How to secrete a recombinant protein from E. coli? What are some secretory pathways that can be used to secrete a recombinant bacterial enzyme from E. coli?

I have a recombinant protein (29kDa) that I will express in E. coli BL21 cells.  For now I have been sonicating E. coli to extract the enzyme, but in the future I would like E. coli to secrete the enzyme.

According to the 2012 iGEM Kyoto team:

  The Twin Arginate Translocation pathway(TAT) is [an endogenous] secretion system in E.coli. This system can carry proteins that have torA signal amino acid sequences at N terminal. TatA, TatB, TatC and TatD compose Tat complex on inner membrane. Tat complex recognizes torA signal peptide and then it transports protein (with torA) from cytoplasm to periplasm. In addition, protein that has passed through TAT pathway cut off the torA signal. Proteins which are secreted by this system have no tag that obstruct the activation of the protein.

The team created a cassette with the TAT genes to increase the expression of the pathway and also included the Kil gene, which perforates the outer membrane, possibly aiding the external diffusion of the secreted protein. They noted, rather tongue-in-cheek, that

  Needless to say, function of outer membrane as membrane is essential for E.coli to survive. In other words, overexpression of Kil causes cell death. In this reason, we must find suitable amount of expression.

Note: according to their lab notebook, the team never observed extracellular GFP via confocal microscope (search that page for 'confocal'). So. Beware :)

Their project page also includes some references to the following literature:

Tracy Palmer and Ben C. Berks "The twin-arginine translocation (Tat) protein export pathway"
J. H. Choi. S. Y. Lee "Secretory and extracellular production of recombinant proteins using Escherichia coli"
G. Miksch · E. Fiedler · P. Dobrowolski · K. Friehs "The kil gene of the ColE1 plasmid of Escherichia coli controlled by a growth-phase-dependent promoter mediates the secretion of a heterologous periplasmic protein during the stationary phase"
Brad A. Seibel* and Patrick J. Walsh "Trimethylamine oxide accumulation in marine animals: relationship to acylglycerol storage"


Proteins in water vs proteins in crystal I am not very familiar with the experimental procedure of x-ray crystallography except that it involves the very delicate matter of producing crystal that contain proteins and then diffracting rays through it to get a pattern that tells us about the shape of the protein.

I am curious though when you crystallize a protein that usually stays in the cellular fluid, does it go through any conformational or size changes. For instance isn't there some pressure applied by the water that would potentially result in protein being smaller then what it might be under less pressure. Or what about hydrophobic\philic effects that play an important role in protein folding. Of course once the protein is folded it is bonded through interactions stronger than hydrophobicity so it is not that delicate. But still a complete change of surrounding environment should count as a big change, should it not? So are there any theoretical or experimental explanations as to whether the protein changes size and\or shape during crystallization? References to both experimental and theoretical work are very welcome. Although I guess experimental evidence would make more sense in this matter since usually potentials are optimized to account for the crystal structure to be the minimum of the energy so it I can't see how theoretical works could potentially help to understand this issue. I guess one way would be to take a native protein structure determined by X-ray and run it through AB initio  molecular mechanics where potentials do not depend on parameters obtained from the native states of proteins on PDB database. I don`t know how theoretically sound that would be though.

Protein crystals are not like crystals of more commonly found substances like salt [NaCl] or diamond [carbon only.]  These materials do not include other atoms in their crystal structures.  For instance, a crystal of NaCl will contain sodium ions and chloride ions.  X-ray crystallography of that material will, after mathematical processing, show electron density peaks of two varieties, each easily distinguished by intensity as either a sodium ion or chloride ion.  Any other electron density peaks will be few and far between, as well as clearly identifiable as an interloper.

Because most proteins have hydrophilic regions on the exterior surface of the structure, crystals of proteins actually contain a considerable fraction of water molecules within the crystal itself.  These water molecules are part of the crystal because they are interacting with those hydrophilic residues on the tertiary surface of the protein, both by hydrogen bonding, in some cases, and less specific polar interactions in other cases.   This is at least one of the reasons why obtaining a crystal of any random protein is not at all a routine endeavor.  The large proportion of water in these crystals make them very fragile once they do form, as well as not necessarily likely to form in the first place.

If you go into the technical literature to look at the electron density maps that the more commonly diagrammed structure maps are derived from, you'll be able to actually trace water molecules surrounding the individual protein molecules.

In fact, in the days of development of protein crystallography, assigning correct specific atoms to the various electron density peaks was a decidedly non-trivial task.

Effectively, despite being a crystal, the microenvironment experienced by the protein within the crystal is very much like that in an aqueous environment.  The hydrophobic interactions & hydrophilic interactions will not be very different from those in solution.

That is, the crystalline state achieved is not, in fact, "a complete change of surrounding environment" to use the phrase that you've used in your post.


What is the precise mechanism by which exercise reduces chance of cancer? Sources like this: http://www.cancerresearchuk.org/about-cancer/causes-of-cancer/physical-activity-and-cancer/how-physical-activity-prevents-cancer point out that we can reduce our risk of some cancers by exercising.

But it seems to just be hypothetical, like "scientists think insulin can turn on signals that tell cells to multiply", and

"This can lead to the cells multiplying much more frequently than usual, to replace dead and damaged cells, increasing the chances of mistakes that could lead to cancer"

But human metabolism significantly increases during and after exercise, implying high rate of cellular division! Therefore, these 'hypotheses' seem questionable in their attempt at saying, "cells don't divide as much". I believe that these may be contributing factors, but I don't believe they're the main cause of most cancers in general. I am deeply skeptical that muscle inflammation requires less cell division than colon inflammation.

I have a hypothesis that exercise simply reduces cancer in the following manner: increase cellular movement, which increases the probability of the following:

1) t-cells tag foreign pathogens
2) white blood-cells capture foreign pathogens
3) damaged cells are repaired/found/killed faster

Statistically, increasing the entropy of a system would allow the individual components to cover a larger area in a shorter amount of time. Since the number of pathogens introduced into the system remains relatively constant while the interal system speeds up, it's like running a high-pressure jet stream of water and soap through pipes to clean them out. The soap (t-cells) and pressure (contractions of heart/blood vessels) together help clean the system effectively.

I'm having trouble finding evidence/support for this hypothesis, so if someone could point out the flaws in my hypothesis or point me to some sources to find out more, I'd be deeply appreciative.

Vigorous exercise (even for five minutes) causes increased DNA damage http://www.ncbi.nlm.nih.gov/pubmed/20839226. The increased DNA damage would stimulate the defenses including the immune system (e.g. natural killer cells) http://www.ncbi.nlm.nih.gov/pubmed/16618710, and the boosted immune system would eliminate cancer cells, reducing cancers based on the immune suppression model of cancer http://www.ncbi.nlm.nih.gov/pubmed/27928220. The reduction of cancers with increased exercise (physical activity) has indeed been observed http://www.ncbi.nlm.nih.gov/pubmed/18506190.


Polydactyly and its genetics One of my friend was saying that her aunt (father's sibling sister) was having polydactyly but none of her cousins (her aunt has two daughters) is having it.

What is the chance that my friend's children inherit polydactyly?

(considering that her partner nor anyone in his generation exhibit polydactyly)

Polydactyly can be dominant or recessive. that is

A single copy of the mutation/s involved result in the phenotype
vs
Both copies of the gene must be mutated to result in the phenotype

When two random people who don't have polydactyly nor a family history of polydactyly have a child, there is around 1/548 (0.18%) chance that child will be polydactyly because the parents were carriers without knowing it, and a 1/11.7 (8.54%) chance the child is a carrier of a single copy

If the aunt's polydactyly is Dominant, then your friend's father hasn't inherited it (he isnt polydactyly) and just has the normal population chance of being a carrier.

In the case of Dominant polydactyly, assuming your friend has a partner with no history of polydactyly, your friend and her partner have the same chance as average of a polydactyly child (1/548)

If the aunt's polydactyly is recessive, meaning she has two copies one from each parent (you friend's grandparents), there is a 1/130 (0.76%)chance your friend's child will have polydactyly (4.2 times more likely), and a 1/4.5 (21.4%) chance of being a carrier (2.6 times more likely)

I'll quickly go through the working/
if you're interested:

Given that the grandparents are both carriers (needed for the aunt to have two copies), then your friend's father has a 2/3 chance of being a carrier of a single copy (1/3 chance no copies, 0/3 chance having two copies because he isn't polydactyly).

Your friend's mother has the usual 1/11.7 chance of being a carrier.

The chance of your friend inheriting a single copy is (chance passes from father) + (chance passes from mother) - (chance of getting two copies)

=0.6600/2 + 0.0854/2 - (0.33*0.0427)

=0.3727 - 0.0140

= 0.3586

35.9% chance your friend carries one copy

Your friend has 1/2.8 chance of carrying and 1/5.6 of passing it on

Friend's partner has the 1/11.7 chance of being a carrier and the 1/23.4 chance of passing it on

Therefore their child has

=0.1793*0.0427 (chance friend passes on * chance partner passes on)

=0.0076

=1/130 chance of having two copies, having polydactyly

=0.1793 + 0.0427 -(0.1793*0.0427) (chance any copies - chance two copies)

=0.2143

=1/4.7 chance of one copy a 2.5 times increase risk


What is the effect of persistent hypothermia on cardiac performance? I define persistent hypothermia in this thread about the mechanisms of persistent hypothermia.
The Graph of Katzung et al. in Pharmacology about Heart Failure:

I am thinking which parts here are critical on temperature.
Temperature has a direct effect of reaction rates of chemical reactions here, for instance NE, AII and probably chemical reactions in endothelin such as ET.

Therefore, I am thinking that the relationship between temperature and cardiac performance cannot be linear at all.
Some have said me that low temperature can decrease metabolism and oxygen consumption.
However, I started to think differently when time goes enough far that is when heart cannot anymore supply enough blood with oxygen. Thus, hypoxia can occur and asymptomatic exodus may occur.

Physiological case

Based on physiology, I can propose that the cardiac output curve shifts to the left (CO1 $\to$ CO2), due to less oxygen being supplied to the heart, similarly EDV1 (end-diastolic volume) shifts $\to$ EDV2 and SV1 (stroke volume) $\to$ SV2.
However, the venous return (VR) curve can shift much more, since I propose that the effect of temperature on smooth musculature is relatively bigger than on heart because of proportional size of tissue.
So the VR1 shifts to VR2, so EDV2 $\to$ EDV3 and SV2 $\to$ SV3.
Consequently, SV3 > SV1, while EDV3 < EDV1.
See my draft figure about this:

where EDV (End Diastolic Volume) in the x-axis and SV (Stroke Volume) in the y-axis.

In a healthy person, who have no hypertrophy of ventricles and elastic myocardium, the heart can tolerate this. So such a condition of cardiac failure as in the figure 13-3 is possible.

However, if flexibility of the myocardium, for instance, is not possible, such a pathway may not be possible.
The autonomic nervous system may enter the picture and increase vagus nerve stimulation (PS more).
However, not sure about the exact pathway.

What is the effect of temperature on cardiac performance?
How can temperature decrease cardiac performance?

Winter swimming and infarcts

The publication Long-term risks of cardiac and cerebral vascular diseases increased following winter swimming in the cold seawater which came out just some weeks ago shows a link between long-term winter swimming and CVD.
I think this is the best evidence so far about the possible link.

WYSIWYG's comment has some good general idea:

  Many processes are affected by temperature including metabolism and
  growth rates. Reaction rates increase with temperature but not in case
  of catalysed reactions where the catalyst can operate at only an
  optimum temperature.

Some related topics

temperature effect on the rate of protein degradation

So further studies

protein degradation in the heart in persistent hypothermia
...

Effect of persistent hypothermia on processes of cAF

[1]

Let's have cAF (chronic atrial fibrillation) here as an target.
Electrophysiological study shows that cAF-related remodeling is typically divided into three categories: 1) electrical, 2) contractile and 3) structural.
They cause respectively

1) shortening of both the action potential (AP) duration and effective refractory period (ERP)
2) possibly a result of impaired Ca2+ intracellular handling
3) changes of cellular level (hypertrophy, glycogen accumulation and modified mitochondrial morphology) and tissue fibrosis

cAF's processes in persistent hypothermia

I cannot say now more anything about persistent hypothermia and cAF by confidence.
Those mechanisms of Koivumäki et al are cellular processes, while the representation of the heart requires integrative analysis in the cellular, tissue and organ levels.

In cellular level

Only some catalyzed reactions can work in persistent hypothermia. TODO consider which enzymes of the heart and body work in low temperature in short-term and long-term cases. Depletion cases too.
Effect of persistent hypothermia on the outflux of Calcium (probably, slows down).

In tissue level

I can say without rigor that electrical coordination is uncoordinated in tissue fibrosis.

In organ level

I say say without rigor that the mean electrical axis should be determined and fixed in the study.
Effect of Arterial hypertension must be fixed. Sokolew-Lyon index can a starting point for the indicator but better indicator is required with higher specificity.

Persistent hypothermia from the extreme side (Sauna)

[2] Regular Sauna is with better hemodynamic function; however, the association of sauna bathing with cardiovascular and all-cause mortality is not known.

so possible effect of persistent hypothermia can be

lower hemodynamic function if no compensation mechanism
better hemodynamic function if some compensation mechanism (genetics; unknown)

Some research topics

Effect of Persistent Hypothermia on the Arterial Hypertension. This may be associated with coagulopathy, especially in the lower limb.
Effect of Persistent Hypothermia on Atherosclerosis. It would be very nice to see long-term study about the effect of regular 4-7 winter swimming on the cardiovascular risk score, SCORE and others.

Sources

In Silico Screening of the Key Cellular Remodeling Targets in Chronic Atrial Fibrillation. Koivumäki et al. Computational Biology.
Association Between Sauna Bathing and Fatal Cardiovascular and All-Cause Mortality Events, here

Please, see the reference of the publication for more better view.


How do I score differential activity of cellular pathways in microarray data (not enrichment)? I would like to identify cellular pathways (KEGG) with discriminative changes in the average activity (expression levels) of their gene members in a two-condition microarray dataset. The goal is to use the average pathway activity for machine learning (sample classification), not to identify pathways enriched in differentially expressed genes (i.e. not performing a classical gene set enrichment analysis).

How do I score differential activity of cellular pathways in microarray data (not enrichment)?

You would look at downstream genes, which are selective for individual pathways - or genes which have binding sites for transcription factors that sit at the end of your pathway. Depending on the existing literature, and your experiment, and the specific pathway, this can include genes, which are themselves part of the pathway (if feedback). For interpretability you would prefer genes, which have previously been established as makers of a pathway in preceding literature.

  I would like to identify cellular pathways (KEGG) with discriminative changes in the average activity (expression levels) of their gene members in a two-condition microarray dataset.

This might be tricky, since the taking the average introduces several assumptions such as: little impact of technical background (expression of most genes of pathway above background), average being representative of the KEGG pathway of interest (and not only of the most abundant pathway members), and enforcing a somewhat arbitrary decision of whether to average log-transformed data (which is justified for many genes, but not genes that don't scale multiplicatively, such as many stress genes), or not log-transforming.

  The goal is to use the average pathway activity for machine learning (sample classification),

You can use this to your advantage, and create multiple features per pathway (e.g.: median, mean, variance, non/log-transformed etc..., manually -curated signature genes of pathways), and then having machine learning choose the best features for your classification (e.g.: as would happen if using Random Forest Classifiers)


Are there any sustained efforts to model existing ecosystems? Are there any ongoing, sustained efforts to obtain enough data about an ecosystem or part of one to build a viable computer simulation of it? All I can find (e.g. in Brazil or by google) appear to be sandboxes for demonstration or experimental purposes.
What I envision is a true model that can predict the future development of an existing system, and of course run simulations to predict the impact of certain external changes: Deforestation, temperature and precipitation patterns, introduction of non-native species etc.
Such a model would require a fairly detailed and complete biological inventory as well as detailed knowledge of the species' interactions, and a detailed map of the physical and chemical makeup of the location or region (water, ground, atmosphere, radiation). This would obviously be a vast undertaking, but with the potential of tremendous insights. Last not least, such a model would be a tremendous planning tool.
Are there any projects attempting this?

Such a model would require a fairly detailed and complete biological inventory as well as detailed knowledge of the species' interactions, and a detailed map of the physical and chemical makeup of the location or region...

I suggest reading about the The Simons Collaboration on Computational Biogeochemical Modeling of Marine Ecosystems (CBIOMES).1 This collaboration has produced ample research concerning the modeling of marine microbial communities in terms of spatial composition, metabolic interactions, nutrient flow, and seasonal variation.
Here are the research efforts highlighted on their website:

Developing New Computational Modeling Frameworks

Developing a New Trait-based Understanding of Microbial Communities Based on Metabolic and Elemental and Macromolecular Constraints (led by Zoe Finkel/Dal)
Constraint-based Modeling of Marine Microbial Community Metabolism and Physiology (led by John Casey/MIT)
Statistical Modeling of Microbial Communities: Niches, Traits, and Interactions (led by Andrew Irwin/Dal)
Thermodynamically Constrained Metabolic Networks for Ocean Modeling (led by Joe Vallino/MBL)
Models of Marine Microbial Biogeography and Biogeochemistry (led by Mick Follows and Stephanie Dutkiewicz/MIT)

Collecting and Compiling Relevant Datasets

Ocean Color and Biogeochemistry (led by Shubha Sathyendranath/PML)
Data and Tools to Define the Biogeography of Marine Microbes (led by Ginger Armbrust/UW)
Microbial Growth, Interactions and Biogeographies from ‘Omics’ Data (led by Jed Fuhrman/USC)

Bringing Together Models with Data

Advanced Statistical Analysis of Marine Microbial Systems (led by Christian Müller/Flatiron Institute)
Unifying Data and Models through Biogeography (led by Chris Follett/MIT)
Data Assimilative Modeling of Marine Ecosystems (led by Chris Edwards/UCSC)
Statistical Network Inference and Time Series Analysis (led by Jacob Bien/USC)

Concerning specific geographic sites, one of the best understood marine ecosystems is the San Pedro Channel off the coast of Los Angeles, which has been studied since 1998 as part of the SPOT project.2 Sampling efforts from this site include sensors that capture continuous in situ measurements of dissolved oxygen, fluorescence, temperature, salinity, and pressure, as well as monthly charters that collect seawater to measure nutrients (nitrate, nitrite, phosphate, silicate) and chlorophyll at 12 discrete water column depths. Peruse the publications section of the SPOT website to better understand the ecological and geochemical research that the SPOT project has enabled.
If you are further interested in the global effort to characterize and model the dynamics of marine microbial communities, I recommend a 2015 review by Fuhrman, Cram, and Needham3, which discusses methods to analyze microbial networks through space and time.

References

https://cbiomes.org/
https://dornsife.usc.edu/spot/
Fuhrman JA, Cram JA, Needham DM. Marine microbial community dynamics and their ecological interpretation. Nat Rev Microbiol. 2015 Mar;13(3):133-46.


Is excretion always necessary? I know we defecate or/and urinate to rid ourselves of toxins and excess undigested food. If I was somehow able to get exactly what my body needed to function.

Let's say that I create a pill (or something) that provides the body with literally and exactly the nutrients and hydration it needs, would there still be a reason to carry out excretion?

Do humans or any animal, absolutely have to excrete?

Yes; there are byproducts of metabolism and maintaining the body that must be excreted, which has nothing to do with taking in unneeded nutrients. For just a few examples, urea is produced normally as part of the constant building and break down of proteins, but must be excreted, the brown color of feces comes from the breakdown of red blood cells, and a substantial weight of the feces is gut bacteria, some of which are necessary for proper digestion of some of the nutrients you take in.


Do Viruses produce a biomagnetic field? From wikipedia:
Biomagnetism is the phenomenon of magnetic fields produced by living organisms.

The present scientific definition took form in the 1970s, when an increasing number of researchers began to measure the magnetic fields produced by the human body. The first valid measurement was actually made in 1963,[1] but the field began to expand only after a low-noise technique was developed in 1970.[2] Today the community of biomagnetic researchers does not have a formal organization, but international conferences are held every two years, with about 600 attendees. Most conference activity centers around the MEG (magnetoencephalogram), the measurement of the magnetic field of the brain.

Do viruses produce such a field?

Every atom produces a magnetic field, so the formally correct answer would be "yes" (assuming that viruses belong to the tree of life, which is disputed -- otherwise, one would not use the prefix 'bio').

However, biomagnetism as a science (and not pseudoscience) is concerned with more measurable effects. The biomagnetism of a virus will be negligible compared to all the surrounding cells, and hardly measurable.


How does changing the shape of ATP synthase specifically prevent the enzyme from working any longer? I am currently stuck on working out how to answer this question:

"A random mutation causes the enzyme ATP synthase to change shape so that it can no longer function. Describe the impact this would have upon respiration and the overall production of ATP."

My question is: How does changing the shape of ATP synthase specifically prevent the enzyme from working any longer?

If you look at an enzyme and its substrate you can also see this as a lock (the enzyme) and the key (the substrate). The key fits the lock and opens it, the substrate fits into the active pocket of the enzyme and a reaction takes place. See this figure for illustration (from here):

If the enzyme (or the substrate) changes its outer shape (this is what happens when amino acids of a protein are changed), this fit will not happen anymore and the reaction which is catalysed by the enzyme will not take place (the lock will not open).


Can vitamin B17 cure cancer? I have heard that a 'vitamin B17' can cure cancer, but that the medical industry never talks about it, since making it legal would cause them loss of billions. But I have never found a reliable report on whether B17 really works or not. There is a question on 'vitamin B17' deficiency as a cause of cancer (see this post), however, not on 'vitamin B17' as a possible medication for cancer. What are the proposed mechanisms? And is there evidence that 'vitamin B17' really works in curing cancer?

Laetrile/Amygdalin has been claimed to be a suitable treatment for 'cancer' (which is a summary term for an extremely heterogeneous class of diseases). Even though laetrile/amygdalin in these claims is often called a vitamin, it in fact is not a vitamin as the molecule is not essential for the metabolism (Greenberg (1980)).

The claimed effects of laetrile/amygdalin are not only based on supplementing the molecule to balance a putative deficiency (with the false assumption that it is in fact necessary), though. Both other putative mechanisms are based on reactions that form HCN/cyanide: the enzyme $\beta$-Glucosidase breaks down laetrile/amygdalin and this reaction releases HCN. The argument now is that tumour cells have higher levels of $\beta$-Glucosidase which leads to accumulation of cyanide in tumour cells - with the effect of killing the tumour cells selectively. This would be great... if healthy and tumour cells actually had different levels of the enzyme. Unfortunately, they seem to have similarly low levels of $\beta$-Glucosidase (Greenberg (1980)). Even more problematic, Greenberg (1980) also reports elevated levels of $\beta$-Glucosidase in the liver and small intestine ... and you would not really want to release cyanide there.

There is a second mechanism, though: The enzyme $\beta$-Glucuronidase is claimed to be at higher levels in cancer tissue than in healthy tissues (leading to the same desirable effect described above). But again, there does not seem to be a difference in enzyme levels between healthy and cancer tissues (Dorr and Paxinos (1977)), and even more: $\beta$-Glucuronidase does not even break down the molecule as laetrile/amygdalin has a glucoside bond - so there is not even any cyanide release in that case (Holzbecher et al. (1984)).

Additionally, there is no clinical evidence that laetrile/amygdalin is an appropriate treatment for any form of cancer. This topic has been reviewed substantially (see Milazzo et al. (2006) for a review and this fairly recent Cochrane review by Milazzo and Horneber (2015)) and none of the studies included and analysed indicate any positive effect of laetrile/amygdalin. On the contrary, the in vivo cyanide formation after laetrile/amygdalin uptake makes the treatment very dangerous as it can lead to cyanide poisoning (and death, eventually) - especially after oral uptake due to higher $\beta$-Glucosidase concentrations in the digestive system. The authors of the Cochrane review therefore conclude that

  The claims that laetrile or amygdalin have beneficial effects for cancer patients are not currently supported by sound clinical data. There is a considerable risk of serious adverse effects from cyanide poisoning after laetrile or amygdalin, especially after oral ingestion. The risk–benefit balance of laetrile or amygdalin as a treatment for cancer is therefore unambiguously negative.


Do cockroaches eat their shells after moulting? I recently witnessed a cockroach eat its shell after it moulted. Do cockroaches always do this?

Yes, it's fairly common for insects to eat their egg casings, shed skin etc. where possible. In a similar vein, as Alex Stone mentions, spiders often eat their webs too. There's generally plenty of valuable protein and nutrients tied up in there, so why not recycle?


Calculating PCR Cycles I have a problem understanding a PCR exercise, it says to calculate the number of cycles to get 1µg of the DNA fragment, starting from 10ng and then from 500ng, I know about 2^n, and the exercise even gave the answers:

For 10ng, we need 29 cycles
and for 500ng, we need 24 cycles

But I don't know how they did it, I tried with 2^n and ended up with something totally different. I would be grateful if someone explained it to me. Thank you.

With every round of PCR, your sample doubles (ideally) and you are right when using $2^n$ for calculating the amount of DNA produced.

The formula would basically be like this:

$$X_{n} = X_0 2^n \\[1em] n=\log_2(X_n/X_0)$$

Just substitute the values of $X_0$ and $X_n$ — 10ng and 1000ng. The answer would be ~6.64 cycles.

The 500ng case is easier to imagine. The amount is doubled between 1µg and 500ng. So it is just one cycle of PCR.

If this was your answer then you are right. If book says otherwise then it is wrong or you could have read the question wrong.


Is it correct that the body only responds to the most painful stimulus? I'm rather ashamed to say that this question is partly based on an episode of House.

I have previously heard that, if there are multiple simultaneous painful stimuli, the mind will only feel the sensation of pain from the most severe injury.  A large amount of googling has turned up nothing and PubMed searches are proving tricky as I cant find the name of this effect (if it exists).

If it does exist, is the mechanism solely effective for pain signals or would we for example only feel cold at our coldest points (i.e. from the face or the hands rather than both) on a frosty morning?

Your question statement is a little bit incorrect or, better say, imprecise.

First of all it is not clear what you mean by the "body response" here? Pain is sensed by peripherial receptors (several types of receptors, mostly purinergic, are assumed to play role in pain preception) and then this sensation is propagated into CNS. So, the local "response to pain" (like swelling, increase of the blood perfusion) is not the response to the pain stimulus, but rather a methabolic response to the cell injures and release of many humoral factors like interleukins, "wound hormones" etc.

And this is true that out of many different pain inputs the one with highest intensity seems to "outshine" all other inputs and ultimately the pain perception is constrained to a single body part. However, if you consciously focus your perception on other parts of your body you may be able to percieve the pain originating from these parts even if this pain is lower.

This principle is known as a smaller particular case of a more general principle known as "the dominance principle of Ukhtomsky". Wikipedia has only the Russian language version about this principle (as well as about Ukhtomsky, a prominent Russian physiologist) and it seems to be not really known outside of the Russian scientific community (this is the only page I found about him in English).

The more general principle of Ukhtomsky postulates the following: one certain input may lead to the formation of the dominance center in the cortex. The domaninace center is characterized by the higher level of nerve cell excitation, whereas the rest of the cortex undergoes an inhibition so that different, even unrelated inputs converge here, helping this center to exist for longer time. The only way how this center can be ceased is to form another dominance center by a extremely high stimulus (for example a startle sound). Here the most insensive pain leads to the formation of such a center and all substantial pain stimuli just contribute to the persistence of this center: the pain is however percieved to originate from the place where the first stimulus, responsible for dominance center formation, originated from.


Is it safe to use an egg incubator to grow bacterial cultures? I've been using a small egg incubator to grow environmental bacteria in petri dishes. I always wear gloves and glasses when I handle the plates and do Gram staining. How likely is it that bacteria grown on dish could become airborne when I open the incubator or the dishes themselves?

A good practice to minimize the contamination of a Petri dish and of the external environment is by never completely removing the lid of the Petri dish: to access the content of the Petri dish with an inoculation loop, lift the lid on one side, slowly: just high enough for the inoculation loop to get in, get some of the content, and get out.


Does a walk after a meal help with digestion? I am a bit confused with the notion that "walking after meals helps you in digestion ",

Some say that it helps, whereas others oppose it. Can someone come up with a valid explanation for this?

apparently walking helps in the movement of food into the stomach and improves digestion. Also helps in decreasing blood sugar after meals, which decreases cardiovascular risk and potential signal diabetes by helping muscles absorb glucose in the blood. Here is the link to a study done comparing the results of walking after food and after a drink. Also a study was conducted where when people with Type 2 diabetes took a 20 minute walk just 15 minutes after eating, their post-meal blood sugar levels were lower than if they had walked before dinner or not walked at all. Here is the link to another similar study.


Species Identification: Spider I usually would search for myself, but I need to be super sure about the identification because I need to know if I need to get an exterminator in here or not. (I think it might be a giant house spider, but don't let me influence your analysis.)

So I live in the northern part of Ireland (About 40 minutes from Derry Northern Ireland over in County Donegal) and I went to my bathroom to a VERY fun surprise this morning. It was this wonderful spider in my bathroom. For reference, the lip of the glasses it is depicted in are 8 - 8.5 cm in diameter.

The missing leg was not my fault either, I was very gentle with the spider and released it outside post photo-shoot. (Warning: these are macro shots of the said spider)

More high resolution photos available on my Flickr (SolarLunix).

Looks like a house spider (Tegenaria domestica)


Why don't plants get sunburned? I just saw a video about the biology between sunburn, UVA and UVB and the different things we know about sunburn in humans. ( http://www.youtube.com/watch?v=ZSJITdsTze0 )

I wonder what keeps plants from getting sunburned?

By sunburned I meant that ultraviolet light injures the plant so that it requires some sort of healing process for the plant to be as healthy/strong/resistant to disease as a plant that isn't harmed.

The following study shows evidence that UVB does damage plant DNA.

Rousseaux et al. Ozone depletion and UVB radiation: Impact on plant DNA damage in southern South America. Proc Natl Acad Sci U S A. 1999 December 21; 96(26): 15310–15315.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC24816/


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

You're right that evolution is largely a gradual progression, but we don't have the luxury of having that gradual progression in the fossil record. We'll have a fossil from, for example, 350 KYA and another from 190 KYA. The older one is clearly not modern human and the more recent one is. So the age of modern humans is set at approximately 200 KYA, especially since genetic calculations confirm that age.

Now, if we find a 400 KYA fossil that is clearly modern human, then there'll be some 'splaining to do, but so far, nothing like that has happened.


Is the six-layer cortex model of the mammalian cortex still the most accepted model? I've been reading a bit about the different layers of the cerebral cortex and its clear that certainly not every region of the cortex has the same number of layers. Thus, the idea that every region has six-layers is clearly false.  And I think this fact is definitely well known.

Do neuroscientists still view the six-layer model as an accurate model? If so, what aspects of it have changed over time that now incorporate the fact not every region has six layers?

Aside:

Let me clarify my question. If not every region has 6 layers, why don't we just say there is a layered cortex and not specify a number? But if we decide to do this, what distinguishes the mammalian "6-layered" cortex from non-mammalian species that have a so-called "3-layer" cortex

See The Microcircuit Concept Applied to Cortical Evolution: from Three-Layer to Six-Layer Cortex by Gordon Shepard for more.

Short answer
The layers in the cortex are histologically and functionally defined. Both 3- and 6-layered cortices are found in the human brain. Hence, the different cortical layers are not models, but classifications based on empirical observations.

Background
The different cortical layers have been defined by histological staining and microscopy. The layered organization of the mammalian cortex is typically explained in textbooks by using the neocortex as an example, which has 6 layers (Fig. 1):

Fig. 1. Layered cortex. Source: What-When-How - Neuroscience.

As one can see in this picture, layer VI can be divided histologically into 2 sub-layers, namely VIa, containing mainly pyramidal cells, and VIb with mainly horizontal cells (Prieto & Weiner, 1999). Hence, a 7-layered cortex could be argued for as well - it is all kind of subjective.

The functions of the 6 layers are illustrated in Fig. 2.

Fig. 2. Functions of the 6 layers. Source: Free-Stock-Illustration.

However, the primary olfactory human cortex (the paleocortex) contains only 3 histological layers, as opposed to the 6 identified layers in the neocortex (Fig. 3). The primary olfactory cortex is part of the allocortex in man.

Fig. 3. Neocortex versus paleocortex. Source: Slideshare.

The primary olfactory cortex receives direct sensory input from mitral cells in the olfactory bulb in the outermost layer Ia. layers Ib, II, and III receive input via local and long-range intracortical connections. Sensory and intracortical inputs converge in layers II and III. The three-layered palaeocortex is different from the six-layered neocortex in sensory areas. In the neocortex, sensory and intracortical microcircuits are distributed to two different layers. Sensory inputs from the thalamus target layer 4. Layer 4 subsequently projects onto layer II/III, which distributes and receives intracortical associative fibers. Note that the olfactory system is exceptional in that it does not relay its information via the thalamus, explaining the absence of layer IV (Wiegand et al., 2011).

Reptilians and birds typically have a 3-layered cortex (Nauman et al., 2015).

References
- Nauman et al., Current Biology; 25(8): R317–R21
- Prieto & Weiner, J Comparative Neurology (1999); 404:332–58
- Wiegand et al., J Neurosci (2011); 31(34):12149 –58


Finding different Proteins with same function Could you help me about finding two different proteins that coming from different ancestors, perform same function?

Thank you

There will be a lot!  Chromosomal dihydrofolate reductase and type II (plasmid) dihydrofolate reductase have not been derived from common  ancestor but catalyze completely the same reaction including stereochemistry by the authority of Brito.

Bacterial phenylalanine hydroxylase too is completely different in sequence of amino acids from phenylalanine hydroxylase from mammals (where plants have no such protin). The literature shows this paper Cloning and nucleotide sequencing of phenylalanine dehydrogenase gene of Bacillus sphaericus.


What do ants do with human finger nails? There is place in my house where I cut my nails. Here, there is an ant hole where an ant colony is seen.

Whenever I cut my nails from here, they take my nails inside their hole. I was wondering what they do with them.

Do they protect their houses with them or feed them to their young ones?

I believe that MattDMo's hypothesis is incorrect.  Only one group of ants, the Attini tribe, cultivates fungus as a food source.  This group is exclusively a New World group, thought to have originated in the Amazon rainforest and spread out from there.  I see from your profile that you are located in India, which is outside the range of the fungus-cultivating ants.

So if the ants aren't using your fingernails for fungus cultivation, what are they doing with them?  Fingernails are primarily composed of keratin, a very tough protein which ants cannot digest.  However, it is likely that the clippings also contain materials like dead skin, nail fungus, or other organic substances that the ants can eat, making them worthwhile for the ants to collect.

References:

U.G. Mueller, T.R. Schultz, C.R. Currie, R.M.M. Adams, & D. Malloch (2001). "The origin of the attine ant-fungus mutualism". Quarterly Review of Biology 76 (2): 169–197. doi:10.1086/393867


Why do ostriches have wings? Wings serve most birds for flying, or (as in penguins) for swimming. But ostriches, which exclusively use only their legs for locomotion, still have wings. Why?

There is a common misconception that a selective process is needed to remove a feature from a population. However, the correct approach is quite the opposite: selective processes normally maintain a feature in a population: if a given feature stops promoting selective advantage, its corresponding genes start to "erode" and the feature disappears from the population (and that can happen in different rates, depending on several factors: have in mind that maladaptative features do exist).

That being said, the maintenance of wings in ostriches indicates us that there must be a reason for it.

It has been hypothesised that wings:

Improve balance when running;
Helps regulating temperature;
Serve as mating display.

(source: University of Washington)


What does (G+) (G++) in terms of male mutation rate and male-heterogametic XY-system? What's the expression for $\alpha_m$ in case of male-heterogametic XY systems (G+)?

Derive the corresponding $\alpha_m$ expression of for (sic) male-heterogametic XY systems (G++)

I have absolutely no idea what they mean with G+ and G++ in the exercises. I have searched the whole Internet and the lecture slides for this but I think I am going crazy. Has it something to do with the gametes? Anyone who knows?
Thanks in advance!

I think you need to provide more context.  When I saw G++, my first thought was the C++ compiler of that name.  I am unaware of any universal use for the term in biology.  It could very well be context specific.  It is common to use that sort of notation when describing alleles in a population, with the pluses following whatever variable name you gave to the allele.  So if we had an allele that we called G, and an individual had two copies of that allele, it would be common to see that individual referred to as G++, with G+ being used to refer to someone with only one copy.  I think it is quite possible that this is what the term means in your context but it is impossible to say for sure without more information on what the question you are being asked is in reference to.  Maybe it would help if you posted questions 1-4 or the blurb that precedes the problem set so we could see what you are actually being asked.


Dimensionless number for blood volume Comments from the question How is the blood volume of a living organism measured without killing it? by @Nico discussed that the time of blood recirculation scales with the size of the organism. I was curious if there were a series of dimensionless numbers that characterize blood flow, blood volume, and time of blood recirculation?

Such dimensionless numbers exists for stride length and drug penetration.

Edit
I like @Nico's comment so much it's going to part of the question. Any description of the circulatory system doesn't necessarily have to be dimensionless. However, I would imagine that one could develop a characteristic time (lets call it Tau) based on blood flow (L/t), cross-sectional area (L^2), and circulation time (t). From that characteristic time Tau, interesting observations and appropriate comparisons about the various ratios and how they vary amongst species.

Blood volume is not a dimensionless number - it's a volume. Historically we used to measure this in patients or volunteers by giving a large carbohydrate molecule like a starch that is not digestible or harmful to the body. Just like every other body fluid compartment volume (i.e. plasma, interstitial fluid, intracellular and extracellular) that we have, blood volume is estimated by intravenously injecting a known concentration of a particular compound. Once that compound equilibrates you take a blood sample and measure the compound's concentration again.

Initial Concentration * Initial Volume = Final Concentration * Final Volume

When you inject a known volume of a known concentration that only fills the "blood" component, and then you measure a final concentration - you can then solve for the "Final Volume" for "blood volume".


qPCR: Accounting for different sample mass when interpreting and comparing Ct I'm trying to use qPCR to quantify the amount of a specific bacteria species in patient sputum, but I don't really have the option to use consistent quantities of sputum to elute DNA from. The qPCR works fine, but once I have the Ct results, what is the best way to account for the fact that I'm using different masses of sputum?

If you are always using a relativ amount of your input yield for each sample, then you'll need to correct your Ct values for the absolute DNA yield of each sample. If you can't measure the DNA yield of each sample, then you'll just have to assume it is directly dependent on the sputum input mass. This assumption is pretty faulty though, since direct DNA measurements are much more exact and are not affected by biases from DNA extraction efficiency differences or batch effects.

Since Ct values represent a single qPCR cycle in the linear phase in which the target DNA is doubled, you need to adjust the CT values by +1 for samples with half DNA input and by -1 for samples with double input (or generally $Ct_{adjusted} = Ct - log_2(inputfactor)$ ). Of course this method of normalising assumes that the relative content of your target DNA in the sample is independent of the total sample yield (which may or may not be true; if your specific bacteria species is proliferating a lot more in one patient compared to the other this might affect both relative and absolute DNA amounts).


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

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

The frequency of the bases in the genome isn't equal to 0.25, the frequency depends on what kind of organism you mean. However let's take a look at some of them:

bacteria, most of the time we can see a bias towards some bases, this could be a GC bias, for example if the bacteria lives in extreme conditions, because GC can vorm three hydrogen bonds compared to AT which can only form two hydrogen bonds. So it's genome is more resistent to extreme temperature, less denaturation chance because the stronger bonds. In bacteria there are also some polymerases which have a bias towards bases, I won't discuss this in depth to keep it short, but from these two points we can already conclude the genome isn't random
Homo Sapien, for example we need CpG Island near our promotor region, to regulate transcription. Further we have higher GC% in gene coding regions to reduce mutation chance, because we don't want to mutate genes wich are needed for survival. Their are also some sequence which are very specific for example TATA box and Poly-A signal, if our genome would be random, so all base would have a frequency of 0.25 these specific sequence could occur at place where we don't want them or they wouldn't occur at places where we want them. We need a promotor (with TATA box) for RNA polymerase binding, if our genome was random we have a big chance we would have genes wihtout a TATA box so no transcription of these genes will occur

There are a lot  more properties of the genome we could discuss but I think this will give you enough insight why the bases in the genome don't have a equally alike frequence of 0.25

UPDATE:

in addition to your second question: I think the chance of finding a genome which has an equally alike distribution is very small. because almost all organisms have undergo evelution, and when we have evolution there is natural selection and natural selection relies on mutations. So (almost) all genomes have udergo mutation, however this sometimes can favor an equally distibution for example if our genome is AGAA and one A mutates to an G we will have an equally alike proportion. So to summarize: maybe you can take a look at NCBI and look for a gc 50% wich means 50% AT so 25% of each base. If you find a genome wich has exact 50% gc, you have found your answer


Regarding cancer cells and radio-frequency ablation Are cancer cells destabilized if near a strong electromagnetic field over a long period of time? I read this technique of using radio-frequency ablation and heat shock to kill cancer cells. I don't know if this is viable but maybe a person could wear a device like a pacemaker right over the area of a tumor that emits  strong E.M. pulses over say a month or a year. Could this destabilize the tumor ?

I think you're referring to radio frequency or microwave ablation. It works by heating the tissues up with electromagnetic radiation, just like you'd use to microwave food, but it's heating you instead. Healthy cells have better repair mechanisms and survive these treatments better. Cancer cells tend to have poor repair ability and can be killed more easily. I've heard of injecting metal nanoparticles which collect in the tumor due to the enhanced permeability and retention (EPR) effect. The nanoparticles respond to the microwaves much more powerfully than cells do and get hotter, burning the tumor from the inside out.


Salmon returning to lay eggs To spawn, salmon return to the river in which they were born. Is it because the individuals remember the specific river, or because populations are genetically conditioned to follow specific environmental cues that guide them to the specific river?

In other words, if a salmon is artificially taken to lay eggs in a different, ("wrong") river, will its progeny return, when grown, to the river where they were born, or that where their mother was born?

If salmon that was grown in a fish-farm is taken to the sea, does it return to a river? How does it choose which?

Answer

The mechanism for salmon natal homing isn't exactly known, but there are really two good hypotheses out there.

Salmon have an extremely good sense of smell. One hypothesis is that they retain an imprint of their birthplace's odor, and manage to recognize it again at a later time (as explained by this article).
Another hypothesis: the Earth's magnetic field guides the salmon to their birthplace via geomagnetic navigation. They then use chemical cues to recognize the stream in which they were born (supported by this scientific article).

These hypotheses were mentioned in this Wikipedia article. Note that there was a third pheromone-related hypothesis which was disproved (as shown here).

I would say that both memory and "genetic conditioning" could potentially be factors in how these animals perform this natal homing, among other things. However, it is difficult to pinpoint which one if any, because neither hypothesis has yet to be confirmed, and both function on completely different mechanisms. Not to mention that we can't tell what exactly a fish is thinking, and also what chemical we're looking for, if there is one.

Finally, for your personal information, salmon aren't the only animals to do this: sea turtles return to their birthplace as well.

TLDR: If a salmon was displaced right before birth, or birthed in a pool, I would imagine it returning to that particular location at sexual maturity.

References

Lohmann, K. J., N. F. Putman, and C. M. F. Lohmann. “Movement Ecology Special Feature: Geomagnetic Imprinting: A Unifying Hypothesis of Long-distance Natal Homing in Salmon and Sea Turtles.” Proceedings of the National Academy of Sciences 105, no. 49 (December 5, 2008): 19096–19101.
Dittman, A., and T. Quinn. “Homing in Pacific Salmon: Mechanisms and Ecological Basis.” Journal of Experimental Biology 199, no. 1 (January 1, 1996): 83–91.
Black, Geoff, and J. Dempson. “A Test of the Hypothesis of Pheromone Attraction in Salmonid Migration.” Environmental Biology of Fishes 15, no. 3 (1986): 229–235.


What moth is this and how do we get rid of them? This bugs are everywhere in my house and we've tried so many home remedies, but they won't leave. Can anyone help us!?

That is an Indian meal moth Plodia interpunctella. Family Pyralidae. They are very common household pests. https://www.doyourownpestcontrol.com/indian_meal_moth.htm
They breed in grains or cereals. You need to look through your pantry, and find out what they have been breeding in. Seal up your grains and cereals in plastic, or put them all in the fridge.


Where can I find free authoritative images of different species of Lagomorphs? I would like to make an infographic showcasing the order Lagomorpha (rabbits, hares, and pikas), which contains a dozen genera and about 100 species. I want to include a picture for most species, or, failing that, a picture for each genus. The difficulty is that I'm not at all an expert on these animals -- I just find them cute and I like infographics -- so if I simply google around for pictures of them, I won't be able to verify that a picture labeled "Bunolagus monticularis" is actually a picture of a Bunolagus monticularis specimen, rather than something else.
Photographs would be ideal, but I'm fine with using sketches instead when no photographs are available. It would also be ideal if the images were free to use and in the public domain (or licensed under some version of Creative Commons)
Is there any source for images of species specimens that is generally considered trustworthy? It's fine if it's limited to lagomorphs, but if it also extends to other animals/plants, that's all the better!

Wikipedia is good for this,
The licence is what you want, and many people will have checked the animal ID.
look up the two pika species, and the rest are under
http://en.wikipedia.org/wiki/Leporidae


How do anticholinesterase pesticides kill nematodes? Compounds that inhibit the enzyme acetylcholinesterase are commonly used as pesticides. In animals with centralized respiratory systems controlled by the nervous system, poisoning with an anticholinesterase would lead to death due to respiratory arrest. I presume that, in insects, the inhibition of AChE would lead to closing of the spiracles necessary for respiration
However, nematodes and other worms rely on diffusion of gasses for respiration and do not have respiratory systems controlled by a nervous system, so how would inhibition of AChE by agents such as aldicarb kill them, especially if the pesticide in question happens to be a reversible inhibitor?

Cholinesterase inhibitors and plant-pathogenic nematodes
While it is true that cholinesterase inhibition does not affect gas exchange in nematodes, it does produce other effects by paralysing motor activity:

Inhibition of larval hatching

Reduced movement to new roots

Impairment of root invasion and feeding

Impairment of copulation

Acetylcholine also has a role in sensory neurotransmission in nematodes, which could further contribute to the toxic effects.
Thus cholinesterase inhibitors do not directly kill nematodes, but only slow down their growth and reproduction. This is why some prefer to use the term 'nematostatic' over 'nematicidal' for these compounds.
Effects on vertebrate pathogens
Pyrantel is a cholinesterase inhibitor used to treat intestinal nematode infections in man and other mammals. Little is known about how exactly it works, except that it causes spastic paralysis of the worms. Possibly, it impairs feeding and reproduction (like its counterparts in plant pathogenic nematodes).

References and further reading:

Wright DJ. Nematicides: modes of action and new approaches to chemical control. In Zuckerman BM, Rohde RA, editors. Plant parasitic nematodes. Vol. 3. New York: Academic Press; 1981. p. 421-449. Link to publisher site.
Martin RJ, Robertson AP. Mode of action of levamisole and pyrantel, anthelmintic resistance, E153 and Q57. Parasitology. 2007 Aug 1;134(8):1093–1104. https://doi.org/10.1017/S0031182007000029


Clarification on RefSeq Genes track on IGV The following picture is a snapshot of the RefSeq Genes track (collapsed) on IGV. I know that the bold blue line indicates exons and the thin one indicates introns.

However, I cannot find what the medium line stands for. Is it part of the exon? Why is it different?

I have checked into the manual but I couldn't find any relevant info.

When you expand the track (bottom picture) even more diverse lines appear.

medium blue line without arrows
medium line with arrows
bold line with arrows

Can anyone explain to me what is the difference between all of them?

The thinnest blue line is intron, so not in your transcript.  The medium thickness segment is untranslated exon, the thickest blue segment is translated.


Why do plants have pith and how is it useful to them? Many plants have pith, from walnut trees to corn to ragweed, but I can't think of anything it does them. What is pith and how is it useful to them?

The pith (medulla) forms part of the ground tissue system of a plant, and specifically it is the ground tissue which lies interior to a plants vascular tissues (xylem, phloem etc.)

The ground tissue system is responsible for much of a plants metabolic functioning, and contains various specialized cell types which aid in photosynthesis and storage of photosynthesis products. The pith is made from parenchyma cells.


Role of Fbx15 in ES cells and its use in assaying for iPS cells (Yamanaka paper and others)? I am trying to understand the assay for iPS cells in the Takahashi & Yamanaka 2006 paper.

They inserted a beta-geo cassette, which contains the neomycin resistance gene, into the Fbx15 gene.  The idea is that the beta-geo cassette will be expressed when Fbx15 will be expressed, thus conferring G418 resistance to only those cells expressing Fbx15.

They say that "Although specifically expressed in mouse ES cells and early embryos, Fbx15 is dispensable for the maintenance of pluripotency and mouse development."  Does this mean that Fbx15 will be expressed in induced pluripotent stem cells, and won't be expressed upon differentiation? (What is special about Fbx15 that will distinguish iPS cells from somatic cells, including those that might derive from iPS cells, as when pluripotency is not maintained?)

Another paper from Yamanaka's group explains Fbx15.

It says:

  Inactivation of Oct3/4 in ES cells led to rapid extinction of Fbx15 expression.

  Fbx15-null ES cells were normal in morphology, proliferation, and differentiation. These data demonstrate that Fbx15 is a novel target of Oct3/4 but is dispensable for ES cell self-renewal, development, and fertility.

So Fbx15 wont be expressed in Oct4⁻ cells.

I haven't seen any paper describing the function of this gene but in the case of cassette insertions the locus would prove useful in expressing the inserts specifically in Oct3/4⁺ cells


What are the environmental conditions for larval Haemonchus contortus to survive? What is known about the environmental limits for Haemonchus contortus to survive outside of a host organism in its larval stages?
I'm interested in knowing:

temperature tolerance levels
preferred humidity levels
pH tolerance
how long can it survive outside of the tolerated ranges?

Lowest temperature
2, 3, 4 and 5 week beakers containing eggs and non-infective larvae in lamb faeces didn't develop into infective larvae (L3) when exposed to fluctuating temperatures ranging from -1 to 15°C:

[...] there were no signiﬁcant differences in the number of harvested larvae
at the different time points for the faeces incubated at 15°C.
However, at 5°C and -1 to 15°C no development of eggs occurred,
although it was found that a small proportion developed into infective
larvae when incubated at 25°C for an extra week.
(1)

Highest temperature

Temperature of 40ºC negatively correlated with the survival rates of
H. contortus L3. [...]
Decreased motility was observed on day 10 after heating. [...]
Heating of L3 at
higher temperatures (45ºC and 50ºC) caused 100% lethality as early on
hour 48 and 24 of exposure
(2)

Desiccation
When it comes to dessication, there are three main things to take into account:

whether the larvae are in exsheathed or ensheathed state matters
they can survive several dessication/rehydration cycles
it is best survived below freezing temperatures

The experiments on desiccation survival showed that, after a few hours
exposure to 47% R.H., all exsheathed larvae died and all ensheathed
larvae survived. (3)

Desiccation protected the larvae against death on storage at
temperatures below freezing, but it was harmful at temperatures above
freezing. (4)

Ruminant larvae were able to survive up to 7 desiccation/rehydration
cycles, and, during anhydrobiosis, metabolic activity was decreased
and survival of the larvae was prolonged both in the laboratory and in
the field. (5)

pH

The effects of temperature on survival and development of the
free-living stages of H. contortus have been studied both by faecal
and by agar-culture methods. [...] with a pH range from 6.5 to 8.5 (6)

How long?
As usual, depends on the current environmental variables and current state of the organism and so forth. Read above sections. The article by P. T. Iliev, A. Ivanov, P. Prelezov has a few tables that can give you a good idea of these times (at least for temperature and humidity).

(1) The development and overwintering
survival of free-living larvae of
Haemonchus contortus in Sweden,
K. Troell, P. Waller and J. Höglund
(2) Effects of temperature and dessication on survival rate of Haemonchus contortus infective larval stage, P. T. Iliev, A. Ivanov, P. Prelezov
(3) Desiccation Survival of the Infective Larva of Haemonchus Contortus,
C. ELLENBY
(4) Effect of dessication on the survival of infective Haemonchus contortus larvae under laboratory conditions,
Kenneth S. Todd, Jr., Norman D. Levine and Paul A. Boatman
(5) Anhydrobiosis increases survival of trichostrongyle nematodes (abstract only),
S E Lettini, Michael Sukhdeo
(6) Trends and Perspectives in Parasitology 2 (page 84),
B. A. Newton


What is this web-like organic matter? I saw this on my window couple of days ago. Does anyone know what it is? I have tried google image search with no luck.

This is a slime mold of the genus Stemonitis, and I'm thinking the species is axifera. They tend to form on dead wood, of which seems to be the case in your picture (assuming that we are in fact looking at the wall just next to your actual window, since the bottom left of your window can be seen at the top right of the picture).


Why can't a human regenerate limbs like some other species? When a person's arm is amputated, the arm will no longer be able to grow back. However, in salamanders, the arm actually grows back.

In comparison to a human, what is really happening to the cells in the wounded area in salamander ?

After salamanders (or certain other amphibians) lose a limb, the epidermis migrates to cover the wound, forming a structure known as the apical epidermal cap. The underlying "stump" then generates a de-differentiated mass of cells from normal tissue. In most cases, these cells will express genes that are vital to the proper formation of limbs, such as HOX genes. This "lump" of cells at the stump of the wound are typically referred to as a blastema. Basically, the blastema continues to grow and regenerate the limb in a way similar to fetal growth. Though mammals (including humans) also have some regenerative capabilities, they are much more limited. In addition, many regenerated limbs will also be mildly deformed (square fingernails). In axolotl salamanders, it was found that certain retrotransposons, such as the LINE-1 element, were prevented from "jumping" around in the developing blastema during limb regeneration. The two active proteins PL1 and PL2 were responsible for inhibiting the activity of LINE-1 and other such retrotransposons. Active retrotransposons can potentially rearrange the genes in germ cells can be detrimental to the mechanisms that allow the blastema to replicate and differentiate, so the PL2 and PL1 proteins play a vital role in their regenerative capabilities. When the PL2 and PL1 proteins were "switched off" in certain axolotl salamanders, their regeneration was much less efficient. Since mammals lack the PL1 and PL2 proteins and have a different LINE-1 retrotransposon, they have reduced regenerative capabilities.

Sources:

Wei Zhu, Dwight Kuo, Jason Nathanson, Akira Satoh, Gerald M. Pao, Gene W. Yeo, Susan V. Bryant, S. Randal Voss, David M. Gardiner, Tony Hunter. Retrotransposon long interspersed nucleotide element-1 (LINE-1) is activated during salamander limb regeneration. Development, Growth & Differentiation, 2012; 54 (7)

Wei Zhu, Gerald M. Pao, Akira Satoh, Gillian Cummings, James R. Monaghan, Timothy T. Harkins, Susan V. Bryant, S. Randal Voss, David M. Gardiner, Tony Hunter. Activation of germline-specific genes is required for limb regeneration in the Mexican axolotl. Developmental Biology, 2012; 370 (1)

Odelberg SJ (August 2004). "Unraveling the Molecular Basis for Regenerative Cellular Plasticity". PLoS Biology 2 (8)


Larva in cat's water dish Can anyone help me identify this tiny larva I found in my cat's water dish and tell me how it got there?

This appears to be the larva of a drain fly (aka moth fly; family Psychodidae).

 Top left is larva; Source: YourWildlife.org; Credit: Matt Bertone
You can use a dichotimous key to help you ID to family. For example, from Bouchard et al. (2004)+:

Body cyclindrical; non-leathery integument...
Head capsule fully visible and completely separated from thorax
Prolegs absent
Thoracic segments not fused or swollen
Abdomen non ending in long respiratory tube
Body segments with 2-3 secondary divisions (annuli); body grey or brown

You can use Arthur Frost's comment to help ID to lower taxonomic levels.
How it got there:
From Orkin:

These pests are particularly likely to be found in bathrooms and kitchens, typically getting into homes through:

Basements
Drains
Windows

 +  Bouchard, R.W., Ferrington, L.C. and Karius, M.L., 2004. Guide to aquatic invertebrates of the Upper Midwest. (Chapoter 13: "Diptera")


What is the purpose of using two layers of gel in SDS- PAGE? I just made a SDS-PAGE with a top layer of stacking gel and a bottom layer of separating gel with different pH values of 0.5M Tris-HCl. The stacking was 6.8 and the separating gel was 8.8. What about this pH change makes the gels different? What effect does this have on the proteins that I ran?

The stacking gel concentrates proteins loaded into the sample wells so that they are resolved as a unified "line" once they enter the stacking gel.  The reason for the lower pH is that this "lower ionic strength implies higher electrical resistance and consequently a higher electric field, provoking the faster movement of the proteins and of every other charged particle in the gel. Such a high electric field coupled with the glycine in the running buffer (that will not go into the resolving gel due to the pH), helps to clean the sample from the Cl- ions from the Tris-HCl buffer. That concludes in a stack of clean, denatured, and equally charged proteins in the boundary with the resolving gel; this will account for a good quality PAGE."

Bassically, in the stacking gel the pore size is larger so it gives a chance for the larger proteins and smaller proteins to equalize with each other.

"As the proteins are denatured and linearized by heating, SDS and dithiothreitol (if there is any di-sulfide bond), the proteins are loaded onto the wells on the stacking gel. The denatured proteins have a uniform mass to negative charge ratio. Since the current run from negative (top) to positive (bottom), the proteins move toward the bottom. When the electricity is turned on, the proteins and Tris-glycine enter the stacking gel. In stacking gel with pH 6.8, the N-terminal amino group of the proteins and amino acids are protonated at equilibrium which makes them less negative. The average electrophoretic mobility is very slow. A Gly-chloride ion boundary is formed since glycine moves slower than chloride ion. However, glycine still runs slightly faster than other proteins. As a result, the glycine keeps pushing the protein towards the chloride ion. In other words, the proteins are trapped between glycine and chloride ion. The proteins form a very tight band inside the stacking gel.

Once the protein reaches the resolving gel, the pH changes from 6.8 to 8.8 and the pores are smaller. As pH increases, the N-terminal amino groups are deprotonated. Amino acids and proteins are more negatively charged at equilibrium than in stacking gel. As a result, glycine moves faster than proteins. Glycine and chloride ions move ahead of the proteins. As the pores are smaller in the resolving gel, the size of the protein determines the mobility (speed). So the smaller the protein is, the faster it will reach the bottom."

SDS-PAGE stacking gel


Why do insects avoid being on their back? I have noticed that when insects are placed on their backs, they tend to turn themselves over quickly or else appear to be in distress. Is there a physiologic, anatomic, or adaptive reason why supine positioning might be unfavorable in insects?

Welcome to Biology.SE

Insects don't "like" being on their back because they can't get back on their legs and they therefore get stuck somewhere where they can gently wait for death to come.

Not all insects are unable to switch back on their legs but some can't do that (or can hardly do that). The reasons for which many insects are not able to get back on their legs (while mammals for example usually can do that) is that they have a exoskeleton. Their exoskeleton limits drastically their movements.


How is duration of efficacy estimated for vaccines? Vaccines, especially those given in adulthood, usually have term limits attached, eg: 10 years for yellow fever or 3 years for typhoid. Since presumably the time course of an immune response is no great respecter of our calendrical conventions, and since there is also presumably a spectrum of responses across the population, how are these durations estimated? What are the criteria for deciding a cutoff time?

Also, do the estimates get revisited and updated as time goes on and new data become available? Do new data become available? Is there continuing follow-up research into this, or does the estimate just get made before the vaccine comes to market and then get taken as gospel?

Duration of efficacy is typically determined by tracking the antibody titers of a cohort of subjects who have gotten the vaccine, and estimating based on the trajectory of those titers where they will eventually cross the threshold to the point where the vaccine no longer confers immune resistance.

These estimates do get revised and estimated as time goes on - you will occasionally see new recommendations for a second or third "booster" dose of a vaccine, which is meant to extend the duration of immunity beyond the duration of the original vaccine.

Two major types of studies track this over time. Phase IV clinical trials, which are clinical trials required post-licensure, and observational epidemiology trials, which tend to be performed when disease transmission starts to occur in supposedly vaccinated populations.

Mechanical snail has raised the issue of viral evolution, so I'll touch on it briefly. The duration of efficacy discussed above is based on how long a patient's body can mount an immune response to a particular challenge. That's a concern for all vaccines.

For some vaccines, there's a secondary process that's of concern - that of the virus evolving in such a way that the antigens targeted by the vaccine are no longer those on the virus itself. This is only a concern for some viruses, notably those that are particularly fast-evolving, like influenza or HIV, and less of an issue for say, measles and HPV.

But that's typically not what people are talking about when they say "duration of efficacy" because it's inherently unpredictable, and less a function of the vaccine and more a function of the virus.


What are the mechanistics of stinging nettles? There is a lot of research on why nettle extracts causes skin irritation and a stinging sensation. However, I cannot find information on how the extract is injected in human skin. Similarly, I haven't been able to find information on  how the pressure is built up in the trichome, nor how the silica tip is inserted in the skin.

Suggestions for articles or books on this topic are welcomed.

The stinging hairs (trichomes) of the common North American nettle (Urtica dioica) are sharp, pointed cells. These nucleated cells are embedded in a base of smaller epidermal cells. The shaft of the trichome is composed of silica. Upon touch, the tip breaks off, leaving a sharp tip similar to a hypodermic needle. The hollow trichome penetrates the skin, and toxin from the base is injected into the skin tissue. The stinging toxin includes a mixture of histamine, acetylcholine and 5-hydroxytryptamine (Online Textbook of Natural History).

Left: schematic of a stinging cell, or trichome of a nettle. Right: trichomes on the stem of Hesperocnide tenella. Source: Online Textbook of Natural History

I couldn't find any info on trichome pressure. It may be that the toxins are released passively. Otherwise, high concentrations of dissolved matter may attract water in the base, increasing the pressure (much like turgor present in many plant cells).


Why isn't vomit corrosive? Vomit comes from gastric acid, right? And in gastric acid there is HCl and HCl is corrosive (strong), how come when I vomit, it doesn't destroy things that it (as the vomit) hits (such as floor, table)?

First of all, it is corrosive. People which are bulimic often get problems with their teeth getting damaged by the permanent exposure to the acidic stomach fluids. See the paper for more information:

Bulimia and tooth erosion

Then it is a matter of concentration. According to Wikipedia, the concentration of the acid in the stomach is around 0.5% which is a pretty low concentration. Additionally the acid gets diluted when you eat or drink things. And last but not least not all things are very susceptible to a fast degradation by acids. Thing tend also not to disappear suddenly, if they come in contact with acids.


Will DNA nanostructures be useful for medical applications? There is a lot of work being done on developing small nanomechanical structures and even small nanomechanical actuators built with DNA.  I have heard researchers motivate this research with claims that it could have biomedical applications.  My question is, how likely is this to be true?  In particular, a few potential problems bother me:

(1) What is the risk that the foreign DNA strands used to build nanomechanical devices will be accidentally incorporated into the host genome?  Are there plausible strategies for avoiding this?

(2) Will it be effective in the presence of an immune system?  If the foreign DNA is not incorporated into the host genome, it seems likely to instead be destroyed by the host immune system.  Is there research addressing this issue?

I think biomedical applications are not an absurd perspective. More specifically, regarding your concerns:

(1) Unless the DNA is first internalized by cells, and then somehow enters the nucleus (both are not very likely, especially considering the small concentrations we're talking about here after dilution in a human body), you would still need the DNA structure to disassemble to become "available", and the strands to be long enough to be incorporated, which is usually not the case. And, of course, you would need some DNA integration mechanism to be at work, such as a recombination with genome sequences that happen to be very similar to the ones used to build the DNA nanostructure (which can be avoided during the design step). In other words, no, it's quite unlikely.

(2) Immune responses might actually be a bigger issue; in particular, some Toll-like receptors (TLR), that activate the innate immune system, can respond to DNA and RNA fragments. But immune responses may not be so problematic if the DNA nanostructures are used for short-term mission, like 1-shot delivery to a specific organ, in which case they do not need to stay around for very long. Additionally, this can be a useful feature; immune recognition can be used to direct the trafficking of nanoparticles to lymph nodes for example, where the efficieny of their payload (e.g. an immune modulator) could be maximized.


Determining whether X chromosome from sperm or egg Is there any way of determining which X chromosome a female inherited from her father and which from her mom ?

yes it is possible... in placenta (trophectoderm) the paternal X is epigenetically silenced [ref].

That is if you do the test in the pre/neo-natal stage. Otherwise, at later stages, you have to check by DNA fingerprinting + karyotyping/FISH as Chris suggested.


Can I use fluorophore conjugated antibody as neutralizing antibody? I need to order a neutralizing antibody to block a protein of interest.
The pure grade functioning antibody (no conjugates) is substantially more expensive than the fluorophore conjugatated ones.
Can I achieve the same by using let's say Ab conjugated with APC/PE as a neutralizing antibody compared to the pure functioning grade ones?
Any insight would be great.

In short, yes, most likely.  When an antibody binds to the antigen at a region (epitope) that is needed for the antigen's activity then the activity is reduced ("neutralized").  The (proper) labeling of an antibody will usually not affect which epitopes it binds to, and so it will work OK (but it may have lower titer than the unlabeled antibody).  As always, there may be some exceptions to this.


Why does mold grow on silicone caulk? I notice mold likes to grow on silicone caulk. I find it odd since silicone is mostly inorganic and doesn't contain any nutrients for mold to grow on unlike soil and clothing. Can mold metabolize silicon?

This product brochure seems to give a reasonable explanation:

  The following conditions help to form mould on sealants:

  High air humidity with little movement of air, eg: in bathrooms, showers, kitchens etc.
  Warmth
  Nutrients in the form of organic deposits. e.g. residues from body care materials
  such as soap, shower gel etc.

  Since elastic silicone joints have low thermal conductivity they are the warmest part of a tiled surface and where mould thrives best, in combination with organic residues and moisture.


How does a "chromogenic mixture" produce such pronounced color differences in this Agar Art? The Forbes.com article Bacteria Become Art Tools In Annual Agar Art Competition says:

...People’s choice winner Zita Pöstényi, a microbiologist at SYNLAB Hungary Ltd, used three agar plates and four different bacteria to create a pattern inspired by Hungarian folk art.
[...]
Pöstényi used another trick to create her colorful plates. “I used a special media for this drawing,” she says,  “It contains a chromogenic mixture which enables the detection of activities of specific enzymes.” Thanks to this special mixture, the four bacteria species she used all showed up in different colors, which allowed her to create the traditional folk art pattern.
Usually, these unique colors tells researchers something interesting about the bacteria, but for the ASM Agar Art competition, these colorful features have become the medium.

Question: How does a "chromogenic mixture" result in different bacteria showing up in different colors in such a vivid way?

American Society for Microbiology Agar Art 2019 Contest, People's Choice. "Hungarian Folk Art," Zita ... [+]ASM / ZITA PÖSTÉNYI

She is referring to a mixture of chromogenic substrates: molecules which are more or less colourless until cleaved by a specific enzyme, releasing a coloured product.

For example X-gal is colourless until the enzyme beta-galactosidase hydrolyzes it, releasing a blue coloured product. If you spread a mixture of bacteria onto a plate, with some expressing beta-galactosidase and some not, you will see both blue and colourless colonies, as seen here:

[source]

Chromogenic substrates are often used to create differential media that allow the differentiation of different species of bacteria. This plate, for example, contains several different chromogenic substrates (a mixture, if you will) for identifying the bacteria commonly found in urinary tract infections:

[source]

If you wanted to make a picture with this plate, you could “paint” with Enterobacter spp. for blue, Staphylococcus aureus for yellow and S. saprophyticus for pink. Each species produces a specific enzyme that acts on a specific chromogenic substrate in the plate, changing its colour.

Alternatively, you could express the desired enzymes recombinantly in one species.


What is a function-triggering antibody? I am reading a journal paper on the effect of a neural cell adhesion molecule on neuronal development and in the abstract of this paper I have come across the following:

The autophosphorylation and activity of Pak1 were enhanced when
isolated growth cones were incubated with NCAM function triggering
antibodies, which mimic the interaction between NCAM and its
extracellular ligands.

In this paper, the NCAM protein becomes activated when it is exposed to NCAM function triggering antibodies. I understand that antibodies are molecules produced by the immune system and bind to antigens. However, I am not sure how incubating growth cones with NCAM triggering antibodies would actually trigger/activate the NCAM protein itself.
Isn't the purpose of an antibody to bind to an antigen  so that it can be removed from the body? I am not sure how exposing an antigen its respective antibody would trigger its function. I have read several other papers about neural cell adhesion molecules where antibodies were used to activate their function. I have searched function-triggering antibodies on Google but I have found no useful results regarding this. Any insights are appreciated.

The term "function-triggering antibodies" is not standard, these are more widely known as cross-linking antibodies. As you may know, an antibody has multiple "arms", with the antigen binding region or Fab (Fragment antigen binding) at the end. IgG antibodies have 2 arms, IgM can have 10. The Fab portion is generally identical on all the arms, although it's possible to engineer them differently. This allows the antibody to bind to multiple antigens at the same time, drawing them close together.
NCAM is a homophilic binding protein, with an extracellular domain that binds to other NCAM molecules, both on neighboring cells and on the same cell. That binding induces structural changes in the intracellular domain which promotes the binding and activation of kinases, proteins that phosphorylate (and thus activate or inhibit) other proteins. This starts a signaling cascade that induces changes in the cell, typically by controlling the activity of transcription factors in the nucleus.
Receptors are generally not spread out evenly over the surface of the cell, they often exist grouped together in membrane structures known as lipid rafts. When drawn close enough together, NCAM molecules can begin their signaling cascades on their own, as adapter proteins bound or recruited to the intracellular domains get activated – the kinases and their substrates are in close proximity as well. To induce this type of signaling in the lab, cells can be treated with cross-linking antibodies that draw the receptors together. This in effect triggers the function of the receptors, beginning their downstream signaling.

Source


Mathematical/statistical models for forecasting population distributions of age, sex, weight, and height I come from a mathematical background but I have no experience with the topic of mathematical biology.
Are there well established mathematical/statistical models for forecasting the evolution of population distributions of biometric parameter such as age, sex, weight, and height? For instance, I have often heard that the proportion of elderly people in the population is projected to increase. What models are being used to generate forecasts such as these?

The term you are looking for is demography - there are literally thousands of papers published on this topic.
Each of your topics mentioned has its own models and prevailing theories, so without an exact question it is very hard to answer as to which model you might find best.
Having said that there are well established models of things like geometric growth of populations (proposed by Thomas Malthus in 1798). The United Nations does a lot of modeling of populations and the like. You might be interested in their freely available publications and information here.


Photosynthesis in oxygen free enviornment If a plant is grown in an oxygen free enviornment would it live longer in light or darkness?

It is evident that oxygen would compete with carbon dioxide during various processes like competing with carbon dioxide for reducing power, also oxygen quenches the excited electron of chlorophyll etc.

But all these effects to me don't give any sense of the extent of oxygen on these reactions. What does the absense of oxygen have on the system? Except ofcourse the plant not being able to respire properly.

If that "environment" is a closed vessel or bell-jar; certainly the plant would survive in light (when it simultaneously perform respiration and photosynthesis), and in darkness (when it can perform only the respiration) it would survive upto certain time due to the oxygen it accumulated. But should die at prolonged darkness when the plant would finish all the oxygen.

(as suggested by Priestley's classic 1870 experiment * there was enough oxygen to keep a mouse for certain time)

(image link)

However, if we look the effect of various concentration of O2 on photosynthesis rate without altering the CO2 concentration; yes the photosynthesis rate get affected; one known effect is called Warburg effect or Inhibition of photosynthesis by O2.

In this effect, photosynthesis rate only decrease if O2 concentration is increased. And in vice-versa, with O2 concentration decrease, photosynthesis rate only increase. (source: this, this, this and this)

This take place due to mainly 2 causes: 1. O2 work in  competitive way with CO2 for binding with the enzyme RuBisCO, the key enzyme for CO2 fixation in plants. 2. And that induces photorespiration (in C3 plants). (Wikipedia shows reference to here). (However this old paper also tells other hypotheses)

There are 2 type of responses in photosynthesis rate in at different O2 concentration in various plant species.

One group of plants ( known to bel C3 plants, those do not have any any CO2 concentrating mechanism) ), is remarkably affected by O2 concentration; i.e. affected by Warburg effect in true sense.

Another group of plants ( known to be C4 plants, those have a certain type of CO2 concentrating mechanism); does not significantly get affected by O2. I.e. doesn't show the Warburg effect.
(see also : table).

By the way, It seems photosynthesis would increase than normal  if we could make the environment "completely oxygen-free" but other parameters same. (due to elimination of O2inhibition) But I could not find any report about such "completely oxygen-free" conditions; and seemingly it is not possible because while doing photosynthesis; some  of the evolving oxygen molecules will pass through the cytoplasm; some will move in the intercellular space, and few molecules will stay diffused in atmosphere around the plant. We can only decrease the concentration of O2

Also; Warburg effect is completely about photosynthesis rate. It is not about plant's overall health. Removal of O2 increase photosynthesis rate... it does NOT mean the plant would live healthiest in oxygen deprived condition

  Sources:

  Fundamentals of Plant Physiology by Dr. V. K. Jain; revised edition; S. Chand Publications, New Delhi.
  * Biochemistry/ Lubert Stryer/ 4th Edition/ W. H. Freeman and Co.


Why do neutrophils need to die after pathogen phagocytosis? From referenced article below, neutrophils need to be removed because its granule contents and oxygen metabolites (used for killing phagocytosed pathogen) are harmful to the surrounding tissue. Thus, the process used for this is that neutrophils undergo apoptosis, then are phagocytosed by macrophages.

However, I do not see why neutrophils need to first die to be phagocytosed by macrophages. Do macrophages not phagocytose living cells?

Source: http://www.sciencebrainwaves.com/the-immune-cell-the-neutrophil-the-good-the-bad-or-the-ugly/

  Once the pathogens have been dealt with, and to completely resolve inflammation, neutrophils need to be cleared from the tissue... For removal, neutrophils firstly need to die.

Macrophages can certainly phagocytose living cells, as you can read in Sompayrac's "How the Immune System Works", Chapter 1 and 2, but they do need an "eat me" signal of some kind in order to do it. For a bacterium that might be lipopolysaccharide and mannose. For endogenous cells, there is a balance of "eat me" and "don't eat me" signals. Apoptosis, in addition to neatly packaging up potentially toxic intracellular components, involves downregulating the don't eat me signals and upregulating the eat me signals. Macrophages can phagocytose live cells that seem to have some sort of problem (for example, tumor cells), but they are much more efficient at phagocytosing apoptotic cells.

As far as why the neutrophil has to die, in addition to making them more efficient targets for phagocytosis, they die pretty quickly anyway. There is some debate about the exact length of their life span, but from the time they're released by the bone marrow, the average circulating life span is probably less than 24 hours, regardless of whether they exit the blood stream as part of an inflammatory process or not. The exact function of this short lifespan is the source of some speculation, but we do know that, after being recruited in the inflammatory response, apoptotic neutrophils help suppress that inflammation, playing an important role in regulating the processes that sent them out into the tissue in the first place.

Sompayrac's book is a good overview, but if you want to read the gory details this is a good review.


Why is the skin of European bog bodies brown? What causes this? Is it to do with decay or is it to do with substances within the bog dying the skin?

The anaerobic decomposition of moss produces tannins in the peat.

  The bog water interacts with the acids in the moss and produce tannin
  and other chemicals that preserve the bodies that fall or are cast
  into the bog; hence the numerous well-preserved bog bodies.
  http://www.digitalmedievalist.com/opinionated-celtic-faqs/bog-bodies/

The tannins tan the bodies just like tanning leather; the color of the bodies darken and the tanning action also preserves them.


How would substances that have anti bacterial characteristics interact with yeast? This question has its origins at home brewers where the question was asked how would substances with anti bacterial qualities interact with yeast a fungus?

No one at home brewers was really sure so I thought I would ask here.

LINK

Substances that exhibit antimicrobial activity do so because the microbe itself is susceptible to the mechanism of action. For example, some bacteria crosslink their peptidoglycan cell wall with a transpeptidase (aka penicillin-binding proteins), and penicillin antibiotics block this step. Other bacteria don't do this, and so if you use penicillin there will be no effect.

Likewise, some antimicrobial methods have very broad efficacy against everything, like drugs that inhibit ribosomes, or at the extreme end, bleach. Being said, ginger as in the homebrew link is shown to have a broad action on microbes as denoted in the following article. The question now is does ginger affect yeast?

Google search "gingerol antifungal" (gingerol is apparently one of the potent effector molecules in ginger) and you get a host of results detailing it's efficacy on C. albicans. This doesn't necessarily mean it has the same efficacy on S. cerevisiae, but it does mean that, and this is just a number out of the literature, but a 10% ginger solution may have deleterious effect on fungal growth.

Outside that, I can't really find anything on the actual antimicrobial mechanism of action for ginger, either, so it's difficult to say other than for some reason, they inhibit microbes. They did show that 6-gingerol induces ROS production in tumor cells, which results in DNA damage, but I'll continue to look for an explanation.

What remains, now, is too broad. The ways that antimicrobials interact with different microorganisms is a lot to consider and I can only be about as broad as I've written above without going into a novel worth of text. Hopefully this was helpful!

You can check out this Sigma page on antibacterial modes of action to get an idea of the ways different antibiotics are made to affect microbes.


Can cancer cells transmit from one organism to another? I know cancer cells are very resilient, so would it be possible for them to survive outside of the original organism for long enough to be absorbed by another? Furthermore, would that type of "infection" be possible?

Yes. Devil facial tumour disease is an example:

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

Look here for other examples of transmissible cancers.

I have not heard of any human transmissible cancer.


What are the units of the band intensities in a western blot image? I have done a Western blot and I am measuring the band intensities in Image J. Using the rectangle tool, I have outlined the band and then calculated the area and the mean intensity of the band. I have then calculated the total intensity of the band by multiplying the area of the band with the mean intensity. I was wondering, what are the units of the band intensities? Are they in arbitrary units? Any insights are appreciated.

The units in your case are arbitrary units.
For instance, you may have taken a photo of the bands with a camera that saved a gray-scale file with an 8-bit depth. That means that the brightness values of each pixel have 256 gradations (or 2^8 values of brightness possible between minimum/blank and maximum/saturated). The program only takes the pixel brightness value anywhere between black (0) and fully white (256) and simply performs the calculations so. There is no real connection between actual band intensity and the output from ImageJ or any software.
Alternatively, you can also have relative units. Say you have a reference: a positive or a negative control. If your reference has a brightness of 10, and your band has a brightness of 7, you could express the band intensity as "0.7 relative units"; here you have to specify your reference, i.e. what you are calibrating your relative units to, hence the term relative.