, the chromosomes are effectively shrinking.  Eventually this chromosome shortening will result in deleting actual genes (at first, 24 chromosomes x 2 chromosome ends = 48 genes).   Not all of those genes are essential for cell viability; and the distance, or length, of DNA between the telomere and the first gene on that end will be variable.  But as soon as the chromosome shortening removes part of an essential gene, then that cell will quickly die.

It would be like erasing the words at both ends of a sentence, one letter at a time.  In the beginning, someone else would still be able to make sense out of your sentence, but eventually they would not be able to fully understand what information you were trying to convey.

Most of the terminally differentiated cells in an adult human are no longer actively dividing, so it is not a problem, they don’t need active telomerase.  However, cancer is a condition of unregulated cell division, and so all cancer cells have to have some mechanism of repairing the ends of their chromosomes.  Reactivation of TERT (Telomerase Reverse Transcriptase, the protein component of the telomerase enzyme) gene expression is extremely common in cancer cells.


What do the negative and positive signs mean in the rotation angles of DNA helices? Does it mean clockwise and anticlockwise?

The signs refer to the direction of rotation. Anticlockwise (right handed helix) is positive whereas clockwise (left handed helix) is negative. The direction of rotation is observed from the side where the helix is ascending towards you (perpendicular to the ascent of helix).

In other words, curl your right hand and extend the thumb out. When viewed from above (thumb points towards you), the fingers curl anticlockwise. This is a right handed (RH) helix. Conversely, you can use your left hand to understand left handed (LH) helices such as that of Z-DNA.

  Obtained from http://biomedapps.curtin.edu.au/biochem/tutorials/prottute/helixfigures.htm. Which, in-turn is modified from Lehninger et al (1993) Principles of Biochemistry 2nd Edition Worth Publishers

   This figure depicts a RH helix. Taken from Wikipedia.

These definitions can be defined in a converse sense too and you would find many web sources that do like that. For example, if you look from below your hand such that the thumb points away from you, then the fingers curl clockwise. However, in physics and mathematics, positive angles are conventionally measured anti-clockwise. So my definition here would be suitable with respect to your question.


Why are the grey matter structures of the inferior medial frontal lobe not directly (not via white matter) connected? I have recently been trying to understand the three dimensional nature of the brain for a neuroanatomy class. Part of this strategy has included learning about structures such as the falx cerebri, tentorium cerebelli, anterior dural girdle, etc in order to understand the physical barriers that surround different parts of the brain and therefore separate them from one another. For example, the reason that the cerebellum and floor of the occipital lobe are not directly continuous is because of the tentorium cerebelli.

One issue that I have recently come across is understanding why the inferior medial component of the frontal lobe, in the region just anterior to the pituitary gland and optic chiasm, are not directly continuous (i.e. the left cortical hemisphere at this location is not continuous with the right cortical hemisphere). I have attached some photos to clarify my confusion:

As you can from this image, the falx cerebri's anterior extent leaves a small opening (indicated by the red line) that would, presumably, permit grey matter from the left hemisphere to be directly continuous with grey matter from the right hemisphere. However, no such connection exists. This is readily confirmed using an inferior view, such as that indicated in the following picture, boxed in red:

As you can see from the boxed area, the medial inferior cortical grey masses from the left and right hemisphere (which are likely the subgenual division of the anterior cingulate gyrus) are distinctly separate. This separation is clearly not related to the falx cerebri, as the anterior descent of the falx cerebri occurs further in front of this area (as indicated by picture 1).

Could anyone offer an explanation as to why these structures are distinctly NOT continuous at this point? Further, if anyone could confirm whether any part of the cortex exhibits grey-matter-continuity (i.e. not via white matter tracts) between the left and right hemisphere, that would be greatly appreciated.

Could anyone offer an explanation as to why these structures are distinctly NOT continuous at this point?

The crista galli physically separates the straight gyrus.

Click to zoom

Click to zoom

  ... that would, presumably, permit grey matter from the left hemisphere to be directly continuous with grey matter from the right hemisphere. However, no such connection exists.

They are not physically touching in that location, elsewhere the two hemispheres are not connected (even though physically touching) by gray matter.

  Further, if anyone could confirm whether any part of the cortex exhibits grey-matter-continuity (i.e. not via white matter tracts) between the left and right hemisphere, that would be greatly appreciated.

Except in rare cases, for example agenesis of the corpus callosum (ACC), communication between the hemispheres is via the anterior commissure and the corpus callosum.

The two halves are separated by a deep longitudinal fissure, see this animation:


Formation of life on other Planets At the present time it looks as if there is no other life in the Universe other than here on Earth . If this is true then why didn't it occur anywhere else ? Is it possible for something to happen only once ? Hundreds of Billions of  other Planets have formed so whatever happened here why wouldn't it have happened again elsewhere ? It is very , very strange indeed .

Issues with the post

I agree that the question is too broad. It is not the only issue, it is also primarily opinion-based (see below for explanations). The post is also somehow unclear (see below for explanations). But here is some kind of an answer that may help you.

If you google your question you will get tons and tons of hits. There is a whole lot of videos on youtube that address this question. You may want to have a look at those and come on StackExchange to ask a more accurate question because for the moment the question is too broad.

As a first short answer to the questions...

  At the present time it looks as if there is no other life in the Universe other than here on Earth

It sounds wrong (as a consequence your question would be primarily opinion based). We haven't found life. This doesn't mean that life doesn't exist elsewhere. Actually most people think that life exist elsewhere. Part of the issue behind this question is the definition of life. Often, people refers to Drake equation (you might want to read about it) which gives you the number of planets where life should exist. However, Drake equation is a speculation that has no solid grounds. It is actually pretty complicated (or impossible because we need to assume things about what the original conditions are) to calculate a probability that life occurs on a given planet. While it sounds pretty intuitive to many people (me, including) that life should exist somewhere else, there is really not much certainty.

  Is it possible for something to happen only once?

Well....yes, the death of Napoleon occurred only once.... I am not quite sure what you mean with this question, it is unclear.


How do red blood cells survive without a nucleus? I was reading this question

Why do mammalian red blood cells lack a nucleus?

According to my understanding, a nucleus is the cell's control center (like the brain). All the functions in the cell are carried out according to  the nucleus's command.

Then how can a red cell survive without a nucleus? Why does it still perform all the functions correctly without the nucleus?

As explained in the previous answer, the RBC loses its nucleus only at maturity. The nucleus contains the DNA and which can in turn produce protein. No nucleus means - no protein/ mRNA synthesis. Also, obviously, the cell loses its capability to divide.

Hemoglobin too is a protein. Knowing that it would lose its nucleus, hemoglobin is synthesized in the precursor stages of RBC. A mature RBC can not synthesize new Hb. Hence, the RBC keeps ready its store of enzymes and structural proteins (not only Hb, all proteins it would need for normal functioning) since it can not form new stuff once it has lost its nuclues.

The lack of a nucleus also limits the cell's repair capabilities. So human RBCs are cleared from circulation once they are about 4 months old. Damage (mostly from oxidative stress) to their structural proteins leads to loss in membrane flexibility. Since, the RBC can't replace the stuff, it gets gulped in by macrophages.

It is not surprising that the cell doesn't have a nucleus. The loss of a nucleus renders it better oxygen carrying capability. Even platelets donot have a nucleus. There too, enzymes are prepared and stored beforehand.

Hope that helps!


Does the genetic material the sperm carries affect its physical properties Basically, what I'm asking is, is the actual sperm cell built from the blueprint in the DNA of the man or is it itself also a consequence of the DNA it carries?

I'd like to know a few more things related to this. For example, which DNA is in the nucleus of a sperm? Is it the same as the DNA of other bodily cells in the man's body, or is it just the DNA it's delivering? Can the sperm's performance be affected by any specific genetic traits that can be observed in a potential human the sperm could make? For example, a sperm swims faster if it's carrying the genetic material that would result in a tall person (probably a silly question).

The original question I had is if the statement that female sperm live longer is true. If it turns out that the man's body makes all the sperm more or less the same and they're just boxes that can swim, then I would guess the answer is no.

I think there is a strong driving force for sperm to be free living haploid versions of human beings.  Since they are a product of meiosis sperm are the product of recombination of both the male chromosome sets.

While I'm sure that if we look closely enough, the germline cells that produce the sperm are contributing some protein and structure to the sperm, the life cycle of the sperm is mostly the result of the genome that it contains within itself.  Sperm are prone to defects.  On the average in human beings about half of sperm are non-motile: simply unable to form the flagellum or power its motion adequately for motility. That's a pretty strong selective force in the life of our other, 'half genome' selves.

Sperm selection - the sorting of which sperm from a single male achieves fertilization is pretty rigorous.  It can take 30 minutes to days.  Once in contact with the ovum, the sperm executes a critical set of transformations and biochemical activations to get past the various layers of the cell.

Sperm are from the man, but they are each living creatures on their own which we hope will deliver themselves up to the ovum to create another human being.  They vary in their genetic quality and effectiveness and this is highly related to their genetic make up.

Because each sperm is the product of two stages of Meiosis, they can be full of genetic defects, most of which would be fatal in a diploid human being.  The functions of the sperm as it goes through its short but competitive life weed out genetic abberations and help assure that the next generation of diploid human beings is as healthy as they can.

So they are not DNA boxes that swim.  I'd be hard pressed to think of a passive role for a cell in biology - they are all working pretty hard... I'd be interested in a comment with suggestions of something that is not under selective pressure in biology.

It sort of reminds me of the old argument about passive mating in females. Behavioral biologists used to think that female animals had little or no active role in mating.   That myth was retired about 30 years ago now.  That link points to an introduction to an entire volume reviewing that whole discussion of active female roles in reproduction in case anyone reading is interested.

BTW I'm not an expert on gametes, but I'd be surprised if the ova also didn't have a complimentary but quite different selective process they had to get through to become a fully presented candidate for fertilization.

Just to add a note about how the functioning sperm genes affect the diploid organism: This is one of the most important things that sperm does.  The genes that function in the living spermatazoan are the same genes the diploid organism uses, or at least a substantial number of them.  Further, these genes are scattered across all the chromosomes and so major chromosomal defects and important genes are functional if fertilization is completed.  As an example here's a cool blog post about how mosquito sperm have been shown to use odorant receptors to orient themselves in the fertilziation process. Those same receptors and the signalling genes that link that signal to the sperm behavior are probably quite useful to the adult mosquito.  I'd be surprised if human sperm also did not use similar pathways to function.

Not to beat a dead horse, but the recent nature has a report of small RNAs in mouse sperm as being an epigenetic carrier for stress.


What are the naming conventions for mutations of proteins? I have been reading about Maltose Binding Proteins. Mutant forms of the molecule seem to be named MalE_ where the _ represents a number, for example MalE36 or MalE50.

Please can someone explain the naming convention for this? i.e. what does the 'E' stand for? Does the number refer to the amino acid that has changed?

What your example is referring to is the change in the glutamic acid (E) amino acid (AA) residue, which is in position 36. This is denoted so that people/scientist would know what has been changed and usually there should be another letter after that number such as Y, which is tyrosine, to denote what it has been changed to, if it is a substitution. Then there is the delta (∆) symbol to denote deletion, and usually a number range e.g. 36-50 or just a number e.g. 70 appears after it to denote if a protein has been truncated in a certain AA range or if the entire protein from that AA is truncated, respectively. Sometimes (quite often now a days) the delta symbol is followed a protein domain name such as SH3 or RA to denote that a protein domain has been deleted and people use all sorts of naming variations for a protein that has been altered from its native sequence, which can be confusing!!

These are just some conventions, which isn't documented very well and you just figure them out when reading a few papers but I would welcome any edits for a good source for protein change annotations.

EDIT:

Since as pointed by Alan Boyd response, MalE is an E. coli gene encoding Maltose Binding Proteins, then my answer will not apply for any protein AA changes as correctly pointed out and elaborated on in Alan Boyd response.


Why are Ramachandran angles of first and the last amino acid not necessary to define the full 3D structure of a protein chain? I have come across an online ppt slide of the bioinformatic algorithm where it is said that first and the last amino acid Ramachandran angle is not necessary to tell all its internal coordinates. Is it really not necessary for any simulations while predicting the 3D structure of proteins? For instance, if we have a protein chain of N amino acid sequence, there will be 2N dihedral angles. Of which we need to specify only the 2N-2 (apart from the first and the last amino acid dihedral angles) dihedral angles. Why the two angles are ignored? Let's assume all the bond angles and bond lengths are provided for the entire chain.
I have seen this statement in the following ppt, slide number -9, titled representation of internal coordinates, under bullet point 3.
https://www.cs.umb.edu/~nurith/cs612/Manipulation.pdf

Think about the case of a chain of N=3 points in space. There are only angles associated with the middle point, the two endpoints don't have angles associated with them because they only have one incident segment rather than two.


Accuracy of best plant growth models? Given a plant $P$, predict its height $H$ at time $t$ since planting given some environmental variables $E_1, \dots, E_n$. How accurate are the state-of-the-art models for such thing? What data is used to make the prediction?

I've worked on a couple of these for biofuel production. The answer varies widely according to plant P and how well studied plant P is. In terms of what data is used, it includes but is not limited to: temperature, insolation, length of the day, cloud cover, rain, soil composition, soil type, soil density, other local effects like wind or pests, altitude, humidity, and pH. For corn(food) and miscanthus(experimental biofuel crop) the models are quite good if the year is pretty normal and you're in a well-studied parameter space, mostly because corn and grass grows straight up. For trees, non-crops, non-corn crops, etc the models are almost completely useless. It's a question of testing nearly every possible combination of parameters for each plant P, and how much people care about how tall it gets.

Given how much data goes in, it surprises me that even under ideal conditions(well-studied) some of the parameters the model spits out are impossible/wrong. There's a measure of leaf overlap(just as an example) that's especially poorly defined but a rough proxy might be "number of leaves that shade a specific point, on average" and it's regularly measured at <10 and regularly predicted at well north of 50.


Is Sugar a stimulatant or a weak sedative? Quite often, I have heard the remark that children become hyperactive when high amounts of sugar are consumed.

But common websites suggest that sugar is a sedative, and the hyperactivity in children is more likely caused by 'artificial dyes and preservatives'. (http://curezone.com/forums/am.asp?i=1444631)

So, is Sugar a stimulant (for adults and children) or is it a sedative? Is there any conclusive research to validate this theory?

The idea that 'dyes and preservatives' cause hyperactivity dates back to this '76 paper by one Dr. Feingold. Despite being disproved neatly in 1978, it's still around.

As far as sugar goes, I recommend this review paper covers both the arguments for and against sugar causing hyperactivity, as well as 12 double-blind placebo controlled studies showing sugar has no effect on children's actual behavior.


Why is the heart not in the middle of the body? All mammals that I can think of have a high degree of bilateral symmetry (In fact, almost every animal I can think of is like this).

So why is the human heart not exactly in the middle of the body? An effect of this is that one lung is slightly smaller. Are there any evolutionary theories on why this came to be?

First of all, let me make it clear that the heart is at the vertical centre of the body -- it is not shifted towards left (or right). However, it is slightly tilted towards the left in most cases.

In some cases, it is tilted towards the right, and the condition is called Dextrocardia. For why it is so, lets look at what the heart does. Below is a diagram of double circulation (from here).

As you see, the highest pressure needs to be generated for pumping oxygenated blood into the body. Thus, the left ventricle needs the thickest muscles for this purpose. And due to these extra muscles, the  heart appears extended and seems shifted towards left.

Coming to the evolutionary perspective, it is important to mention that humans are not the only organisms with this feature. Indeed, displacement of the heart towards the left is a conserved feature in all vertebrates (Fishman et al, 1997). See this answer for more information.

Coming to genes, bending of the heart towards one side is actually controlled by the NODAL gene during development. See this diagram (from Jensen et al, 2013):

Tilting occurs in two phases, one during the first four and a half months of intrauterine life and the other, which is actually a 45° rotation to the median plane, later. During the early development of the heart, a process called cardiac looping happens and the straight heart tube develops a bend (see diagram). The NODAL gene, along with the Lefty1 and Lefty2 genes, regulates the speed and direction of cardiomyocyte movement during the development of the heart, leading to this asymmetry. To confirm it, researchers knocked out the spaw/nodal gene from a zebrafish and found randomized development of heart, even symmetric heart, as the result(!) (see Walmsley, 1958 and Rohr et al, 2008).

Now, talking about why this happened in the first place, and why it is so conserved among vertebrates, we need to ask ourselves a basic question: what good would a symmetrical heart be? External symmetry is preferred (probably) because it helps in locomotion; it would be quite difficult to move with your two legs placed away from your center of gravity. But when we talk about internal symmetry, conditions drastically change. We get a major restrictive factor here: space. And limited space always dominates other factors. Seeing that the structure of the heart is necessarily pointed towards one side, it becomes difficult to make it symmetrical. (The only option IMO is to have another pointed end at the right side.) In this case again, what advantage would a symmetrical heart provide? None. And it might even be harmful since having an even bigger heart would mean making both lungs smaller. Thus, a symmetrical heart would only prove to be a liability rather than an asset. See this question for more information.


Confusion about mitochondrial electron transport chain Complex I Wikipedia article title The Wikipedia article title for Complex I (the NADH dehydrogenase enzyme complex) is "NADH dehydrogenase (ubiquinone)". This is confusing to me because this title sounds like ubiquinone is another name for NADH dehydrogenase, but ubiquinone is in fact the Coenzym Q, which is reduced by the hydrogen transferred from NADH through Complex I. What is the reason behind this title? I mean, what is the point of having "ubiquinone" in parentheses in the title?

I've changed the title of the article. The reason for the title was just poor writing (I agree that it seems to imply that the enzyme is ubiquinone) but also the fact that someone had previously tried to change the title to the accepted name tht @xusr has mentioned but they did so incorrectly.


Total dark deprivation at day-neutral plants First of all, I am not a biologist.

Almost for a week, a question has come to my mind:
"Is it harmful ceaselessly exposing a plant to light?"
(I mean with natural & artificial light with proper spectrum)
I have been searching for a week, and I stumble upon many weird and wonderful things, and by them, I have become able to consider this topic more deeply, and refine my original question. However I have still not found the answer.
I am already familiar with these topics:

Light-dependent reactions
Light-independent reactions
Calvin cycle
Photoperiodism
Phytochrome
Cryptochrome
Long-day, Short-day, Day-neutral plants
Grow light

So my main question:
Does ceaseless light exposure with proper spectrum adversely affect a day-neutral plant?
As a layman I have started to fumble towards light-independent reactions, but I have not found strong claim. I have learnt that there are processes which taking place during dark phase, but are these reactions impossible in presence of light?
But probably there are other factors.

My resources were: Google, Wikipedia, (a tons of) academic paper, many article from Botanical Gazette, many blog & webpages about botany & greenhouses etc.

I cannot say anything about the general case, or specifically for day-neutral plants. However, Sforza et al. (2012) have studied the effects of light conditions on algae (used for biofuel production), and their results indicate several problems with continuous light. In continuous light conditions they find lower chlorophyll contents and higher carotenoid concentrations in cells, which leads to lower photosynthetic efficiency.

This figure shows chlorophyll contents (black) and chlorophyll/carotenoid ratio (red) under different conditions, with the two treatments to the left representing continuous light. (graph from Plos One)

  Results show that Nannochloropsis can efficiently exploit even very intense light, provided that dark cycles occur to allow for re-oxidation of the electron transporters of the photosynthetic apparatus. If alternation of light and dark is not optimal, algae undergo radiation damage and photosynthetic productivity is greatly reduced.

However, they also experiment with pulsed light, which in some cases lead to even lower rates of photosynthesis:

  However, similar experiments, at different frequencies, also showed that alternating dark and light may be detrimental, as demonstrated by the growth inhibition observed in the 1200-1 and −5 Hz curves. These cells showed a decrease in Fv/Fm values similar to that observed under constant strong light, indicating that the inhibition of growth was due to photoinhibition.

They also find that light pulses can be very short, and still allow for the photosystem to reset:

  The optimal duration of light pulses was found to be around 10 ms, which is consistent with the suggested PSII turnover rate in whole cells [4], [46]. Accordingly, after photon absorption by the photosystem, 1–15 ms are needed to reset the system, before it is ready to receive another photon [22]. If the illumination is this short, most photons are exploited for photosynthesis and do not lead to the formation of ROS which then causes photoinhibition. These results indicate that even strong light does not cause damage if it only lasts a short time. Conversely, longer exposure allows the generation of ROS and damage and, in this case, the abrupt changes in illumination undergone by the cells are as harmful to the photosynthetic apparatus as constant high light.

Different species of plants can have mechanisms to handle light stress in different ways, so the effects on different species and types of plants are likely to differ. However, their results should generalize to some extent/for some plant species.

You may also find this paper by Li et al. (2013) interesting.


Is this aquatic plant duckweed or something else? This plant has been growing in my pond for quite a time now. It multiplies in large numbers rapidly.
 Some told me it is duckweed or is it something else?

That looks very much like a duckweed.

The multiple roots rule out most genera within this group and so this is probably a Spirodela.

The apparently relatively large size and red undersides are consistent with this being Spirodela polyrhiza.

Picture by Christian Fischer available under Creative Commons Attribution-Share Alike 3.0 Unported.


What does entering of sex chromosomes to gametes mean during meiosis I? I am reading one answer about meiosis:

  During meiosis I, the sex chromosomes separate and enter different
  sperm or egg cells (gametes).

I assume that sex chromosomes refer here to homologous chromosomes that experience crossing-over after meiosis that is exchange of genetical information.

Meiosis I refers here to female meiosis I and to male meiosis I.
In both cases, homologous chromosomes separate resulting in haploid cells after meiosis I.
These homologous chromosomes enter sperm or egg cells according to the writer, which I cannot understand, since the given chromosomes, now sister chromatids after meiosis I, do not enter physically anything, they just divide into haploid cells, gametes, after meiosis II.

What is the meaning of the word "enter" in the given sentence?

I am confused by the word "enter".
I am assuming that the word refers to enter something physically which is not the case in my opinion here.

I seem to now understand the sentence. I read the clause in other words:

  During meiosis I, the sex chromosomes of the gametogonia separate in
  anaphase I and II and become eventually different sperm or egg cells
  after cell differentiation and maturation: male spermiogenesis and
  female maturation into ovum.

Female thing does not seem to have a special name for the maturation thing.
Female does not seem to have differentiation part at the last part similarly as male, since only one ovum is formed after the sequence of events.
Sex chromosomes refer to your parents genotypes. [jg89]

Problem seems to be solved now.

I would not personally use the word "enter" in a such sequence. It is a shortcut. Better would be "enter eventually" or "enter after a sequence of events". I prefer explicity instead of implicity.


Is ovum + ovum fertilization possible for human? In humans is it possible to fertilize a ovum with another ovum from the same female subject?

I already found some works in which the ovum is fertilized by a somatic cell (see e.g.  this ), but I am looking for fertilization specifically by another ovum.

Around a year ago I found in the internet a Japanese (ongoing) study on this, but cannot locate it any more.

I would greatly appreciate any help.

Using a somatic cell in an a ovum is what is typically done in the process of cloning.  It was the same process used to create Dolly the Sheep. What you're asking about is something very different:

Consider that somatic cells are properly diploid.  Whereas an ovum itself just contains a haploid number of chromosomes. In typical sexual reproduction the sperm fertilizes the ovum which would than bring the chromosome number to to correct tally.  So combining the genetic material in two ovum should bring the chromosome count to the correct tally as well, but scientists would need to somehow motivate the  activities that happen when typical  sexual reproduction occurs. It's likely very challenging to do that if not highly improbable. Should it work, this process could only produce female children.


Calcium for Humans: Supplements vs Fortified Sources I'm trying to be vegan, and purely natural foods lack sufficient calcium for the Recommended Daily Intake. Links 2 to 4 (but not 1) assert a correlation between calcium supplements and disease.

  [1. WebMD :] "Keep in mind that there's really not that much difference between getting calcium in a supplement and calcium in food."
  "Calcium-fortified foods -- such as cereals, some juices, and soy milk -- are excellent sources of the mineral, experts tell WebMD."

  [2. health.harvard.edu :] An 8-ounce portion of off-the-shelf orange juice contains about 300 mg of calcium. The calcium in fortified soy milk also compares favorably to whole milk.
  Breakfast cereals (which are also fortified) contain substantial amounts of calcium, especially when combined with low-fat milk.
  A portion of oatmeal on its own contains just 100 mg of calcium. “But if you cut up some dried figs and add it to a bowl of oatmeal with milk, you easily get about half of what you need without having any supplements,” Dr. Hauser says.

  [3. NY Times Blog :] All the researchers agree that, given the widespread use of supplemental calcium, better studies are needed to clarify possible risks and benefits, and to whom they may apply.

  Until such information is available, consumers seeking to preserve their bones would be wise to rely primarily on dietary sources of the mineral and to pursue regular weight-bearing or strength-building exercises, or both. Walking, running, weight lifting and working out on resistance machines is unquestionably effective and safe for most adults, if done properly.

  [4. NY Times :]  The institute’s expert committee, which included bone specialists, concluded that most people don’t need supplements of these critical nutrients and warned of serious health risks from the high doses some now take — including kidney stones and heart disease linked to calcium supplements, and the very falls and fractures that vitamin D is meant to protect against.

5. How and why would the calcium carbonate from calcium supplements be asserted as worse than that in the fortified foods?

6. Isn't solid calcium carbonate (e.g. in supplements) chemically the same as aqueous calcium carbonate (e.g. in fortified drinks)?

7. Are calcium supplements really worse than fortified foods with calcium?

This is close to a personal medical question, so I'll try and be vague and avoid advice.

There's nothing inherently bad about calcium supplements, and those links and thousands of others that are easy to find tend to all say that same thing.  Basically, for typical people on a typical diet, enough calcium is supplied through food that supplements are unnecessary.  The problem arises when people take too many supplements, such that their intake is significantly higher than the daily recommended intake.  These people can experience a number of symptoms, including kidney and heart failure.  Fortified food and supplements are, as best as I can tell, no different, except that food is simpler route for intake with built-in limit-setting.  That is, you can easily pop five calcium pills (BAD IDEA) but nobody is ever going to drink five containers of fortified soy "milk" on a whim.

My go-to example is that of astronauts.  Astronauts who are in space for extended periods of time must take calcium supplements, in addition to a strict exercise regimen to help stem the tide of bone loss.  Bone loss still occurs, however, because they can only take so much calcium before it starts to cause serious heart problems.  There's nothing inherently wrong with calcium supplements but for most people they are completely unnecessary.  You should talk to your primary care physician and perhaps a dietician.


The fundamental importance of R.E.M. Sleep. (Rapid Eye Movement) Question:
I know that experiments have been conducted to determine the importance of R.E.M. sleep in our sleep cycle. It is particularly important for learning, information synthesis, and recovery from distress. Why else is R.E.M. sleep important? What experiments have been done/observations been made to determine the neurological mechanisms underlying R.E.M. sleep? I know that we exhibit high frequency $\alpha$ waves, similar to the waves we experience during wakefulness.
Wiki:
During REM sleep, high levels of acetylcholine in the hippocampus suppress feedback from hippocampus to the neocortex, and lower levels of acetylcholine and norepinephrine in the neocortex encourage the spread of associational activity within neocortical areas without control from the hippocampus. This is in contrast to waking consciousness, where higher levels of norepinephrine and acetylcholine inhibit recurrent connections in the neocortex. REM sleep through this process adds creativity by allowing "neocortical structures to reorganise associative hierarchies, in which information from the hippocampus would be reinterpreted in relation to previous semantic representations or nodes.
Do these reorganized neocortical hierarchies remain this way?
Just HOW integral is R.E.M. sleep to our brain development?

REM sleep stimulates the brain regions used in learning. This may be
  important for normal brain development during infancy, which would
  explain why infants spend much more time in REM sleep than adults (see
  Sleep: A Dynamic Activity ). Like deep sleep, REM sleep is associated
  with increased production of proteins. One study found that REM sleep
  affects learning of certain mental skills. People taught a skill and
  then deprived of non-REM sleep could recall what they had learned
  after sleeping, while people deprived of REM sleep could not.

  Some scientists believe dreams are the cortex's attempt to find
  meaning in the random signals that it receives during REM sleep. The
  cortex is the part of the brain that interprets and organizes
  information from the environment during consciousness. It may be that,
  given random signals from the pons during REM sleep, the cortex tries
  to interpret these signals as well, creating a "story" out of
  fragmented brain activity.

Source: link


What is the energy cost of an action potential? As I understand it, ions flow down their electrochemical potentials through ion channels during a neuron's action potential. Otherwise, ion pumps work to restore and maintain the resting membrane potential. What is the energy cost of a neuron's action potential? That is, how much work must the ion pumps perform to restore the resting membrane potential after an action potential occurs?

There's a few [1, 2, 3] sources that claim it's on the order of $10^8$ ATPs per action potential. The first paper (which is a review that cites the second paper) also has some equations for converting from ATPs to free energy, although that's going to be very context dependent.

If you can't access the third paper, someone has helpfully entered the relevant figures into the bionumbers site.


Have there been new discoveries concerning the perception of taste for the last 10 years? What are the last discoveries concerning the perception of taste for the last 10 years?
We discovered the 5th flavour: umami.
Also the 6th and 7th: oleogustus and starchy.
Anything else?
Maybe in genetics, as we all have genetic predisposition?
Or concerning the creation of the systems in charge of the perception of taste during the embryo-genesis?

I'm not quite clear on exactly what you're interested in, but the short answer is yes, there have been discoveries related to the perception within the last 10 years.
The example that comes to mind is the role of the cannabinoid 1 receptor in the sense of taste of lipids.  The full text of a good article is available online here.

Source:
Brissard L et al. 2018. Orosensory Detection of Dietary Fatty Acids Is Altered in CB1R−/− Mice. Nutrients 10(10): 1347.


How do gene locations change during crossing over events? Suppose you have two variants from the same species, which have slightly different chromosomes I's to each other. Genes may be in slightly different positions on the chromosome, and the lengths of the chromosomes might be somewhat different. Suppose these are crossed to produce offspring. If a crossing over event occurs in the offspring during meiosis, what happens to the positions of the genes?
A concrete example of what I'm asking is the following. Suppose that in the above scenario, the first chromatid is 1Mb long and the second is 1.05Mb long. "Gene A" occurs between 6kb-8kb on the first chromatid and 10kb-12kb on the second. If the crossing over occurs and replaces the first 9kb on the first chromatid, what happens to gene A there? Does it cease to exist? Or does the crossing-over process somehow know to grab DNA from above 12kb from the second chromatid?

It depends on the regions of sequence homology between the two chromosomes. Crossing over occurs through pairing of homologous regions. If there's a substantial stretch of chromosome without a matching homologous region on its pair, that non-homologous region should loop out and not be involved in crossing over. Crossovers will occur only in paired homologous regions.
For example, if you have a chromosome I and I' as follows:
I   ABCDEFG
I'  ACDEHFGM
They should pair as:

A-(A)
B
C-(C)
D-(D)
E-(E)
(H)
F-(F)
G-(G)
(M)

Crossovers should not happen in the B, H, or M regions lacking homology with the other chromsome. Crossovers in a homologous region will just result in a new chromosome containing the left end of one crossover partner and the right end of the other.
Using I and I' above, a crossover in region E would produce either:
ABCDEHFGM or ACDEFG
Now, if you have repeated regions of homology in one or both chromosomes, or regions inverted on one chromosome vs. the other, pairing possibilities expand rapidly and all kinds of weird things can happen (and do in real life).


During weight loss, do we inhale more oxygen? During weight loss, triglycerides which are composed of carbon, hydrogen and oxygen, are broken down. During respiration, the inhaled $O_2$ is bonded to a carbon atom to form $CO_2$ which we exhale. However this process happens anyway, even one isn’t trying to lose weight. So that suggests to me that during weight loss people must inhale more oxygen, otherwise where are all those extra carbon atoms that we now have going?

First one needs to make it clear that oxidation of foodstuffs, either those in the diet or from deposited reserves, occurs in order to generate energy (ATP) for life’s processes — the most evident to the non-biochemist being to perform muscular work. So, as the poster correctly implies, this will occur in both fasting and non-fasting individuals, and the fairest comparison would be between the same individual performing the same amount of energy-requiring processes.

Let us consider this comparison in the simplest situation where the person “losing weight” is fasting, i.e. has no food intake (rather than being on some fancy diet). After his glycogen has been depleted, the fasting individual will be producing all the energy for his various needs by oxidizing triglycerides that had been deposited previously in his fat cells. The amount of oxygen he inhales (assuming this is strictly related to requirement — I’m not a physiologist, so I don't know) will be that required to oxidize the triglycerides to produce this required energy.

Now compare this to the same individual, not fasting. His energy needs have been assumed to be the same as in the fasting state, but he is generating this energy from his food intake. Making the unlikely assumption for comparison that this were all triglyceride, the amount of oxygen needed to oxidize this would be exactly the same as the fasting individual.

I think that deals with the fallacy in the question, perhaps caused by not reflecting on what the oxygen inhaled by the non-fasting individual is used for. Technically one should admit that if the simplistic assumptions do not hold, the strict equivalence would not either. Different foodstuffs (carbohydrates, fats, proteins) are in different oxidation states, so the amount of oxygen required to oxidize them in the fed individual would depend on diet. If the food intake of the fed individual were greater than his needs and he was depositing glycogen or fat, extra ATP would be required to do this, which would likely be generated by oxidative phosphorylation. No doubt one can think of other possibilities, but these were not the focus of the question.


Isolating the gene of interest for protein production For protein production, the gene of interest is inserted in an expression vector and introduced into a suitable host for expression. But how is the gene of interest for the desired protein isolated from the organism which possesses it?

One way could be to synthetically make the DNA sequence coding for that protein. Another could be to identify the gene of interest from a pre-existing genomic library or cDNA library of that organism. Are they the only methods?

The organism's entire genome could be taken and cleaved with restriction endonucleases, and a Southern blotting technique (i.e. electrophoresis followed by probe hybridisation and autoradiography) could be used to screen the gene of interest from the fragments produced. Of course, for this the gene sequence must be known beforehand, in order to synthesise the probe. Is this method also adopted? It seems inefficient - given that the fragments are assumed to have the intact gene of interest, and the gene should have been sequenced beforehand.

As you already wrote there are two basic ideas: Synthesis of the desired gene sequence and use of existing DNA.

DNA Synthesis is getting cheaper so it is becoming the method of choice for generating DNA-samples up to about 5000 bp (for example see the IDT-page for commercial gene synthesis). If this is too short for your desired sequence there is the possibility to split the gene to different of those synthetic sequences and to fuse them using Gibson-Cloning (Gibson et al. 2009) - after adjusting the synthetic sequences so that there is an overlapping sequence. Alternatively you could use classical cloning - provided there are suitable cleaving sites in your sequence.

If you don't want to synthesize the DNA and have a template available you could design suitable primers and amplify the gene from the template using PCR and purify it by gel-electrophoresis. Inserting the sequence into a vector then requires that you find suitable cleaving sites within the sequence and the vector.


Low-tech or low-cost technique for quantitative estimation in enzymology If an accurate measurement of enzymologic quantities is needed, then following established methods in the field is necessary.
However, it is sometime of great usefulness to ballpark a value before committing to taking the necessary time for protein purification, or buying the necessary equipment/reagents.
For such purpose a little "hack" can go a long way. This often involve using an available equipment
to substitute for another (e.g. maybe I have a FACS readily availably, however no HPLC).
I am seeking examples of "unconventional" use of lab technique that
can be used to determine enzymologic quantities ($K_d$, $V_{max}$, $K_i$ ...) as a first estimate -- whether you have partaked in such heresies, or have merely seen them used, possibly even in a non-formal/DIY environment.

If there is a way to:

Make the replication of a common culture organism (e.g. E. coli) dependent
upon the inhibitor or substrate of interest, possibly with a restrictive media.
Express the enzyme of interest in a relatively controlled manner in such organism (e.g. well caracterized promoter in plasmid with well characterized copy number),

Then you can get good mileage out of some serial dilutions and a OD600 meter. Even better with a plate reader.
Exact protocol will depend on the quantity under consideration, but mostly will amount to substituting around in the enzyme kinetics equations until the quantity of interest is a function of the concentration, and devise a scheme to cancel out the other unknown quantities (often substrate concentration ramp + starting OD ramp + curve fitting)