Circadian clocks in enzymes I'm aware of the existence of circadian clocks, but I don't understand exactly how circadian clocks regulate other circadian mechanisms. For example, if an enzyme is found to have a circadian rythm, how is this rhythm produced? Is it because of one or more clock genes?

Molecular feedback mechanisms create rhythmic patterns. The circadian rhythm is driven by a handful of genes, which in turn can regulate a number of downstream factors.

Here is a very nice explanation of the Drosophila circadian clock, which gives you an idea how this works. The video shows the same animation adding more factors every time to guide you through how the system works on the genetic/protein level.

A brief summary: The genes period and timeless are transcribed over night. Their proteins stabilize each other and build up in the cell. At the same time they block their own transcription, limiting the amount of proteins.
Other factors destabilize the proteins and evoke their degradation. One of them is the light activated protein Cryptochrome. This helps entraining the clock and results in the removal of Period and Timeless protein during the day. The negative feedback of their blockage is removed and transcription starts anew at night, when Cryptochrome is inactive.

These clock genes do not only regulate themselves but can also activate or deactivate other factors resulting in daytime-dependent transcription of genes or protein activity.

The whole picture is of course a bit more complicated and involves a lot of additional factors. But also in humans and other mammals you find very similar mechanisms.


Soma-soma paired neurons I'm reading this paper about how neurons can connect. Wikipedia says, typically neurons connect via axon (transmitter) and dendrites (receiver) but there are also special cases where dendrites connect with dendrites, axons with with another axon, neurons with no axon etc.

Now in the paper they refer to the soma-soma paired neurons and their strength of their cholinergic synapse.
Does that now mean that they neurons do directly interact via their soma? If so, how much different is that process to the generic axon->dendrite pathway?

Yep, the soma-soma synapse in that paper appears to be a chemical synapse between two cell bodies. There are no axons or dendrites in that preparation so the synapse must be between the somas. They are using two snail neurons that are far from each other (in different ganglia) in vivo, but which are known to synapse. This in vivo synapse is long-range and so must be mediated by an axon. In the dish, they can encourage the  synapse to form even without encouraging axons and dendrites to grow.

Note that this is an artificial in vitro preparation and they are, in some sense, forcing a synapse to occur in an unusual way in a cell culture dish. They do this because it makes it easy to study certain aspects of the signalling mechanisms for generating synapses. In your paper, they appear to be using it as an easy preparation for a proof of principle for the interface between a biological neuron and a non-biological semiconductor substrate.

The paper you cited references this paper that outlines the soma-soma preparation with a pretty picture to make things clear: http://www.jneurosci.org/content/19/21/9306


Species Identification: Beetle having trunk! Today morning I found this beetle in Cynodon dactylon grass. It had this beautiful head bearing a trunk like structure. I'm wondering what beetle it is

Images:

Approximate size: 1.75 cm
Temperature: 29°C
Location: Uttar Pradesh, India

This is a weevil called Cleonis japonica. Here is a link to a specimen which was collected in 1904. (http://weevil.info/sites/weevil.info/files/Cleonis_japonica.jpg)
Here is a link to same site and one other which show where it was found.
(http://weevil.info/content/cleonis) and (https://www.iso.org/obp/ui/#search)
NP means nepal. Here is a link to something which I hope is a little more descriptive.

https://www.zin.ru/Animalia/Coleoptera/pdf/arzanov_grebennikov_2017_cleonini.pdf

I wish you had taken better pictures.


Purpose of antibody wash It is common practice after surface staining cells for flow cytometry analysis to wash the antibody out of solution before analyzing a sample. I have tried analysis with and without washing the antibody out and notice no significant difference by flow. So is there a reason people do this step that maybe I'm just not noticing?

Two reasons for antibody wash:

To limit non-specific epitope binding. All ABs have specificity.  Washing is usually trying to remove weaker binding to non-intended targets.
For flow, excess AB that is not bound, if also pre-conjugated to a fluorophore, may allow for excitation of the fluorophore while going through flow even though the antibody isn't bound to the cell type of interest.

If you had a very specific AB, and very little excess, you may not notice a thing. I'm sure there are additional reasons; these are the two that immediately come to mind based on my own flow cytometry experiments.


How much oxygen does a plant use up at night? Given the fact that plants cannot do photosynthesis at night but need respiration for their energy needs, they use up oxygen and generate carbon dioxide. But how much is this? If I fill a room with plants thoroughly, what composition will the air in this room be in the morning? Are different plant species vastly different in this regard?

Roughly, half of the CO2 assimilated annually through photosynthesis
  is released back to the atmosphere by plant respiration (Gifford,
  1994; Amthor, 1995).

Source:

https://academic.oup.com/aob/article/94/5/647/151785/Plant-Respiration-and-Elevated-Atmospheric-CO2

Furthermore, it appears like plant respiration rates do not change much with changing temperature, and that larger plants have higher respiration rates.


Is the number of nucleoli in a nucleus fixed? A nucleus can have multiple nucleoli. But are there any constraints on the number of nucleoli in a nucleus?

Can cells of individuals of different species have a different number of nucleoli?
Can cells of different individuals of the same species have a different number of nucleoli?
Can cells of different types have a different number of nucleoli?
Can different cells of the same type have a different number of nucleoli?

I've found snippets of information implying the number of nucleoli is fixed per species, but none authoritative enough to stoke my doubts.

I'll directly go to your fourth question, as all of them can be answered with a yes. This rather old mouse paper already got to the point. Sadly, only the abstract is freely available. Briefly, the number can be variable in the smallest unit you are interested in, the cell type. From the abstract:

The distribution of the number of nucleoli in many diploid cells
exhibited a mode of two or three nucleoli per nucleus, and a range
from 1 to 6 nucleoli.

In the paper, there are histogram of different cell types of mouse and all of them seem to be variable in their number of nucleoli.


Are there pre-synaptic alpha 2 receptors in the post-ganglionic synapses of the heart? Are there pre-synaptic alpha 2 receptors in the post-ganglionic synapses of the heart?

I haven't found any sources that clearly state whether they do or not. I'm also not sure if they exist in most post-ganglionic synapses, or if they do in just specific ones. The reason I ask is wanting to understand the reflex tachycardia non-selective alpha blockers like phenoxybenzamine cause.

One of the side effects of phenoxybenzamine is reflex tachycardia, caused by, from my understanding, partly a reflex to the initially decreased blood pressure and due to the blocking of alpha 2 receptors, increasing nor-adrenaline release. Does this occur by :

Blocking alpha 2 receptors at other sites, causing increased blood levels of nor-adrenaline, which then cause increased heart rate.

OR

Blocking alpha 2 receptors in the heart, increasing local increase of nor-adrenaline?

The heart of course does have Alpha 2 pre synaptic receptors , the definition states that alpha 2 receptors are present on sympathetic postganglionic endings , so I don't see why heart should be an exception .
I will explain to you how reflex tachycardia occurs .
When you give non selective blockers , presynaptic Alpha 2 are blocked , therefore the pre synaptic neurons cannot sense NE amount in synaptic cleft , so they release large amounts of NE . BUT , post synaptic alpha1 is also blocked , so this large amount of NE cannot act BUT THE HEART DOES NOT HAVE alpha 1 it has BETA 1 receptors which are perfectly capable of being stimulated by this large amount of NE that is released , hence causing tachycardia.


Can one switch the DNA present in a sperm cell? Can a donated sperm cell be stripped of its original owners DNA and be replaced with DNA of another person to make a biological child of a man who has low production in sperm?

Not with present technology. There is next to no cytoplasm in a sperm cell. You cannot suck out its nucleus. If your remove its nucleus, the whole thing will just collapses on itself.

As for you question of replacing nucleus?. One current technique (Intra-cytoplasmic sperm injection - ICSI)  is to  inject a single sperm of a man with low sperm count with minimal mobility directly into an oocyte. (Ie sperm that is so bad that they effectively cannot swim on their own)

Unfortunately there is some indication, that this technology has made an entire generation of sons, who have also inherited their father's low sperm count and limited mobility. And now have a higher than average chance of needing IVF assistance.
https://www.newscientist.com/article/2108218-male-fertility-treatment-seems-to-pass-infertility-on-to-sons/


What is this insect? These photographs were taken today in Marseille, in the Mediterranean coast of France. My French friends inform me that these beasties are called cousins because they are "cousins" of mosquitoes (whatever that means).

The thing is, we are absolutely infested by them. They seem to be more active at dawn and dusk (like mosquitoes) but we have dozens flying around the house every evening. I would like to know the species' name to see if I can learn anything about them. Do they have cycles like cicadas? Are they linked to stagnant waters like mosquitoes? Why are there so many of them this year?

Here's one with my hand next to it to give you an indication of their size:

It is indeed a Crane fly, superfamily Tipuloidea, which is part of two-winged insects (Diptera). There are >15000 species worldwide. Their systematics is somewhat uncertain (used to be a single family, now a superfamily). They are placed in the same suborder as mosquitoes (Nematocera). The adults feed on nectar or not at all (they do not prey on mosquitoes), and the larvae usually feeds on litter, roots, fungi etc, but some aquatic species are predatory. Larvae of some species develop in soil and others in water. Adults of many species are attracted by light, which is why you often find them inside houses. I dont know why you find so many this year where you live, but winter conditions affecting survival is a possible explanation.


Function and expression of pseudogenes Can pseudogenes be transcribed into mRNA and translated into functional proteins, or should they be regarded as functionless mutated genes?

A subset of pseudogenes can have a function - even if not translated: For one possibility see the official record for PTENP1, which acts as a tumor suppressor by providing a decoy for PTEN targeting miRNAs
A subset of pseudogenes can be translated. There is a selection for preserving the length of the reading frame, which suggests (but does not formally show) the presence of a translation-dependent function of (at least a subset of) those pseudogenes. - See Xu et Zhang 2016: Are human translated Pseudogenes Functional? (paywall)
As indicated by the above, it seems likely that quite some pseudogenes have a function, which just has not been discovered yet - and that the mode of action can differ between different pseudogenes.


What is this very tiny (3mm) centipede-like insect? My kid found this little guy in his bedroom. It’s about 2-3mm long. Lots of legs, and white rings around its abdomen.

Any idea what it is?

Edit: Location in San Jose, CA.

That is a dermestid larva. A beetle from the family Dermestidae https://en.wikipedia.org/wiki/Dermestidae, common name, skin beetle. They eat dried skin, or flesh, and are generally the last insect to feed on a carcass. They are the bane of insect collectors, because they eat dried insects right off the pin.


Splice in with CRISPR/Cas I need to splice a gene into a human cell genome, with highest rate possible. I mean, doesn't really matter where the gene enters, nor does it matter if some cells die as a result of this.

CRISPR know to knock-in genes with very high specifically, this reduce the success rate if we have a low amount of gRNA and/or of the protein.

I need to insert the gene, without the need of targeting some specific place.

Is this possible in some way with CRISPR?

I know that there may be better technique to do this, but I can only use CRISPR.

A paper was published about a week ago in Nature Biotechnology and adresses your question, Maruyama T et al., 2015. I must say I found the authors' strategy extremely clever.

It is not about increasing efficiency by reducing specificity, but simply increasing efficiency (which is your ultimate goal anyway). What the authors did was to inhibit nonhomologous end joining (NHEJ) to promote homology-directed repair (HDR), two DNA repair mechanisms that compete in cells and of course HDR is the mechanism needed for the CRISPR/Cas9 system.

They achieve NHEJ inhibition using the molecule Scr7, a DNA ligase IV inhibitor which in turns perturbes NHEJ.

Using Scr7 they boosted by 3 to 19 fold (depending on the cell line) the insertion of the target gene. Here the graph showing these results

See paper figures

Moreover using 1μM of Scr7 over 24h on DC2.4 cells increased the % of transfected cells from 4.58% to 58.3%, a neat ~13-fold increase. Here their results:

See paper figures

Hopefully this should give you some ideas.


Chromosome 2 fusion? I read this article by Jeffrey Tomkins and Jerry Bergman claiming to debunk chromosome 2 fusion. Is there anything wrong with these conclusions?

" 1.The reputed fusion site is located in a peri-centric region with suppressed recombination and should exhibit a reasonable degree of tandem telomere motif conservation. Instead, the region is highly degenerate—a notable feature reported by a previous investigation.

In a 30 kb region surrounding the fusion site, there exists a paucity of intact telomere motifs (forward and reverse) and very few of them are in tandem or in frame.
Telomere motifs, both forward and reverse (TTAGGG and CCTAAA), populate both sides of the purported fusion site. Forward motifs should only be found on the left side of the fusion site and reverse motifs on the right side
The 798-base core fusion-site sequence is not unique to the purported fusion site, but found throughout the genome with 80% or greater identity internally on nearly every chromosome; indicating that it is some type of ubiquitous higher-order repeat.
No evidence of synteny with chimp for the purported fusion site was found. The 798-base core fusion-site sequence does not align to its predicted orthologous telomeric regions in the chimp genome on chromsomes 2A and 2B.
Queries against the chimp genome with the human alphoid sequences found at the purported cryptic centromere site on human 2qfus produced no homologous hits using two different algorithms (BLAT and BLASTN).
Alphoid sequences at the putative cryptic centromere site are diverse, form three separate sub-groups in alignment analyses, and do not cluster with known functional human centromeric alphoid elements."

I've also heard them say that there has to be a fusion in every living thing that evolved or evolution isn't true.  Is that true or not?

The article is here

Part one
Part two

Regarding the Papers referenced above:

If the authors maintain that the evidence at the site of fusion is not clear and that explanations as to how this happened are flawed that is possibly concedable.   They would need to do more homework than these papers.  The discussion of vestigial centromere sequences and telomere motifs being inverted is interesting, though contrary views have been written up elsewhere.  I'm not going to review that evidence as I think its not primary to the question at hand...

I would point out that the centromere and telomere sequences are highly repetitive - they are so repetitive that they are often associated with unreliable sequencing in a typical genome build.  While its possible some will be found in future builds of the human genome, such sequences are just as likely to have been excised during mitosis or by mutation.  There would be strong selection pressure for them to be excised quickly; having two centromeres on one chromosome would probably be a fatal trait and the same is probably true for telomerase susceptible sequences in the middle of a chromosomal arm is too.  A lot has happened at the point of fusion and 150 kB of DNA seems to have included itself which is not from the original Chr 2A or 2B.

I think there is some confusion here: The fusion models examined do not predict the fusion from the local configuration of bases.  The main evidence for fusion has always been the fact that the two pieces of human chromosome 2 are nearly identical to chromosomes 2A and 2B of apes - typically 96-98% identical.  The genes are almost entirely in the same order, the inter-genic regions are very similar All along the 2A/2B length - millions of bases.  The site of fusion ad models for its occurrence is merely confirming what we already - there are two chromosomes somehow stuck together.  Since both papers focus on the site of combination and do not adequately address this primary piece of information, they seem to be missing this point.

The chances are infinitesimal that human chr 2 were to resemble those of other primates at random.   This is what you say in science when you mean 'impossible'.  One simply doesn't see a segment of DNA the size of Chr 2A and 2B being so similar for such a length when we look at rats, dogs, worms or any more distantly related living thing.  But for every primate the relationship corresponds to humans the same way.  In addition studies show that these highly similar blocks of DNA sit right next to the site of fusion and show a crossover where the fusion probably occurred.  Some recent hominids - Neanderthals and Denisovans had the chr 2 fusion as well.

I have to say is that there's always a chance that chromosome 2 fusion did not happen though in my view there's a tremendous amount of evidence that it did.  The second most likely explanation is that all the other apes had their chromosome 2 break into 2 pieces at some susceptible site.

I don't quite agree that chromosome 2 fusion is an indispensable or even leading piece of evidence that means that humans and the other primates are interrelated.  That question is a different kettle of fish and the relationship between Human chromosome 2 and the chromosomes of other primates is just one contributing point.  All the other chromosome sequences in primates are the same, and nearly every gene in human beings is closer to primates than to other animals.  If they had not found chromosome 2 fusion in the genome sequences few if anybody would have worried about it.

As to your last question - I don't know if its necessary that chromosomal fusion must occur in every living thing, but it appears that it has.  In fact what we see as we look at all the diverse chromosomes being sequenced, is that most chromosomes have been merged or rearranged over and over again.  Over long periods of evolutionary time, a typical chromosome looks like a patchwork quilt stitched up from pieces of other chromosomes.  These relationships are called synteny, which reaffirm the thesis that all living things came from a single point of origin, if you go back far enough.  Really, the fusion point of Chr2 is interesting because its a relatively new event; by picking through the pieces we might find some understanding of something that appears to be a common phenomenon in genome dynamics.

The above image comes from a review of methods to identify syntenic regions.  It identifies regions of human chromosome 7 and similar regions of mouse chromosomes, identifying regions on mouse chromosomes 6, 9, 11, and 12 with substantial similarities as well as a little bit of chr 2.  Hu chr 7 is 158 million bases long, so even a small band (> 1/1000th of the full length) on this chart means 100,000s of bases.

If all these syntenic relationships are considered together they can construct chromosomal rearrangement events that compare with the phylogenetic tree and typically verify speciation events that separate the two organisms being compared.

Whoops - just found this.  Take a look at this Biology.SE question: it refers to Robertsonian translocation where the long arms of several of the chromosomes chr 14, 15, 16, 21 and 22 are known to sometimes fuse, resulting in viability.  The answer there is useful - these variants don't tend to produce offspring, but it only takes one time.  Its only happened once in the past 5 million years or so.  So another point of view there.

That should't discourage the authors from trying again.

All this being said, as a scientific question I'd rather have a discussion like this, based on evidence and facts that anyone can evaluate.  The authors did quite a bit of homework and read some of the literature that is out there.  This is the right direction some of the creationists are taking here and I personally hope that they keep at it.

If science is to have any merit (or fun) at all, its because any idea can be called into question and be re-evaluated at any time by anyone.


What would happen if a person had the right side of their body totally removed (including the brain)? What would happen (in reality or theoretically) if the entire right side of a human's body was removed?

Could they live (aside from all the probable infections and such)?

I would guess that humans can live without part of the liver or brain.

The left brain controls the right side of the body.

What do you think (or know) will happen?

Thank you very much in advance!

They would die.

Let's imagine that we perfectly cut a person down the middle. That would mean cutting the spinal cord in half, probably damaging the tissue so much that the remaining half wouldn't work well. The liver would be gone. The intestines and bladder would just be open. The heart would have to be adjusted to the left. The surgery would probably cause so much blood loss that they wouldn't even survive to die of other organ failure.

And you already alluded to the mismatch between what side of the brain controls what side of the body, so if you kept the pseudocorpse "alive" on an IV, heart lung machine, and hemodialysis, they'd probably still be paralyzed.


Plumage as indicator of health in birds Anybody know which traits of bird plumage are accurate indicators of a birds health? For example feather coloration, feather brightness, amount of feather wear, number of feathers, moult timing, moult duration etc.

This resource provides a short list of which general components of plumage are good indicators of a healthy bird.

Your pet's plumage should be. . .
Soft - feathers should be strong, yet flexible.
Smooth - no rough feather shafts; no uneven or split edges
Glossy - sheen extends over the entire coat
Full - thick, where it needs to be
Vivid - color should be deep, bright and uniform
Clean - free of dust, dander, waste, or soil
Parasite-Free - no lice or mites

Also, this website page discusses the signs of malnutrition or disease in plumage in more detail.
Stress bars, dark lines which transect a feather, are directly caused by an inefficient absorption or lack of required nutrients. Stress bars can be found on all feathers during the period of malnutrition, and remain even after this period.
Assymetrical moulting is also a sign of bad health. There should not be any bald patches present during the moult.
The resource states that if a moult is delayed due to malnutrition, an incorrect photoperiod or a metabolic problem, plumage will become depigmented. However, the appearance of "dirty" feathers can also be due to overpreening or damage done to feathers by physical contact.
Finally, a change in the usual plumage color of the bird in question is indicative of a lack  or oversupply of a particular nutrient.


Programs/software to graph biological data I am curious about what sort of programs people in my field of academia are using to graph their data. I am a master student in biochemistry, and have more or less only used excel (on rare occasions I have used the statistical program R).

I know my question is very general, but I would like to hear suggestions for programs that could be useful when I want to compute numbers or make good graphical representation (in the life science fields, e.g. microbiology, biochemistry, biotechnology, biophysical chemistry).

Also, are the other programs to create good graphic illustrations? I am currently using Inkscape to produce molecular illustrations, and I think this is one of the most typical programs to use?

There is no standard software, programming language, or library used for computing and graphing biological data. The R language is commonly used for statistical work, but Python (in conjunction with the SciPy stack) and C++ also gets used a lot.

Before going further, I should point out you are asking two questions. One about computation and the other about presentation.

Computation:

You mentioned R. That is a programming language (with specialized software built around it). When it comes to programming language choice, the three most important factors are personal preference, available libraries, and the language already in use if you are joining a project with a pre-existing code-base. You might notice performance is not on this short list. The reason for this is that modern languages on modern hardware are efficient enough to, very often, make language choice irrelevant from a performance perspective. Most computational tasks suitable for R are also suitable for languages like Python and Julia.

R's strength is in its focus for statistical work. Whereas Python's standard library comes with many bells and whistles intended to ease the design of small to moderate sized pieces of software across many situations, R comes with many features focused specifically on easing the task of writing code for complicated statistical calculations. Due to it being so common in academia, R one language you are very likely to encounter in academic, computational work. That makes knowing it a helpful skill (whether you regularly use it or not). R, having such a strong suite of tools and large userbase, is also the basis for many third-party tools. One interesting example is Bioconductor

That being said, there are also advantages to using (or at least knowing) Python. It is one of the most common languages in programming in general. That means it has a diverse assortment of libraries designed for it by members of the community. When it comes to nonstatistical libraries, few languages have as many options. When it comes to statistical work, Python does not have as many options as R, but it does still have a lot. The SciPy stack, which includes the NumPy and Pandas libraries, is a big part of that. Another benefit that comes from Python's popularity in the programming world is that you will have an easier time finding programmers to help you on a large project if you decide to look for help outside of your field. (For example, far more computer science majors will know Python than R ...multiple times over.)

As far as the Julia language goes, it is still new. It is being developed as a competitor to R and Python, but it is not mature enough to be a serious contender just yet. However, since your question is about what people use, I would be remiss to ignore it. It may become a serious contender, but for right now, it is still trying to grow and prove its worth.

If performance becomes a serious issue, you would probably be forced to dump R, Python, or whatever very high level language you are using in favor of C or C++. Both are far more efficient than the so-called "batteries included" languages. C and C++ are system programming languages. They are often used in operating systems, databases, video games, and other large pieces of software which you would not want slowed down due to features being included which you did not explicitly program in. (C and C++ are also used in small projects, but I digress.) However, taking advantage of this efficiency requires some insight into how computers actually work. This is not a difficult task, and any good tutorial or book will cover such topics. Using C or C++ without this basic understanding will likely be counter productive, as doing so can lead to you inadvertently creating a program far slower than it needs to be, which could be an issue if performance is becoming a serious concern.

A non-performance benefit of C is the large library selection. As I mentioned above, few languages can compare to Python's library selection. C is definitely one of those few. Actually, C is essentially the lingua franca of libraries (due to its age, its dominant position, and aforementioned efficiency). This means you might find yourself needing to use some highly specialized library with no bindings to languages like Python or R. I have come across a few.

Presentation:

R is also a nice language for graphing data. It comes with a package known as ggplot2, which is responsible for this functionality. This is a common source of data visualizations. However, this does not mean you must use R if you want to create graphs that follow the norms of academia. First off, many people use other pieces of software for plotting. Secondly, there is the library for Python called matplotlib. It is fully featured and is capable imitating the visual appearance of ggplot. One of its built-in style sheets was included just for this purpose. Not surprisingly, matplotlib is the graphing library used in SciPy.

There are many other graphing/plotting libraries, and many of them are fairly language agnostic. Presentation is not often a deciding factor in what language to use for computation. However, if you found yourself needing to use a specific language for its presentation options, doing computations in one language and then feeding the results into another for presentation is not unheard of.

Software:

I include this as a third category because this is more complicated than deciding on programming language A or B or choosing a plotting utility. Non-computer scientists often confuse software with languages. You have to use software when writing a program in a given language, but all the work is done by the program you write. Large software suites, on the other hand, do work for you in many ways. They often come with some sort of quasi-programming language included, but that is only one part of a larger whole. While R comes with a number of software tools, Matlab and Mathematica are better example of this. Free, open source alternatives to these proprietary suites would be Octave and Scilab, although such open source software traditionally has not very competitive with the likes of Matlab. SciPy is a recent example of open source software closing the feature gap (which is a very good thing in terms of avoiding vendor lock).

Beyond that, it is hard to say what you would encounter or what is common. Most large software tools are proprietary. Different companies, universities, and individual projects will use different software, and you will not know what to expect until you you are recruited by a team.

This is why projects sticking to programming languages over large software is preferable in terms of ease of recruitment. Also, programming code can be published with papers a lot easier than describing how you used a piece of software (which is big if open data is important to you). That being said, it can not always be avoided. Many machines in biology require specialized software and many kinds of data are most easily manipulated with proprietary software. Do not worry about such situations. It, obviously, will not affect your current work from being presented in a standard way.

EDIT:

Sorry for the wall of text. The question was broad and this is a complicated issue. It was hard to summarize.


Is there a web tool for species identification? I know this stack exchange provides the ability to post photographs of animals/plants for species identification, but is there a web resource that can automatically identify a plant/animal using image processing/correlation tools - so the user doesn't have to painstakingly work with keys?

I'm going to go out on a limb and say NO. I'm a professional biologist developing a natural history website, and I've never encountered such a thing.


laboratory mice, nutrition, and humans It seems that many nutrition experiments [directed at human diet] are carried on laboratory mice. Is there any justification that nutrition that is good or bad for laboratory mice will also be same way applicable to humans ?

I wonder because mice and humans, although both being mammals, are separated probably by tens millions years of separate evolution.  By the "mammals" logic, dolphins, cows, wolves, and goats, all being mammals, shall have same diet as mice ?

Sometimes one man's food is another man's poison (lactose differences for example, due to genetic differences). That's man to man, same species. On what is "transfer of nutritional information" from species to species based ?

2) Was it ever established, or the opposite, that all humans have same best diet. Other than known lactose metabolism difference.

Whether using quantitative models, or "animal models", I think this is a useful quote to keep in mind:

  A model is a lie that helps you see the truth.

  -- Howard Skipper

As for evidence that using mice models for human nutrition is justified -- I believe there has been a good deal of research that has provided useful insight on the influence of genetics on the susceptibility to diabetes in humans using mouse models, so ... yes?


Are proteins a different shape in space? Is the shape of a protein affected by gravity? In space, will the shape of a protein be different to what it is on Earth?

If the structure and shape is in fact affected, then would it be enough of a change to cause a change in protein function?

I've found studies from NASA saying that when protein crystals are grown in space, they are larger and form more perfect crystals than on Earth but I want to know about the effect of gravity on proteins that have already been formed.

Thanks!

Proteins are not made to be one way up or the other as they flow around and surround cells, so sea-level to space gravity gradient will not be the major cause of change to proteins at different altitudes.

Pressure is more of a factor on proteins, and it has been studies very much, both for protein shape and protein interaction with elements and other molecules.

http://www.annualreviews.org/doi/abs/10.1146/annurev.pc.44.100193.000513?journalCode=physchem

People have awesome health when they are born and raised at altitudes of 4000 meters, there are even people living at 4800 meters OK. the pressure gradient there is halfway in between sea level and space. 100m depth also stresses nitrogen toxicity and other severe effects more than proteins, but deep sea fish do have specially adapted proteins because depths at 10000 meters require different proteins than the surface.


Laemmli-SDS-PAGE problems I did Laemmli-SDS-PAGE for my Ammonium sulphate precipitate but I had very weak band and have very weird part at the end of gel. Please help me to solve that problem. Thanks

Your gel looks just fine to me. It simply indicates that your ammonium sulfate precipitate contains massive amounts of this small protein at the bottom (whatever this is). The upper bands look fine, the amount loaded is appropriate: they are not overloaded like the bottom one, but not too faint either. The fact that your first and last lanes look a bit smeary is because of the massive amount of the small protein (lanes do look smeary when overloaded this much). The bottom band is definitely really some protein, and not a staining artifact; I have seen this shape before with purified proteins overloaded on SDS-PAGE.

One thing you could do, assuming you still have enough of these samples, is to run a complementary gel with 100 times less material. Dilute by a factor of 1/100 in 1X Laemmli denaturation buffer, and load a new gel with the same volume as for this one. You won't see the upper bands anymore, but you will have a much cleaner bottom band that you will hopefully be able to assign an apparent molecular weight to (or even cut out for mass spec identification; wear gloves and use clean tools if you do that, otherwise they will mostly detect keratin from your skin).

Assuming the point of this gel was to check the outcome of ammonium sulfate precipitation used as a purification step, well obviously it didn't work well to separate all these bands, and you might need to repeat and try different concentrations. But if the bottom band is the one you are trying to purify, then you were successful (the top bands represent less than 10% contamination, I would say by eyeball estimation). If you're interested in one of the top bands, then it clearly didn't work.

Is one of these lanes the supernatant? If so, you also have massive amounts of the small protein there (it's in every lane). Such a high enrichment looks suspicious: could that be purified lysozyme that you added during the purification procedure to help break down bacterial cell wall? (assuming you're trying to purify a protein over-expressed in E. coli).


How could pharmaceutical metabolizing bacteria be used to synthesize them? Lets say I have a pharmaceutical "P". It can be broken down by enzymes of one strain of bacteria into two molecules one of which can be further metabolized enzymatically by a different strain of bacteria. Both strains as a result can decompose "P" to the simplest metabolites.

Could one hope to reverse the reaction using the same enzymes and have the two bacteria produce "P" from basic nutrients and if so, how would the conditions have to be altered? Or perhaps would it be possible ex vivo?

In principle yes, because almost all reactions exist in an equilibrium and enzymes are catalysts (meaning they affect mainly the activation energy for a specific reaction).

The best approach is to purify the enzymes in question (probably not even from their original species, but from another transgenic bacterium), since this reduces your total systems from two different organisms and all their enzymes and metabolites to a very specific set of two enzymes and a handful of metabolites.

But ...

The natural equilibrium of the reaction might favor the more basic metabolites.
Even if you speed up the generation of "P", that won't help much if only a fraction is converted in the first place. Many biological systems deal with this problem by coupling unfavourable steps with hydrolysis of high energy molecules (like ATP), but linking to this to a given enzyme would be a very challenging process.
The enzyme(s) might not be overly specific for "P".
Many enzymes that remove or break down 'unwanted' products can act on multiple similar molecules. This make sense for cells, since its much more efficient to have one enzyme taking care of multiple 'bad things'. However, this makes reversing the process tricky since your reaction will yield multiple products of which only one is interesting. Optimising the enzyme to be more specific is relatively straight forward using in vitro evolution though.
'Basic metabolites' is not a clearly defined thing.
Many pharmaceuticals are pretty complex, and enzymes that break them down likely literally chop it into two pieces. Whether these pieces are actually easy to obtain chemicals that can be used as input for an enzymatic reaction is a different question. Depending on the complexity of 'P' you might have to use a pretty large number of enzymes (all of which may come with the above mentioned problems) to be able to start from reasonably basic molecules.


How do I calculate the change in allele frequency in a haploid population under selection? From this book

For simplicity, let us consider a haploid organism and assume that the frequencies of alleles $A_1$ and $A_2$ are given by $x$ and $y=1-x$, respectively. We also assume that the fitnesses of $A_1$ and $A_2$ are $w_1 = 1$ and $w_2 = 1-s$, respectively. In this case the mean fitness $\bar w$ is given by $x + (1-x)(1-s)= 1-sy$, and the allele frequency change per generation becomes
$$\Delta x =  \frac{dx}{dt} = \frac{sxy}{1-sy}$$

If I would have to find what $\frac{dx}{dt}$ equals I would use the Wright-Fisher equation and find that:
$$\frac{dx}{dt} = \frac{w_1 \cdot x}{\bar w} = \frac{x}{1-sy}$$
, which is obviously not the same result as what the author found...
What am I missing? How did the author find out this result $\frac{dx}{dt} = \frac{sxy}{1-sy}$?

Here is my full derivation to the book example you gave, hopefully it'll help you clear up what went wrong:

You need to remember that after there is selection acting on the population, you no longer have a total of 1 after selection. Think of selection as "killing" individuals, which means the total is now 1 minus what has been "selected out". sy is what is selected out, therefore the new total is 1-sy. Which means you now divide each of your frequencies by 1-s*y (see picture).

Please comment if you need more explaining.


Structure separating the left atrium from the ascending aorta? With reference to the (adult) anatomy of the human heart:

The left atrium (LA) and the proximal part of the ascending aorta (Ao) abut one another, as shown nicely in this image [1].  Is there a name for the wall(s) separating the LA and Ao?  And is this a single structure (i.e. septum), or is there a sinus?

[1] http://www.radiologyassistant.nl/data/bin/w440/a5097978b829cd_3-chamber.jpg

There isn't any particular structure there: you have the wall of the aorta/adventitia, and if you have an explanted heart there is a space and then the auricle of the left atrium on one side and the right atrium on the other. These would all be contained within the pericardium.

Where the aorta is most "touching" the left atrium is where the pulmonary veins come in: I think this picture from Gray is most helpful.

Figure 494. Henry Gray (1825–1861).  Anatomy of the Human Body.  1918.

There really isn't much to distinguish these veins from the non-auricle part of the atrium, similar to the vena cava on the right side. If you were to cut along the veins eventually you would just open up into the atrium.

The Visible Heart Lab is another good reference http://www.vhlab.umn.edu/atlas/aorta for cardiac anatomy.


What is pQTL and why do we need eQTL? eQTLs are genomic loci that contribute to variation in expression levels of mRNAs (wikipedia).

There is data out there that shows that ~60% of the time, the amount of mRNA in a cell is directly proportional to the level of protein coded by that mRNA.[1]

It means that even if the abundance of mRNA is high, we cannot be sure that the abundance of protein is high as well. Why do we still need eQTL if we cannot derive abundance of protein from mRNA transcripts? In the end, the abundance of protein influences the disease rather than the abundance of a transcript.

Does a pQTL implement the idea of a relationship between a genetic variance and the abundance of a protein? I do not understand how a genetic variance can influence the protein level. I assume it is related with a post-transcriptional modification but how?

Genetic variation can affect the levels of protein; consider a variant that reduces the amount of mRNA transcribed, this could have a profound effect on the amount of mRNA available to translate into a protein.

Consider another variant that does not affect the abundance of the mRNA transcribed, but alters one of the many important sequences that are required for translation (co-factor binding sites, ribosomal binding sites, start site, etc.).

These are just a couple of examples that first came to mind, but there are many more. For instance, a variant may increase expression of a particular microRNA that in turn inhibits the translation of another mRNA molecule. I have not included any references as this is more a logical exercise - doubtless there are many more ways a genetic variant can affect protein abundance.


How is yellow elastic cartilage a true cartilage? My book has only mentioned the fact but no reason is given so I would like to know the reason for it. I would like to know what more to add in the body but the question just doesn't get posted.

True cartilage is something of a simplification or a misnomer, they are saying that it truly a form of cartilage and not another elastic tissue type. in fact
"true cartilage" is a term coined by your book. They could have also said it's part of the cartilage family of cell/tissue types.

It's similar to cartilage under a microscope, structurally and has similar consituents, although yellow cartilage also contains elastin. If you were to dissect humans, you would probably find that there are a lot of variations of cartilage of different elasticity, midway in between both forms.

this page is full of info and pics:

It's a good idea to check wikipedia and 2-3 pages to find results to that kind of query, you will find fabulous resources, whereas on stack it is really for studies that take more than 20 minutes via google.


Will neurons live after the death of a human? If so, how long? I don't know if this is correct or not, but I have heard this from a friend and I want to get a clear explanation about this.I hope there is some one who can help me.

I think that depends somewhat on how the human dies - in particular on the conditions. If they die in a very cold environment (say at the top of some icy mountain range), they'll freeze and metabolic processes will slow down considerably, and so will cell death. But such hypothermia-based slowing down is a special case. Normally, if your heart stops or you are not getting oxygen to your brain (perhaps due to a stroke), your neurons will start dying pretty quickly. Within many minutes there will certainly be considerable permanent cell loss - certainly within hours. If oxygen is significantly depleted, ATP production will also significantly drop. If this happens, the various ATP-dependent processes will slow to a crawl (including the Na/K ATPase and other ion pumps and channels that are needed for maintaining and changing the voltage difference between the inside and outside of the cell). This in itself is bad enough as a lot of the enzymes and mechanisms that are dependent on the voltage difference will fail (and probably enough of a reason for many cells to start dying), but one of the effects of this is apparently an increase in the extracellular glutamate, which ultimately leads to (via NMDA receptors for example) an influx of calcium ions into the neurons. Too much of the calcium ions is once again toxic for a variety of the processes inside the cell and is an additional and big reason for neuronal cell death.

In short, as far as I know, neurons don't have a good time living without sufficient oxygen and therefore after a typical human death.


What is an aromatic cage and what does it do? Epigenetics, 2. ed, Chapter 3.6:

  Similarly, methylated lysine residues embedded in histone tails can be
  read by “aromatic cages” present in chromodomains, or similar domains
  (e.g., MBT, Tudor) contained within complexes that facilitate
  downstream chromatin modulating events (see Ch. 7 [Patel 2014] for
  structural insights

I understand it is something like a protein motif, but I cannot find a good definition using google.

It refers to the structures in the PHD-finger domain and chromodomains. The aromatic amino acid residues form a cage like structure which covers and interacts with the methylated ammonium of lysine via a cation-pi interaction.

  The BPTF-PHD structures reveal the main characteristics of PHD fingers that can read H3K4me3. The binding occurs through an aromatic cage where a trimethyl ammonium group is stabilized by van der Waals and cation-–π interaction, which is similar to the ones observed in chromodomain, MBT, PWWP, and Tudor domains. This aromatic cage is composed of one Trp and three Tyr residues; and it has three faces and a 'lid' that is beyond the tip of H3K4me3. Subsequently determined structures of other fingers in complex with the H3K4me3 peptides show that the cage varies and can contain a combination of two to four aromatic and hydrophobic residues.

 Margueron et al., 2009


Can endometriosis be considered a form of cancer? In endometriosis the lesions form their own vasculature and compromise organs, arteries, and nerves. It can spread and embed throughout the body. It's difficult to treat as the adhesions resulting from repeated surgeries can cause the same symptoms as the lesions. Treatment often leaves patients with the original level of disability after the 2 year mark.

My question is, for these reasons could one treat and research endometriosis as if it were a form of cancer?

Could the immune system be utilized in treatment as the lesions induce high levels of certain cytokines?

Why or why not?

According to Endometriosis: benign, malignant, or something in between? (PubMed, 2017), endometriosis is not considered cancerous because:

Does not appear as an expansille tumor mass
Is not destructive
The cells in the lesions are normal, like in the uteral endometrium
Is not lethal

Immunotherapy of endometriosis is in the experimental phase - you can read more here: Novel Therapies Targeting Endometriosis (PubMed, 2011). Other treatments mentioned are anti-inflammatory drugs, selective estrogen or progesterone modulators, statins and antiangiogenic agents. There is also a study Open Label Immunotherapy of Endometriosis running - it is briefly described on ClinicalTrials.gov.

Chemotherapy, which is effective in some cancers, is based on killing quickly-dividing cells, but cells in endometriosis do not divide so quickly, so you can't treat it by chemotherapy in the same way.


Before I move my arm the brain sends signals - what causes the brain to send signals? Please tell me what causes the brain to send signals, how does the brain send signals?
can you tell me what happens between the point when you make an intention to pick up a glass of water, and before the brains sends signals to the body which excites the muscles.

So what happens at the moment when you make the intention to pick up a glass of water but before the brains sends signals after you reach to pick up a glass of water.

Action potential - I haven't read through the entire Wikipedia article so I can't vouch for its accuracy (not that my neurophysiology is good enough to critique it), but it's probably a good start.
Broadly speaking: the brain contains different regions that are each responsible for fairly specific tasks. In the case of picking up a glass of water we can, at a high level, describe the mechanism behind thirst. Your blood contains electrolytes in water; you can consider the electrolytes as being like cordial (reduce the water and you have a higher concentration of cordial / electrolytes). A sensing mechanism (beyond the scope of this answer) will trigger action potentials between the relevant areas of the brain (motor, memory, etc.) to result in the final movement.


LCMS/MS versus Western Blot I have a general question regarding which method would you recommend me to use if I would like to investigate the difference in the level of several proteins in tissue samples and compare different treatment groups. I could either do an LCMS/MS or a Western blot. Which one would you recommend and would you do both for validation? I am looking for time- and cost-effective techniques.
I'll appreciate any suggestions.
Thanks!

Western blot, though is a commonly used technique and is relatively simple to do, has some issues:

Low throughput: it is difficult to analyse multiple proteins simultaneously
Limited cross comparability: since antibodies to different proteins can have different affinities, they cannot be compared with each other.
Low sensitivity
Not very quantitative

LCMS addresses all the above limitations of western blot. It is also possible to do targeted proteomics i.e. study just some few proteins instead of the entire proteome.
An LCMS system has a high initial setting up cost but a relatively lower run cost. However, the mass spectrometer has to be maintained and it is not an easy job; you basically need a facility and a dedicated technical staff.

  Which one would you recommend and would you do both for validation?

Which technique to use depends on what you really want to see and what resources you have at hand. It is a commonly practised approach to do a western blot for re-validating a few selected genes identified from LCMS experiment, which is just to prove that the result can be obtained using another technique too.


How to pipe Bwa-mem output without saving SAM file I'm trying to find circular ARN using the program CIRI2. CIRI2 takes as input SAM file from BWA-mem, but I would like to go straight to CIRI2 output without saving SAM file.
Is there a way to achieve this?

I never used CIRI2 but I think you can do the same way as I used to pipe with samtools:

bwa mem genome.fa reads.fastq | samtools sort -O BAM -o output.bam -

So it would be something like:

bwa mem genome.fa reads.fastq | CIRI2 <your options>

I think you will need to precise that CIRI2 input is STDIN.
I hope it will help,


How do I prepare a PDB for submission to the Protein Data Bank? I have a couple structures that are nearly ready to be deposited in the PDB.  Out of curiosity, I ran them through the ADIT's precheck tool and they failed with one error after another, as I lacked all sorts of additional records (TER, SEQRES, HETNAM, etc.) that my refinement and modelling tools don't seem to care about.

From what I understand/guess, the online submission tool will help fill in all the metadata (REMARKs, etc.), but how do I turn my coordinates into something acceptable?

These two links go through the specifications required for the PDB format:

Link1: http://deposit.rcsb.org/adit/docs/pdb_atom_format.html

Link1 primarily goes through the specs. required if you say have a NMR file you would therefore require the MODEL statement. It also goes through other statements such as when to use TER and how each ATOM line should look etc...

Link2: http://www.wwpdb.org/documentation/format33/v3.3.html

Link2 goes through the other statements such as HEADER, REMARKS and TITLE


To what extent do gonads affect differences in gendered behaviour? I'm not sure whether this question makes sense, but someone said that they result in gender differentiation on an organisational level in the brain. I'm wondering how important these changes are, in terms of magnitude of average differences in neural structure between males and females?

Yes

During embryonic life,there is formation of new synapses by a process termed as exuberant synaptogenesis.
Their differential formation in the males and females could be due to the effect produced by the gene PCDH11X/Y located in the allosomes.

  PCDH11Y is a gene unique to human males that encodes Protocadherin 11Y, aprotein that guides the development of nerve cells. PCDH11X, located on the X chromosome, is common, in both sexes, to humans and our nearest relative, thechimpanzee; however, PCDH11Y, located on the Y chromosome, is unique to males.[3]
  ...PCDH11X/Y are cadherin family genes. They make proteins, involved in signalling, that attach to the surface of nerve cells.[4] PCDH11X and PCDH11Y, respond in different ways to Retinoic acid, a chemical involved in the development of embryos. The acid stimulates the activity of PCDH11Y but suppresses PCDH11X. This is likely one of the explanations for the differences between the brains of men and women.[3]
  [source]

About the parts of the brain which are deemed"sexually dimorphised" a few of them are:

1.hemispherical differences due to which inter hemispherical functioning is better is females
 whereas intra hemispherical functioning in males

2.hippocampal and amygdaloid laterisation

  on average males had larger grey matter volume in bilateral amygdalae,hippocampi, anterior parahippocampal gyri, posterior cingulate gyri, precuneus,putamen and temporal poles, areas in the left posterior and anterior cingulate gyri
  ...females on average had larger grey matter volume at the rightfrontal pole, inferior and middle frontal gyri, pars triangularis, planum temporale/parietal operculum, anterior cingulate gyrus, insular cortex, and Heschl's gyrus; bilateral thalami andprecuneus; the left parahippocampal gyrus and lateral occipital cortex
  Source:Neuroscience of sex differences

Furthur,since synaptogenesis may occur throughout one's lifespan perhaps not as greatly as during embryonic life and as receptors for gonadal hormones are present in the brain it can be said that the gonads may affect the phenomenon,though mainly after puberty when their concentrations are higher than during childhood.


In the Lineweaver-Burk Plot, why does the x-intercept = -1/Km? Taking the reciprocal of both sides of the Michaelis-Menten equation yields the Lineweaver-Burk Equation:

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

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

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

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

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


Is the heart more relaxed when stretched or contracted, and how does it affect cross-bridge interactions? In the heart, are stretched muscles during the diastole more relaxed or are the contracted muscles more relaxed? Depending on the answer, are there then more cross-bridge interactions in cardiac muscle cells when the heart is stretched or contracted?

The muscular portion of the heart is comprised of cardiac myocytes, elongated cells filled with bundles of actin and myosin called sarcomeres. These cells are similar in many respects to skeletal muscles, but are shorter, have only one nucleus, and slightly different isoforms (versions) of the proteins involved. The purpose of this cell, like the skeletal muscle cell, is contraction, or shortening on activation.

This image of cardiac muscle cells shows how full they are with long bands of proteins (proteins stain pink).

Because the heart is a muscular chamber, instead of simply a band of muscle (like the bicep), the relevant dimension for the organ is volume instead of length. Where your bicep gets shorter when it contracts (and pulls your forearm toward your upper arm, bending at the elbow joint), when your heart muscle contracts, it twists and squeezes against the fibrous part of the organ, decreasing the volume of the chamber.

Since there is no air in a healthy live heart, when the heart contracts, reducing the volume of the container, the blood is forced out of the heart (ejection) through whatever opening is available. This is called systole. When the heart relaxes, the volume of the container increases, and blood enters the container through whatever opening is available. this is called diastole.

Now, how is this related to cross-bridge interactions?

The mechanism for contraction itself, in both skeletal and cardiac muscle, is cross-bridge cycling. Those pink bundles of actin, myosin, and associated proteins in the picture above form bonds, change conformation, break bonds, change conformation, and form new bonds:

This cross-bridge cycling occurs during contraction when $Ca^{++}$ enters the cell as part of the cardiac action potential. Relaxation occurs when $Ca^{++}$ concentrations decrease, through the action of the $Ca^{++}$-ATPase, causing cross bridge interactions to decrease.


Do Black Pepper and Black Nightshade share specific characteristics? In my textbook, I read that two organisms of the same species share specific or fundamental characters. Piper nigrum (Black pepper) and solanum nigrum (Black nightshade) share the same specific epithet despite belonging to different families. Is this because they share common fundamental characters ?

Short answer
Nigrum is Latin for 'black'. As you write in your post, it's black pepper and black nightshade. Not until the level of Class and Phylum do they share the same taxonomic classification. Hence, the species suffix nigrum doesn't tell you anything about their kinships, other than their physical appearance (they're both black).

Background
In general, the species part of the linnaeus nomenclature has nothing to do with evolutionary relationships. Instead, it is the higher classifications that denote kinships, for example, as you already suggest, the genus name, that may have various related species in it (Fig. 1). The species you mention are of a different genus.

The Species: Piper nigrum belongs to the Genus Piper, Family: Piperaceae, Order: Piperales, Class: Magnoliopsida, Phylum (Division): Magnoliophyta, Kingdom: Plantae, and Domain: Eukarya
The Species Solanum niger belongs to the Genus Solanum, Family: Solanaceae, Order: Solanales, Class: Magnoliopsida (Dicotyledons), Phylum (Division): Magnoliophyta, Kingdom: Plantae, and Domain: Eukarya.

They share only the same Class (and hence Phylum, Kingdom, Domain). For comparison, in the Kingdom of Animalia, we have the Phylum Chordata (vertebrates), that splits up into the Classes Mammalia (Mammals), Actinopterygii (Bony Fish), Chondrichthyes (Cartilaginous Fish), Aves (Birds), Amphibia (Amphibians) and Reptilia (Reptiles). So your two plant species share as much in common at the taxonomical level, as Mammals and bony fish.

Piper nigrum (or black pepper), is a climbing vine in the Piperaceae (pepper family) native to the Malabar region of southwestern India. Black pepper is grown in various tropical regions, including India, Indonesia, and Brazil, as it is one of the most important spices in the world.

Solanum nigrum (or European black nightshade) is a species in the Solanum genus, native to Eurasia and introduced in the Americas, Australasia, and South Africa. It is also known as black nightshade, duscle, garden nightshade, Indian nightshade, garden huckleberry, hound's berry, petty morel, wonder berry, small-fruited black nightshade, or popolo.

Fig. 1. Linnaeus nomenclature


why prokaryotic ribosomes have 30s and40s subunits and eukaryotic ribosomes have 40sand 60s subunits? Ribosomes are protein factories of cell and are composed of two subunits; one smaller and other larger unit I want to know that why ,ribosomes of eukaryotes have a 40s and 60s subunit and prokaryotic ribosomes have 30s and50s subunits ?If we combine 30s and 50s subunits shouldn't it be 80s ribosome instead of 70s ribosome .

I think I can get the point after your second comment.

Not only protein composition, but rRNA composition and sequence length of Bacterial and Eukaryotic ribosome is very different. And the difference of sequence lengths (and hence mass) in both take part in the difference.


What's inside the males body in the space where females have the ovaries and the uterus? The male penis and scrotum are external extremities, whereas the female sex organs are placed "inside" the body. So as females have the bladder, rectum, other stuff just like males. Does this mean overall females have larger volume of organs? Is this why females have wider hips? Because male penis and scrotum is extral appendages just like female breasts.

Any good animation, videos, references are welcome. Any reason for how these changes came to be from a evolutionary view point are all extra information I would love.

Wider hips in females is not contributed because of large volume of organs.

Broadening of the hip bones happens as a feature of the female pubertal process, and estrogens (the overwhelming sex hormones in females) cause an enlarging of the pelvis as a piece of sexual separation. Consequently females for the most part have more extensive hips, allowing labor.

However, I found this article from International Business Times that states >>

  Women have not evolved wider pelvises despite it being difficult and
  dangerous to give birth – yet they may have developed some physical
  features that help during labour.

  Barbara Fischer, from the University of Oslo, has found a link between
  pelvis shape and statue and head circumference of both baby and
  mother.

There was, however, no sufficient evidence to back this article, but it is quite an interesting approach otherwise.

Males are not needed to have any extra organs, but females have just more space in the pelvis region. That space can be linked to idea of uterus expanding to hold the fetus during gestation as mentioned by @BryanKrause.


Can Anyone Identify This strange cockroach looking bug I am looking for someone to identify this bug:
location india. It flew from my window in my room, killed it by spraying cockroach killer spray, it could fly like cockroach.

That is a mole cricket. Family Gryllotalpidae. They generally live underground, but as you noticed, they can fly. https://en.wikipedia.org/wiki/Mole_cricket


Europe: big fly with black/yellow striped body: I'm guessing a horse fly? This one made a summer night visit to the room and tried to escape by banging against the ceiling. What is it? I found nothing which corresponds, though "horse fly" might be a close match.

Location: Central Europe, Luxembourg
Locality: Where the suburb morphs into the not-yet-conquered countryside
Time: Late August, Nighttime
Weather: Quite warm (~27°C). Dry.

Here is an MP4 of the beast: https://i.imgur.com/F5yqMQ8.mp4

It is about 2 cm (0.8 inch) large. Relatively plump, keels over and likes to clean itself a lot.

Large head, large eyes, a bit hairy, two black stripes

Once it falls on its back it wallows a bit, there is clearly a probabilistic algorithm to get itself out of the predicament:

At first, because of the size and shape, I thought that it was a horsefly, but no horsefly looks like that (at least not in Luxembourg). It turns out that it was a hoverfly, just as Karl Kjer said. The species is Volucella zonaria, or the hornet mimic hoverfly. This hoverfly lives in most of Europe (including Luxembourg) and is 15-25 mm in length, consistent with your 20 mm estimate.

In this image you can see the same coloration and abdominal markings as your insect.

The markings in your photo are very difficult to see but are there.

Wikipedia page

original image source


Are there any major noticeable limitations to genome sequence compression methods that use reference templates? Recently, I have been researching about big data analytics in biochemistry, and started wondering about how genome sequence compression could affect analysis.

Of all the method listed on the Wikipedia page, the reference template method is my favourite as, it not only seems effective, but also was the idea that popped into my head before I did any study regarding this topic.

But, before I implement it in a project I am working on, I wanted to know if there are any common and obvious drawbacks/limitations that the bioinformatics industry faces quite often when using this scheme.

The most obvious drawback of the reference template method is that if you use it, you've already analysed data.

Usually, you get data from wet biologists. They sequence samples and upload sequences to a server. Often an uploading process is already automated. If you sequence in-house, the data is already on your server. If not - biologists do not want to do an extra job. Moreover, if it is not a big project you do not have that much data that transferring and storing it is the problem. So you'll get the data as *.fastq.gz files.

Then you make QC, align reads and make an SNV-calling or expression analysis or whatever you want. Aligning and SNV-calling could be painful, complicated (Copy Number Variation, heterozygosity etc) and time-consuming. It is the problem. Resulting data usually is stored as Variant Call Format (VCF). Under the influence of CRAM and 1K Genome Project which uses it, VCF has been developed.


What bird makes this sound? It sounds like some kind of crow but not really. Here is my recording: https://www.youtube.com/watch?v=4TsKFUugot8&feature=youtu.be#t=06s

This bird always wakes me up at 04:00 and this started in late June. I live in a village in Hungary.

I really need to know and don't know where to ask.

It can't be confirmed but it sounds like a pelican.


Is there a binding affinity metric for interactions not in equilibria? I am investigating the strength of binding of a small peptide to a protein by isolating the bound version and subjecting it to collisions with gas molecules (CID mass spectrometry) to dissociate the complex.
When I plot the collision energy against the proportion of bound and unbound proteins I get a curve that looks like a Kd curve.  However, as the interaction isn't in equilibria (i.e. it is in the gas phase) calculating the Kd value wouldn't be correct.

So is there another value I could calculate to describe the strength of the interaction?

You should be looking at the interactions in terms of kinetics and not thermodynamics. k_on and k_off should do the trick.


What is the reason for fear induced defecation? I started to handle mice for my job and noticed that they tend to defecate and/or urinate when they are scared. The fear is induced by me, because I need a long time (due to inexperience) to grab the mice and then move them from one cage to a new one. My question is why?

I tried to look up literature for this behavior and there are different fear behaviors for different animals some shake in fear, some play dead but I could not find something for fear induced defecation. Therefore my question: What is the reason behind the "Fear induced defecation"?

I am especially interested into the neuroscience pathway behind it.

If your mice are stressed or scared during those manipulations, as we can expect them to be, defecation can be a consequence of the "Fight-or-Flight response": in this situation, the organism try to focus its energy to act quickly, and a wave of specific neurotransmitters (noradrenaline in particular) is released. In consequence, mice's bladders relaxe, which cause them to urinate, the digestion stops, but the transit of the faeces in the colon is accelerated: they defecate.

This is all controlled by the activity of the sympathetic nervous system, which secrets acethylcholine and noradrenaline.


How two genomes adopt when cell goes to recipient's body from donor's body? We often give blood to another following the blood giving compatibility chart. Heart transplant and similar transplants also brings one's cell to another's body.
My curiosity is, when a cell goes to the recipient's body from the donor's body, what actually happens with respect to the genome?
If the genomes do not merge to one, then how to identify one identically? How does DNA fingerprints, parent detection etc. work correctly? More generally, how does it maintain consistency?
Remarks:
My assumption was : "All the cells of one particular person's body carry the same genome or DNA information. And every individual has a distinct genome or DNA information". But after some study and some comments, I found that the statement is actually wrong.
However,  this article led me to break my wrong notion.

My previous answer was to the original question which focused on red blood cells which do not contain DNA. Now the question has been revised to focus on tissue transplantation, where the cells do contain foreign DNA, my amended answer deals with a couple of the points raised, but only briefly with the question of identification.

Incorporation of foreign DNA into the human genome

It is extremely unlikely that any of the DNA from the tissue of the donor would be incorporated into the DNA of the cells of the recipient. The donor cells would have to be broken (i.e. die) to release the DNA, which is most likely to be degraded in the process. Even if it survived it would then have to be taken up by the host cells, which is unlikely as there is no specific mechanism to allow this. However if foreign DNA somehow got to the nucleus it would need specific machinery to be incorporated into the host DNA. This involves enzymes making staggered cuts in the foreign and host DNA to allow annealing and enzymes to ligate the two together. We know about this sort of thing because retroviruses and viruses that can exist in the genome in a latent state have specific mechanisms for doing this. It is unlikely to happen just by chance.

Even if foreign DNA did get incorporated, it still has to be in an environment that allows it to be expressed (appropriate promoters). A more likely possibility is insertion in a position that affects a host gene. This can result in uncontrolled division of cells, i.e. they become cancerous, and is a problem that has been encountered using viruses of the type mentioned to insert genes into genomes in gene therapy.

Do the differences in the DNA of transplanted tissue matter?

Obviously differences in the DNA of different individuals has an effect on the individual. It is genetic differences that cause people to differ in size, shape, features, hair colour etc. Oh, and some are girls and some are boys. But when the tissues and organs have finished developing it probably doesn't matter if a piece of transplanted liver is from a male or female donor. The genetic programme that causes sexual differentiation and function isn't the one being expressed in the adult liver. The genes that are being expressed are those for the enzymes the liver needs to play its metabolic role (too numerous to list), and if they work, they work, even if the proteins differ in amino acid sequence by the odd amino acid that doesn’t impair its function.

The problem of identification by DNA

I would have thought that this would not really be a problem. After all, if you want to take a DNA sample from a person you can do it with hair roots, white blood cells or scrapings from mouth skin. You wouldn't need to resort to liver biopsies and the like.

Doctor of Philosophy

Finally, I can see there is a general philosophical concern over who one is if one has tissue or organs from another donor, but until we have brain transplantation I’m not going to worry about that. (And when that comes, I won’t be answering questions on the subject.)


Is it possible to combine live attenuated and non-live vaccines? There are many combination vaccines available but I've noticed that there don't seem to be any with both live and non-live components, e.g. DTaP/IPV/MMR. Such combinations could be useful in some cases, since most developed countries give a second dose of MMR (or MMRV) at the same time as DTaP/IPV. Is there a biological reason that this is difficult?

First let me point out that for the US, I'm not knowledgeable enough to speak for the rest of the world, you are correct.

There are no approved live attenuated vaccines mixed with componet/subunit/inactivated vaccines.

Background:

Before we go into why that's true, let's work a little to show that's true.  The FDA publishes a wonderful list of every approved vaccine for use in the US.  Of the 78 vaccines listed (and there is a lot of redundancy due to different manufacturers etc), only 16 are live attenuated (or about 20%).

Another thing to notice is that we have vaccines to both viruses and bacteria.   Technically, some of the vaccines are to bacterial toxins, not bacteria themselves, but for the sake of simplicity, we're going to group all bacterial component, subunit, and inactivated vaccine preparations together in one group.

First you will note that there is only one live attenuated vaccine for bacteria, Mycobacterium bovis (more on this exception later).  There are several reasons for this, but as a general rule, you don't want to put a foreign object capable of self replication inside a person.  Viruses cannot self replicate, they are obligate parasites by definition, so they don't fall under this rule.  One could, however engineer bacteria that were sufficiently deficient in replication that this might not be an issue.  Another safety concern with live attenuated bacteria is sepsis.  Again by choosing a delivery route that doesn't involve injections, you might be able to mitigate this risk.

I also want to be clear that I think live attenuated bacterial/fungal (yeast mostly) vaccines can work more broadly, and are likely to be used in innovative vaccine strategies.

The main obstacle to a live attenuated bacteria vaccine is that the component and subunit vaccines work.  Sometimes they work even better by only supply the part of an organism that is known to provide broad neutralization (getting rid of) of the pathogen.  And if you know that you can provide protection with out the risk of putting the live organism in a person, why would you take that risk?

Quite simply you don't.  Back to M. bovis.  For the most part, humans are not vaccinated with M. bovis (BCG) to prevent M. Bovis infection (though zoonotic infections can occur).  Instead it is to prevent M. tuberculosis (MTB) infection.  Attenuation of MTB is difficult, and not complete.  Indeed we don't have a subunit or component vaccine that has worked for MTB, and an inactivated MTB has more safety concerns than BCG.  Thus we choose a related organism, M. Bovis, which naturally doesn't cause disease in humans (or rarely), but can provide some protection against TB.  Even the product insert admits that efficacy of the vaccine is in question.

The same pattern of necessity holds true for viral live attenuated vaccines.  They are used when you need a more immunogenic vaccine, and where we haven't been able to make safe and effective, inactivated, subunit, or VLP vaccines.  Thus when you need a live attenuated vaccine, you really do need it to be alive for it work.

Answering the core question:

As @MattDMo pointed out, the storage conditions are very different for live attenuated vaccines.  Not only that, but most of the preservatives used in many inactivated vaccines cause titer loss (though there is work to find alternatives).

On the theory that a picture is worth a thousand words, I did a little experiment just for this post (and also I was cleaning out an -80).  I took a high titer stock of measles virus that has a protein tag on one of the proteins so we can easily detect it (F is Flag tagged).  Then I spiked 3 different tubes of virus in ether PBS (saline) or DTaP (an actual dose, just past expiration), and left them in the refrigerator (4oC) for 8h.  Note that Merk thinks you should toss the measles vaccine if you don't use it within 8/hours (also note their comment on preservatives).  Then I infected some cells that grow up measles, and harvested the cells in a total cell lysate.  Finally I ran equal amounts of total protein form each preparation on a gel for a western blot:

You should notice the three pairs of bands, in each case the lighter band (indicating less protein) belongs to the DTaP group.  That is to say less measles F protein (something you want to make antibodies to) came from the samples that were put into the DTaP vaccine compared to PBS.

Another serious problem is cold chain:

Again we need the virus to be "alive" when we give a person a vaccine.  This almost always means that we have to keep it frozen or at least refrigerated from the manufacturer, all the way up until moments before it goes into a person's arm.  There are many good reviews on cold chain to be found.  Quite simply, inactivated and component vaccines do not have the thermo-stability requirements that live vaccines do.  It would be a waste of energy in most cases to chill all of the vaccines which could be left at room temperature, and it would remove one of their clear advantages.

As far as the immunology is concerned, there is probably not a real limit on what the body can react to.  Indeed, as you point out, they are often administered at the same time in developed countries.  It is merely a question of how you can keep live-attenuated vaccines "alive" in the same preparation.  It is certainly possible that there is a solution to this, and vaccine stability is an active field of research.  Hopefully in 10-20 years we will be able to adjust this answer to say that such a vaccine has been made, and that it's safe enough for approval.


Original Lotka–Volterra model I am looking for the articles in which Lotka and Volterra published their original predator prey model. I couldn’t find the model presented in many textbooks in Lotka’s book Elements of Physical Biology or Volterra’s paper Fluctuations in the Abundance of a Species considered Mathematically.

Is there really Lotka–Volterra model for dynamics of two  competing species? On Wikipedia and Murray’s book Mathematical Biology: an Introduction, it is written that it exists but I couldn’t find it in their papers.

Volterra’s Variations and Fluctuations of the Number of Individuals in Animal Species living together features what is nowadays often called the generalised Lotka–Volterra model.
Thus it captures competition between and with populations.
In particular, Section 2 is titled:

  Biological Association of two Species which contend for the same Food.


First pass protein structure prediction I'm working with a protein that doesn't have any homology to other proteins so it will likely require ab initio structure prediction. However, since I don't work for a structure prediction lab and I don't have a stringent requirement to have a high resolution structure, I'm fine with a 6-10 angstrom resolution prediction to help me visualize the protein.

I'm imagining I-TASSER to get an initial idea of the topology. SWISS-MODEL doesn't find any homologs to template against. I'm trying to avoid using Robetta since it will probably take a month. What other low-resolution webservers should I test?

Alternatively, you could just tell me to suck it up and submit it to a month-long prediction.

Have you used hhpred to search for homologues? What was your criteria for defining there was no homologues? You could potentially go down to around 30% sequence identity to model.

I would submit the the query sequence to both I-Tasser and Rosetta and see if both of the servers agree on the topology. I-Tasser will always provide 5 models of your query sequence (even if they are rubbish) ranked by a confidence score.

While you wait for the above servers to finish, I would submit the sequence to a number of secondary structure prediction servers to come to a general consensus for the secondary structure of your protein. Some servers you could use are:

Predict Protein
Phyre2
Raptor X
Jpred
Psi-Pred

If the servers come to a consensus, compare the secondary structure prediction with that of the secondary strucutre of the models, to see if the ab initio modelling concurs with that of the secondary strucutre prediction. This will give you more reason to be confident in your model.

I would then validate your models using:

Prosa - This calculates a Z-score, and plots where it fits with structures with a similar amino acid length, from the PDB.
DOPE Score - This is employed in Modeller and measures the "nativeness" of your model, the lower the score the better. But you will need to install Python and have some knowledge of how to use the command line. I can provide the code to Run Dope with modeller.

Finally, are there any constraints you could introduce such a oligomerisation site or a protein-protein interaction site, to help with the modelling?


Genetics... Translocation Can a Translocation of chromosomal parts occur between an autosome and an allosome?
If it occurs in between allosomes,what could be the effect of Robertsonian Translocation between an X and a Y chromosome considering the fact that the small product of a Robertsonian Translocation is mostly lost!??!

Can a Translocation of chromosomal parts occur between an autosome and an allosome?

In short, yes. A quick scan of a few abstracts gives both clinical and model organism examples.

  [I]f it occurs in between allosomes,what could be the effect of Robertsonian Translocation between an X and a Y...

It seems Robertsonian translocations are not ubiquitous amongst the chromosomes and only involve 13, 14, 15, 21 and 22.

HTH.


How to compute properties of peptides ? I have been tasked with writing a program for computing properties of a give set of peptides. These peptides are given as 1-letter amino acid sequences and I need to compute the following :

Length of peptide
Number of Each Amino Acid
Percent composition of each amino acid
Molecular weight
Net charge of peptide
Positive charge
Negative charge
Isoelectric point (pI)
Hydropathicity
Percent polar amino acids
Percent positive amino acids
Percent negative amino acids
Percent hydrophobic amino acids
Hydrophobicity
Lipophilicity
Amphiphilicity
Water-Octanol Partition Coefficient
Steric Bulk
Side chain bulk
Net donated hydrogen bonds
Percent \alpha helix
Percent random coil
Percent \beta sheet

While some of these properties are self explanatory ( eg. size, num. of amino acids, percentage of amino acids. ) and easy to compute. Other properties ( like Molecular weight, Net. charge, Positive charge, Hydorphobicity etc ) have been difficult for me.

I donot have Chemistry or Biology background and hence have found these difficult to compute. I would be appreciative if someone could point me in the correct direction ( I have already been through Wikipedia ) containing methods to compute the above mentioned properties or to a standard text which would explain the above mentioned properties and also provide methods to compute them. Thank you all.

Biopython and the other bio-programming languages typically have examples of how to do this kind of thing.

For example here is some python code for calculating some of these:

http://biopython.org/w/index.php?title=ProtParam&redirect=no

Many of the propensity scales are in this database:
http://www.genome.jp/aaindex/

And there are also biojava classes for accessing these. Essentially you will need to know what these physicochemical properties are and get access to a scale for converting the letter to a numerical value.


What is the lipid membrane of SARS-CoV-2 made of? SARS-CoV-2 is an enveloped virus: in structural diagrams it is drawn with membrane glycoprotein (M), envelope protein (E) and spike protein (S) embedded in a lipid membrane.
What specifically is the lipid membrane made of?
I assume it is derived (somehow) from the host cell membrane, and would have a similar composition.  It doesn't necessarily have the same composition.  If it just host membrane from a typical mammalian cell, it may be mostly phosphatidylcholine (PC) and cholesterol on the outside, and phosphatidylethanolamine (PE), PC and cholesterol on the inside.  It should equilibrate over time, since the virus does not contain a flippase to keep an asymmetrical distribution.
Related questions: Does the composition depend on the cell that the virus was assembled in?  Does it have any selectivity, or does it simply pick a random piece of the host membrane?  How exactly is the viral membrane detached from the host?
Probably most important question: Does the infectivity of the virus depend on the composition of the membrane?

I don't know if this questions has been studied in detail even for SARS, let alone SARS-CoV-2. As noted in a comment by reuns, the virus lipid envelope is most likely derived from that of the endoplasmic reticulum.

What we know however from from some studies on influenza viruses, that's hardly the end of the story though:

  Using rigorous virus purification, marked differences between virions and host were observed. Over 125 phospholipid species have been quantitated for three strains of influenza (HKx31- H3N2, PR8- H1N1, and VN1203- H5N1) grown in eggs. The glycerophospholipid composition of purified virions differs from that of the host or that of typical mammalian cells. Phosphatidylcholine is the major component in most mammalian cell membranes, while in purified virions phosphatidylethanolamine dominates. Due to its effects on membrane curvature, it is likely that the variations in its content are important to viral processing during infection.

And this part is a bit of a "reverse answer", but lipid rafts on the membrane of the target cells are thought to be important for the entry of coronaviruses, including SARS. One experiment found that depleting cholesterol from the cell membranes dramatically slowed SARS virus' ability to enter them.

(Regarding how SARS-CoV-2 might come out [with different envelopes] from different cells: we only had confirmation very recently that it substantially infects intestinal enterocytes. So expecting a lot of extra details on that is a bit premature right now.)


What is the connection between exercise and muscle growth From a physiological perspective, all that is done during exercise is the expending of energy in the form of ATP to fuel muscle contraction and extension.

When I looked up why muscle grow due to exercise, there is the claim that recovery of micro lesions formed during exercise enables slight growth of muscle. I am not sure how micro lesions are formed and intuitively, these micro lesions should cause atrophy of the muscle rather than strengthening of the muscle fibers.

Further there is no logical connection as to why muscle fibers would be strengthened rather than just restored to its previous form during rest.

Can someone help me make the mental leap from the consumption of ATP through exercise to muscle growth?

Muscle growth and development is mediated by "trophic factors" not biochemical reactions (ATP) or muscle contraction directly. The best method of releasing tropic factors is exercise and not electrical stimulation or biochemical reactions (ATP) or biomechanical contraction.

Nerve ending release growth or tropic factors which stimulate muscle growth and for example if the nerves die off either due to injury or disease (ALS) the muscles will atrophy.

Not all of the tropic factors are as of yet known, but it is these tropic factors that stimulate muscle growth, not the biochemical or biomechanical reaction of the muscle (contraction). One can not as of yet stimulate muscle growth by delivering electrical energy to the muscle, for example (it has been tried to in an effort to maintain muscle mass in critically ill patients).

There is a review of the trophic factors here - http://neuromuscular.wustl.edu/lab/trophic.htm

And a review of electrical stimulation - http://www.medword.com/MedwordStore/PCP/EMS_truth.html

There are many claims of benefit for electrical stimulation, such as regeneration of the facial nerve in facial paralysis, such as Bell's palsy.

The "problem" is that the prognosis in Bell's palsy is very good, even without electrical stimulation, and so it is difficult to "prove" benefit with electrical stimulation:

  With or without treatment, most individuals begin to get better within 2 weeks after the initial onset of symptoms and most recover completely, returning to normal function within 3 to 6 months.

http://www.ninds.nih.gov/disorders/bells/detail_bells.htm

  Statistically, the natural history without treatment was described in a study of 1011 patients in 1982 [8]. One-third had an incomplete paralysis, and two-thirds had complete paralysis. Overall, 85 percent showed signs of recovery within three weeks, 71 percent had complete recovery, 13 percent had slight sequelae, and 16 percent had residual weakness, synkinesis and/or contracture. Patients with incomplete lesions had a 94 percent rate of return to normal function, while only 60 percent of those with clinically complete lesions returned to normal function.


Can "human exclusion zones" in national parks for preserving Wolves and Grizzlies be a good idea? There are National Preserves in the National Parks where some human activities are permitted. But can it make sense to create "exclusion zones" so no human would be permitted in a certain area, not even scientists or researchers just so Grizzlies and Wolves can have a whole world to themselves ?

I know we won't be able to find out how those species are doing, but would there be any benefit ? Has any country ever tried that ?

I think it is a neat idea that should be discussed.
Not just for wolves or large predators but for all wildlife situations
There should be small habitats for all wildlife to refuge scattered around. Of course national parks, reserves and refuges are there for this purpose, but humans have become far too abundant on this planet to coexist anymore, and maybe we need to take it a step further? Again, it's something that should be discussed and awareness made of the issue.

And by far the best reason for this if nothing else is to have a scientific "control" spot for environmental research. It is important to have a control in all experiments, and to have a human exclusion zone helps create that control. If we had that, maybe someone could actually prove how much humans really are screwing up the planet, or maybe someone will prove they aren't :D


How does a sperm cell die? What causes an animal sperm cell to die? Does it die somehow from being outside its original environment?

I've studied the Wikipedia page
 on sperm and I see a lot of information on what makes up a sperm cell, but can't quite figure out its lifecycle and exactly how it dies.

So most cells require growth factors and survival factors to stay alive in an organism. Cells which stop receiving survival factors, such as sperm, undergo a process of programmed cell death (PCD) called apoptosis. Some cells will also undergo necrosis, or autophagy, among other types of PCD. Lachaud et al. performed a study in 2004 on the contribution of apoptosis and necrosis in ejaculated sperm. They make note in the intro that from other literature that we see some hallmarks of apoptosis like externalized phosphatidylserine, fragmented DNA, etc. despite inactivated nuclei and a small cytoplasm. Their data notes that ejaculate sperm cell death mainly occurs from necrosis, however, because sperm themselves lack the ability to initiate apoptosis. However, in the testes, there's data to note that apoptosis plays a role, and the presence of apoptotic spermatozoa in the ejactulate may be result of the inititation of apoptosis by factors which still inside the body. Apoptosis of spermatozoa in the testes is currently under investigation in male infertility, and damage in cryopreservation.

Just to give you an idea of the difference, necrosis is a much messier outcome derived from physical factors, or those factors external to the cell. Apoptosis is organized, controlled, and modulated by cellular signals.


How do liver and lung metastases cause death? Metastasis to the liver and lungs are the main causes of death in colorectal cancer.(1)
I understand that colorectal cancer may have metastases. But how do these metastases cause death?

Reference

(1) A. Bolocan, D. Ion, D.N. Ciocan, D.N Paduraru. Chirurgia (2012) 107:555-563. Introduction.

Metastasis is the spreading of cancerous cells to a new site within the body where they form a secondary tumour.  There is nothing special about how these metastases cause death, they do so in the same ways as the primary cancer eventually might:

Replacing functional cells with non-functional cancerous cells
Eroding into other tissues and disrupting normal body architecture
Causing haemorrhage
Putting pressure onto other structures

If we apply those principles to lung and liver secondary tumours, it is easy to see why they are likely to contribute significantly to mortality.

Cancerous masses in the lungs reduce the surface area available for gas exchange, reducing oxygen saturation of the patient.  The tumour may also erode into a primary bronchus, which if obstructed would cause lung collapse, or into the mediastinum.  If the mediastinum is involved then the great vessels or heart may be invaded into with significant consequences.

Liver metastases are more likely to cause problems due to the reduction of liver function as the cancer grows. This causes a plethora of problems as the liver is involved in so many pathways within the body.  Examples of serious effects would include the patient becoming coagulopathic due to a reduction in production of clotting factors, making bleeding much more severe.  The liver can begin to fail to clear toxins from the blood, leading to the risk of acidosis or hepatic encephalopathy (leading to coma and eventual death).  If the tumour were to invade the portal vein, this can cause portal hypertension, which in turn shunts pressure into the systemic venous system.  This can cause oesophageal varices which are prone to spontaneous and catastrophic bleeding. Similarly a tumour invading the common bile duct (or other part of the biliary tree) can cause obstructive jaundice and associated problems.

The reason your quote suggests that most deaths are from metastases than the primary tumour is probably because tumours in these locations have greater negative effects at a smaller size because they are in crucial tissues.

There may be another contributing factor in the form of data interpretation, however.  Tumours are often 'staged' via the TNM staging system, the last component of which is the presence of metastases.  The presence of distal metastases automatically makes colorectal cancer Stage 4.  This is often considered not to be curable, meaning a move to more palliative treatment options.  This may affect the survival curves for those with distal metastases and those without.