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Is there a command line molecular cloning tool?
There are many software applications such as SnapGene, Geneious, Vector NTI, ApE, Gentle and others for assistance with cloning. Their key functions are:

Making maps of plasmids
Annotating plasmids with common features
Finding restriction sites
Mapping Sanger sequencing reads
Showing sequence, reverse complement of the sequence, translations in different frames
Designing primers for specific applications (such as Gibson cloning)

Is there a tool that does functions such as these, but runs from a command line?

Note: My intent is not so much to get recommendations for what to use, but to get an idea of what software is currently available. Obviously there exist many CLI tools which can be made to serve also these purposes, up to and including general purpose text editors like vi.
I'm interested in what effort has already been made to produce CLI software specifically intended for cloning (by which I mean the functions described above).

Why does it need to be command line? Are you trying to batch these operations? And it would seem like any command line implementation of these would have very complex commands.

I agree with @user137 on this! For protein alignment you have things like Clustal W/Clustal X, which you can find from http://www.clustal.org but for your request it's far too complicated and you might be better off with GUI such as the ones listed. Many, including myself use R for bioinformatics related work and I have came across this (http://www.bioconductor.org/packages/release/bioc/html/ecolitk.html), which can address one of your points but I don't know of any unified CLI for the points you have said. If this answers you question, please let me know so that I can post it as an answer.

@user137 I suspect that I will find the command line to be a more efficient interface for these functions, and it would be much more convenient for integrating the tools into my own scripts.

@Bez I was aware of but not familiar with Bioconductor. If you could explain specifically what parts of the package perform the functions I want, that would be a great answer. Otherwise, I think just mentioning Bioconductor itself is a fair response.

I haven't worked with that specific package itself but if you have R or RStudio, which is my preferred IDE, you simply have to enter the command source("http://bioconductor.org/biocLite.R") command to upload the biocLite package and prepare R for download from the bioconductor database/depository and then execute the command biocLite("ecolitk"). Its mostly for plotting functions to work with circular genomics and can be used with other genomes/plasmids according to the package description http://www.bioconductor.org/packages/release/bioc/manuals/ecolitk/man/ecolitk.pdf

Making maps of plasmids Annotating plasmids with common features

Plasmapper works through commandline

Finding restriction sites

Simple regex searches can do that

Mapping Sanger sequencing reads

BLAST will do it.

Showing sequence, reverse complement of the sequence, translations in
  different frames

EMBOSS has a collection of tools for these things. (getorf is a tool for finding ORFs)

Designing primers for specific applications (such as
  Gibson cloning)

Primer3 works through commandline

You can just download the entire EMBOSS collection. It has many useful tools.

+1 for plasmapper, but the others aren't quite what I'm looking for. They are general tools which, in principle (and with some work) can be adapted for the purposes I mention. They are not a streamlined pipeline explicitly designed for it.

I always used BLAST for aligning Sanger-sequencing reads. You should find a lot of tools in EMBOSS collection (usual stuff like finding ORF, Reverse complement etc). I don't think there is a tool for designing primers for Gibson assembly. BTW plasmapper also annotates common restriction sites.

For protein alignment you have things like Clustal W/Clustal X. Many, including myself use R for bioinformatics related work and I have came across this package which can be found in Bioconductor, which can address one of your points but I don't know of any unified CLI for the points you have said.
I haven't worked with that specific package itself but if you have R or RStudio, which is my preferred IDE, you simply have to enter the command
source("bioconductor.org/biocLite.R")

command to upload the biocLite package and prepare R for download from the bioconductor database/depository and then execute the command
biocLite("ecolitk")

It's mostly for plotting functions to work with circular genomics and can be used with other genomes/plasmids according to the package description.

pydna is a python package designed for cloning. Disclaimer: I am the developer. It can be used in a Jupyter notebook to create executable scripts that result in the sequence of a some genetic construct. Restriction cloning, gibson assembly/homologous recombination are supported.

Welcome to Biology.SE. As written this would be more appropriate as a comment. We're looking for long answers that provide some explanation and context. Please don't post one-line or link-only answers; instead explain why your answer is right, ideally with citations. In this case I personally would preferred the question be closed as opinion based (off-topic), but since it wasn't you could provide a summary of what your package does and how it is an improvement over existing tools. ——— Please take the [tour] and consult the [help] starting with [ask] and [answer] for details.


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Are brain cells replaced over time?
You know how your cells die all the time and new ones are made to replace them, so you practically have a new body every maybe 5 years?
Many people say you become a completely different person every several years, but what about neural cells, do they get replaced?
I believe it would cause a lot of information to get lost if this happened.

I just would like to comment that while others have, correctly, emphasized the existence of neurogenesis, it is more the exception than the rule. Outside the hippocampus and confined cortical regions, typically neurons do not regenerate.

By brain cells, I'll assume you mean neurons (the other type are called glial cells). Yes, new neurons arise in a least certain parts of the brain, and yes, they do cause memories to weaken or disappear. This has been shown in mice, guinea pigs and degus.
It would be wrong to assume that neurogenesis occurs with the frequency of, say, gastric cell or skin turnover. Up until recently, it was not thought to occur at all.
Learning and remembering use various cortical structures, including the hippocampus.Throughout life, new neurons (neurogenesis) are continuously added to the dentate gyrus. These additions remodel hippocampal circuits, and when this occurs after memory formation, this neurogenesis leads to degradation or forgetting of established memories. This was shown in adult mice. Conversely, decreasing neurogenesis after memory formation decreased forgetting.[1]
It is not only plasticity that makes the brain adaptable to continuous changes in environmental demands. Adult-born neurons integrate into preexisting neuronal networks and participate in information processing. Adult neurogenesis itself is a type of circuit plasticity required for hippocampus-dependent learning and memory recall. Adult hippocampal neurogenesis may also promote forgetting.[2]
The more neurogenesis there is, the more memories are broken down. Since we retain many memories over our lifetime, it's pretty safe to say out brains don't "turn over" every five years (or even over longer periods); some parts of our brain don't seem to undergo neurogenesis at all.[3]
[1] Hippocampal Neurogenesis Regulates Forgetting During Adulthood and Infancy Science 9 May 2014
[2] A Price to Pay for Adult Neurogenesis Science 9 May 2014
[3] Neurogenesis in the Adult Brain The Journal of Neuroscience February 1, 2002

I liked that article [1]. Forgetfulness of babies explained.

Very interesting! Is there any data on increase in brain size due to neurogenesis (in micro or perhaps millimeters?)

What about other neurons, which are not involved in adult neurogenesis? How frequently are they replaced?

Addition to anongoodnurse's answer.
Different organisms have different numbers of neurogenic niches (regions where neurons form). For example zebrafish[1] has six niches compared to two in mammals and it is known to have active neurogenesis throughout life. In mammals, apart from the dentate gyrus (subgranular zone) of hippocampus, the other prominent neurogenic niche is the subventricular zone (SVZ) - the region adjoining the ventricles. Immature neurons born at the SVZ migrate to olfactory bulb via the rostral migratory stream[2, 3].
You can also refer to this detailed review [4] on Adult Neurogenesis.

References:
[1] Lindsey, Benjamin W., Audrey Darabie, and Vincent Tropepe. "The cellular composition of neurogenic periventricular zones in the adult zebrafish forebrain." Journal of Comparative Neurology 520.10 (2012): 2275-2316.
[2] Pencea, Viorica, et al. "Neurogenesis in the subventricular zone and rostral migratory stream of the neonatal and adult primate forebrain." Experimental neurology 172.1 (2001): 1-16.
[3] Bath KG, Lee FS. "Neurotrophic Factor Control of Adult SVZ Neurogenesis". Developmental neurobiology. 2010;70(5):339-349
[4] Ming, Guo-li, and Hongjun Song. "Adult neurogenesis in the mammalian brain: significant answers and significant questions." Neuron 70.4 (2011): 687-702.

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Does pupil size affect image focus in persons with no lens?
If an individual has no lens like Claude Monet (who had them removed).
They should be able to still focus the images they see in a well light area if they shrink their pupils to a very small size like the Moken people right?
But they won't be able to see well at all in dim light, as focusing would require them to dilate their pupils which would make everything  very blurred.
Is this right?

This is right. People with slightly defective eyesight (like me) often don't need glasses or lenses under very bright conditions, but vision blurs when it gets darker. Chris' answer nicely explains why this is the case.

PS: A nice analogy comes from photography: With a high f-stop (= small pupil size) the photo will have a high depth of field, i.e. you don't need to focus a lot, whereas a photo at low f-stops (= wide open pupil) requires careful focussing to display an object sharply.

Very nice question! You are right, in that small pupils will help to reduce the blurriness of vision caused by refractive errors.
Removal of the lens (aphakia) results in farsightedness. It is caused by a focus point that falls behind the retina as the absence of the lens prevents focusing of the image, causing a blurred image. The amount of blur is proportional to the pupil size (Colichia et al., 2008). See their figure 2 below:.
In the upper part you see a hyperopic eye, which has a lens that cannot accommodate sufficiently, comparable to an aphakic eye. the bottom part shows the result of when a pinhole is applied, namely a reduction of the blurred circle and improvement of the focus. This could also be achieved by having very small pupils such as when ambient light is very bright (and a characteristic of the Moken peoples when diving (Gislén et al., 2003). And indeed, under conditions of low lighting the pupil size will increase and hence blurring will be worse.

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What is the nature of plasmids?
What are the plasmids composed of? Are they composed of genomic or non-genomic DNA?
I guess the answer is "genomic DNA" but I'm not sure.

Is this a homework question? What definitions of "plasmid" and "genetic DNA" are you going by?

No...it's not a homework q...just one of my classmates was arguing about this....Actually I think you guys are just PARANOID about homework q....if it was a homework q. I think I have enough sense to put a 'homework' tag....

You probably mean genomic and non-genomic DNA - Plasmids are small rings of non-genomic double-stranded DNA in Bacteria. They replicate mostly indepently of the genomic DNA can can occur from a few to several hundred copies per cell. See the illustration from the Wikipedia:

Not only in bacteria.

@chris, yeah...


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Loss in DNA band size extracted from polyacrylamide gel
I'm using cDNA AFLP teq.. I extracted 670 bp band from polyacrylamide (urea) gel and I have amplified with PCR  but on agarose gel it stops at nearly 350 bp.it happened for most of other bands before. I always extracted the precise bands.  I repeated with both pre and selective primers with the same PCR program before done for amplification of digested cDNA and same size bands observed in agarose gel.I wonder maybe secondary structure causes losses in band size (before running in polyacrylamide samples treated in 94 degree for 5 min), but how I can recognize?  i should notice 350 bp band i mentioned above is very sharp. what other thing I'm wondering is can dye uses in agarose gel alternate the DNA charge and reduces the speed of movement . The big  matter is the rate of losses in band size almost is same for almost all of the bands for one primer. Is it happened for anyone before? can i trust on my extracted bands for doing cloning?

Urea-PAGE is a denaturing gel. The mobilities are likely to be different from the normal agarose gel. Can you put the gel pictures up?

I ran dna ladder in both acrylamide andagarose gel, if mobilities affected it should be true about the ladder!

What ladder was it. Urea will denature dsDNA

I don't know realy. I always thought ladder is dsDNA. is there any ssDNA ladder. I should check it. I'll let you know soon. however thanks for your help.

Thanks. with your guide I could find the problem, really there was no problem! DNA ladder I used was double strand DNA, and somewhere I read ladder's mobilization profile in denaturing gels differs depending on gel percent. I ran the PCR product of extracted band in polyacrylamide gel again. And I found what I expected, the same size -670bp. I think denaturing gel affected sample DNAs and ladder mobilization but because of their size and sequence (GC content for producing secondary structure)difference the influence was not same and it 's not predictable.


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what the best E-value cutoff in the miRNA homology search
I'm trying to use miRBase database to annotate some microRNA sequences in length 22-24bp. I highly appreciate if someone let me know whether I should do this BLAST against mature miRNA or stem-loop sequence database? and the other main question is that which number of E-value is reasonably accepted as a lowest E-Value in the miRNA BLAST results? Also, what tool you suggest to perform miRNA enrichment analysis? for example we can use DAVID for gene (coding sequence) enrichment analysis. Using such analysis we are able to assign probable functions and biological roles to a group of miRNA (not only one miRNA). Any comments and idea is welcomed.

If you are using BLAST for short nucleotide searches then you should reduce your word size to <=7. It is better to align with mature sequences.
E-value depends on the database size. If your target database is huge then you should increase the e-value cutoff. If miRBase (for a few organisms) is your database then there is no need to run BLAST, also. You can simply run SSEARCH (Smith-Waterman Local alignment algorithm).
If you are running BLAST against miRbase you can set the e-value cutoff at 10. This is fine because there are many similar looking miRNAs with different function. If you reduce the e-value cutoff then you may lose these.
There are some other criteria for miRNA conservation- e.g there should be very high (almost exact) similarity at the seed region. After the BLAST, make sure that seed region is conserved.

Can we can use DAVID for miRNA functional analysis.

I don't think DAVID can be directly used (miRNAs have to be annotated in their database). What you can do is that you can predict the targets of your miRNA and then pass them to DAVID. DAVID won't do the predictions but there are other programs (see this post). You can also try BioMart (provided by ENSEMBL) for getting GO details. Even BioMart does not provide functional annotation for miRNAs (I just tried, to verify). So best thing is to check for the targets.

Thanks for your feedback. I want to use miRBase to do this blast that its default word size is 4, is nice for short sequence homology search, but the E-value cutoff is 10 by default that seems a bit high for miRNA (short sequence) in my opinion since the probability of having good alinment by chance is increased as the sequence length is decreased, is it right or no?

Yes that's true. Also that probability increases when the database size increases. If you find the answer suitable then you can accept it (A tick mark on the left).

Ok. Regarding what we discuses, could you please suggest me what is the best E-value cutoff in the case of miRNA homology search? I'm a bit confused about the selection this parameter.

Dear friend, as you said, DAVID can not be directly used for miRNA analysis. Also, miRNA target analysis using this tool is a different story. at the moment My focus is on miRNA not their targets.

@Mary- edited the answer. No you cannot directly annotate miRNA. You need to find its targets first. E-value of 10 is fine (don't go below this).

Thanks a lot for being with me! what about the mature miRNA and stem-loop sequence database, both available in miRBase! which one should I choose as a database? my concern about this topic is that I should confirmed the best hit of the blast with what I looking for it in the laboratory.

I mentioned in the answer- align against mature. Other regions are not that well conserved.

10? Really? I haven't worked with miRs but 10 seems extremely high. In fact, working on short nucleotide sequences, I wouldn't recommend using the evalue at all. I'd go for plain %id and % coverage instead.

@terdon 10 is safe. I think the online BLAST asks for evalue cutoff. It assigns 10 by default for short nucleotide searches. But for miRNA, I think more parameters should be defined. I think gap start penalty should be high (5` region should match perfectly). Using a short read aligner like bowtie is also not a bad idea. It allows you to set a seed sequence and lets you define allowed mismatches in seed and non seed regions separately.

Absolutely. Your parameters sound fine. I just wouldn't use an evalue of 10 as a way of determining whether a hit was interesting. I'd leave it at 10 or higher to be sure to get everything and then ignore it and filter on other things as you suggest.


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How does proximal centriole of human sperm function?
I've read that the human's unfertilized oocyte ( stuck at metaphase 2 of meiosis ) lacks centrioles and that it completes meiosis 2 after fertilization as sperm gives its proximal centriole. Then what about the centrioles required for mitosis of zygote?? How does proximal centriole function?


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Do wolves bury food like dogs?
Many breeds of domestic dogs seem to like burying food, presumably in preparation for leaner times.
Assuming that dogs evolved from animals similar to the modern wolves through a mix of natural and artificial selection, is this burying behavior novel in dogs, or inherited from wild wolves? Do wild wolves also habitually bury food, and return to their caches when hungry?

The habit of burying food in modern dogs is an instinct that came from the grey wolf (Canis lupus) long ago, and originates from a phenomenon called surplus killing, where a carnivore would kill more than it could eat, and often use it at a later time.

Many, if not all, carnivores possess behaviour patterns which allow utilization of a kill at a later time, or allow other members of the same social unit or offspring to use the food.

When the prey is small enough to transport, and there are pups, it is often returned to the den.

Pups will usually remain in their den for the first three or four weeks of their lives before mother allows them to venture forth into the light. During this time the mother is quite dependant on her mate and other pack members to bring her food in the form of meat that is often regurgitated for her.

It is then fed on by the litter, and the excess buried for later use.
This is called 'caching', and is still seen today in the domestic dog (Canis familiaris).


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If human eyes watch an area, what's the shape of its capturing shape? Rectangular? Half spherical?
A normal camera can capture a rectangular image. If human eyes watch an area, what's the shape of the captured region? Rectangular? Half-spherical?

The info posted about retinal response shape area is quite useful, but when you ask about  the shape of the image you perceive, you are diving head-first into the neurological field of optical sensing.  What little I know is that what we "think" we see is largely made up out of history and good guessing by our optical processing center in the brain.  Our apparent perceived region is somewhat less than a hemisphere IIRC.

Mapping the output of a camera's photon sensors as a rectangular grid of pixels is an explicit and arbitrary decision made by the designer of the camera (and driver/firmware architects). Because the output of a human eye is not visualized on a monitor, and consciousness itself is a very controversial phenomenon, I think this question is ill-posed. A better question would be, "how does human visual acuity change over the FOV?".

@Superbest On the other hand, regardless of how the sensory input is used, the eye still, physically, has a definite viewing volume (i.e. a definite range of angles such that photons passing through the lens at those angles interact with the retina). E.g. no matter how you feel about consciousness, a ray of light arriving at the back of your head will not strike your retina.

The capture area of the eye is a bit fuzzier and harder to define than that of a camera.
A camera captures consistent, fully detailed data right up to the edge of its sensor, and no data at all beyond it. Captured data is clipped by an ideally uniform sensor, augmented a bit by the lens, and is well-defined during design and manufacturing.
The eye can capture higher "resolution" near the center of its capture area and also has very little information about color near the edges (see also Peripheral Vision); so it's not quite as clean cut depending on your goal of "capture area". The eye also has a bit of a "blind spot" near the middle, which our brains basically Photoshop out. Additionally, it varies from person to person.
The effective capture area would really depend on your application (e.g. the "capture area" for, say, reading text, would be narrower than the area for, say, detecting motion).
Here is a typical diagram for a single eye, showing just the ability to see something in that area (does not show details related to peripheral vision quality):

Here is a typical diagram for both eyes combined, the solid white area is the overlap:

Both of those images are from a 1964 NASA report detailing aspects of the human visual field. If you want the detailed answer to your question and more, you probably want to take a look at that.
Note that our field of vision is very wide, those diagrams may not do it justice. As an experiment, close one eye, stare straight ahead and hold your arms straight out to the sides. Wiggle your fingers and slowly bring your arms forward until you can just see your wiggling fingers in your peripheral vision, and you will get an idea. As an added experiment, hold a piece of paper with text on it, and repeat the same experiment until you can read the text - this region will be extremely narrow and will give you an idea of how the quality of vision changes across the field. Also try with a colored object and bring it in until you can clearly identify the color.
There are also some simplified mentions of it in wikipedia:

http://en.wikipedia.org/wiki/Field_of_view#Humans_and_animals
http://en.wikipedia.org/wiki/Human_eye#Field_of_view
http://en.wikipedia.org/wiki/Visual_field#Normal_limits

A good set of search keywords is "human field of vision". There is also a nice related article entitled The Camera Versus the Human Eye.

Great answer, but the illustrations hide (as you say in the text) the order of magnitude difference in resolution between the middle of the field and the sides. For a camera, all of the pixels are almost equal, for an eye they are not.

@Peteris Yeah... I added the bit about doing an added experiment to try to make up for inadequacies in the diagrams. When I have a better internet connection I'll try to find better diagrams.

Perhaps add a reference to how the brain makes you feel you have a more cinematic and even visual field (more Photoshopping) e.g. http://en.wikipedia.org/wiki/Saccade - this depends a little on what the OP means by "watch an area". Unless effort is made to keep eyes still, watching is naturally and unconsciously an active scanning process. Edit: Scratch that, that is very nicely covered in your last link (The Camera Versus the Human Eye).

+1 for making me roll my eyes around until I realized I can't see my cheek, but I can see my mustache.

The link to the 1964 NASA report is now broken; if someone can find a better link (or a real citation) that would be a nice update. I tried but failed.

@eclarkso Thanks. I've replace it with an archive.org link.

I don't know why I didn't think of the Wayback!  For posterity, the citation is to Webb, P., Ed.  Bioastronautics Data Book: NASA SP-3006.  NASA Special Publication: Washington D. C., 1964.  An updated and more recent citation for the diagram is also in Parker Jr, J.F. and West, V.R., Eds. Bioastronautics Data Book: NASA SP-3006. NASA Special Publication, 2nd Ed., 1973, p. 631.

One eye captures a roughly circular area.  Because we have two overlapping fields of vision for depth perception, between our two eyes we capture a roughly elliptical shape.

To add to this - Cameras capture in rectangular shapes because that is the shape of their CCD sensor, so I imagine that the shape of an image received by an eye will correspond to our "sensor" i.e., our optical nerve.

@Kitchi Picking anatomical nits: Our "sensor" is called the retina. The optic nerve itself cannot sense light.

@JasonC - Ah, right. Thanks! I thought the retina was part of the "optics", i.e., the focusing and lenses etc.

@Kitchi Indeed, the spot where the optical nerve is attached to the retina is called the blind spot, as mentioned in Jason's answer. (The demonstration on that page is pretty cool by the way – try it out.)

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Rosemary room temperature at winter
I consistently read in non-scientific resources that I have to put my rosemary to low temperature (about 10°C) in winter (unless I don't want it to freeze). I googled, but I fail to find a scientific resource about why room temperature is not good for it. Do you have any explanation (with scientific references ofc.)?

can you provide any reference to the article where you got the info?...cause your q is not too clear...like, in winter you want to keep the plant in low temperature, in order not to freeze it....it's ridiculous...

@souvikbhattacharya It doesn't freeze by 10°C, which is lower than standard room temperature 20°C. What don't you understand?

Either the rosemary is a naturally cold-weather plant and just prefers colder temperatures, or the plant needs cold weather to trigger winter behavior. Some plants need to hibernate during the cold months.

@JeremyKemball What if I don't trigger the winter behavior? Ohh actually that is the main question as well...

I have no idea. You might be able to find someone who knows a lot about rosemary on gardening.stackexchange.com ? The tree equivalent is called vernalization and can apparently out and out kill a tree. I have no idea why, but there you go.

@JeremyKemball Do you think this is off-topic and should be moved to gardening?

I mean you'd have to reword it to something more like 'what happens if I don't properly overwinter my rosemary' but this isn't entirely off-topic here. It might be unanswerable due to lack of research, but on-topic nonetheless.

@JeremyKemball I created a topic in gardening as well. The result is unconclusive yet. Some of them claims that it would survive in room temperature, some of them claims the opposite. :-) I'll try to find articles about mediterran plant hibernation meanwhile.

I did not find scientific articles in the topic. Non scientific resources claim that is is possible to overwinter rosemary at room temperature, but it is hard. It requires at least 8 hours of light, humidity, and almost, but not totally dry soil. I'll give it a try.

As a bioassay, I have for years seen rosemary growing in the median strips of highways in Downtown Las Vegas, a pretty warm place most of the time. You can Google Vegas weather data, but it has to be well over 100 F in those medians much of the year. Right next to Bellagio they had rosemary growing in the medians for years, not sure if it is still there.

@LynnGriffith I asked a botanist. According to her, it can withstand -15°C degrees, so I left it outside. It's still alive! :-)


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How does rate of evolution/innovation scale with population size?
I understand that there will be many other factors that affect rate of evolution/innovation. However, other things being equal, how will the rate of evolution vary between two populations of different sizes? Does doubling the population size double the rate of introduction of new traits?
Is this answerable for evolving life in general, or do different forms of life have different scaling laws? For example, is it different for sexual and asexual life?

I'm no evolutionary biologist but surely the rate (meaning the frequency) for a given mutation won't change if two populations are of different size, but the likelihood of observing it at a given time probably will. Obviously I'm assuming any mating won't change/affect the rates. But I could be totally wrong!

@Bez you mean the rate for an individual will be the same, but its rate of occurrence in the population will be proportional to the population size?

Yes! that sounds about right!

@Bez I can see intuitively that the rate of appearance of a given mutuation (good/bad/neutral) will be proportional to the population size, but it isn't clear to me whether the same will apply to new traits being adopted. For example, if a trait requires 3 separate mutations to occur in a specific order, will its probability of occurring still scale linearly?

It still should since you can calculate the probability of a sequential mutation just as you can calculate what are the chances of getting a 4, 5 and 6 in that order after throwing the dice exactly 3 times! The higher the number of throws, the higher its probability of occurrence but the overall chances of getting that particular order won't change! Obviously I'm discarding the concept of selection pressure etc!

One thing I expect to make a difference is the time taken for a new trait to spread sufficiently, before the next trait that builds on it can occur. Would doubling the population mean that the next trait occurs in half the time, but subsequent traits take longer?

Let us continue this discussion in chat.

Interesting question (+1) but not that easy to answer. I'll give a try!
First, the rate of evolution and rate of adaptation are two different things.
There are two main thing processes that quantitatively differ in populations of different sizes. 1) population-wide mutation rate and 2) genetic drift.
1. Population-wide mutation rate
Large populations create more mutations at each generation and therefore if the rate of evolution or the rate of adaptation is limited by the genetic variance, then one can expect large population to have higher rate of evolution and higher rate of adaptation.
--> Large populations may have higher rate of evolution and higher rate of adaptation
2. Genetic drift
However, small population have higher drift, resulting in a higher probability of fixation for new neutral (or slightly deleterious) mutations. It results that a small population will fix (fixed: frequency = 1) a higher proportions of the new mutations through time than large populations.nActually the probability of fixation of a neutral mutation is \frac{1}{2N}. Therefore, the rate at which neutral alleles fix is $\mu\cdot 2N \frac{1}{2N} = \mu$, where $\mu$ is the mutation rate. So, the rate of fixation of neutral alleles is independent of the population size.
--> Small populations have more drift but this doesn't necessarily yield to higher rate of evolution
Other and comments
Shifting balance theory
If adaptation is limited by the genetic architecture, that is, only mutation of very big effect on phenotype can be advantageous, then small population have the advantage to be able to accumulate slightly deleterious mutations, so that they can get off a local peak on the adaptive landscape and eventually manage to evolve toward a new higher fitness peak.
--> Small population may have higher rate of adaptation
Population-wide mutation rate vs genetic drift
Weighting the relative importance of rate of production of neutral (or quasi-neutral) mutations (See population-wide mutation rate above and the probability of fixation of neutral (or quasi-neutral) mutations (See Genetic drift above) depends also on the probability distribution of mutational effects (=probability distribution of the effect on fitness of a given new mutation).
Ceteris Paribus
The comparison between large and small populations are dependent on the state of other parameters. So even when saying all else being equal (ceteris paribus), we need to know what these other parameters are equal to, in order to answer the question because there are interactions between populations size and other parameters in explaining the rate of adaptation and rate of evolution.
Other impact of population size on genetic features
Population size has many impacts on various genetic features, such as pattern of genetic diversity, distribution of per locus Fst between subpopulation, and other things. This paper is likely of interest

There is probably other processes I forget about. Also, there is probably some sources that offer some quantitative measure of the general effect of population size on adaptation.

On point 2: for strictly neutral mutations, the increase in fixation probability ($1/N$) in small populations is exactly canceled by the reduction in the mutation flux ($N\mu$), so the rate of evolution is independent of population size.

@DanielWeissman I'd be interested to see an answer expanding on this.

@Remi.b I'm not sure I understand your comment. Drake's Rule refers to the product of the per-base mutation rate and the genome size, not the population size.

Oops. You are totally right! Temporary brain malfunctioning! To defend myself more than I should, I would note that I would expect a rough tendency for species with small genome size to have large population size. I deleted my comment above. Thanks!

It looks like that we humans can’t estimate this for now (to answer this in binary way Yes/No). Is it?


text:
Are there any known mutual symbiotic relationships that has more than two agents?
We are all familiar with the examples of symbiotic relationships in nature consisting of two agents, like lichen or the co-evolvement between certain birds and flowering plants.
Do we know of any mutually symbiotic relationships that has three of a even higher number of agents?
Edit: To make a implicit distinction clear, let's specify that the agents in question have distinctive and fully interdependent roles in the symbiosis. In contrast to a scenario where a range of bird species might co-evolve for a single specific flower and have the same role as pollinators in the symbiosis.
This image represents my current models in thinking about this:

The type I'm searching for here is mainly the "3-agent symbiosis", but the bidirectional one is of interest as well.

I think what you are asking for is "Multiple Mutualism". Normally,

Most of the known cases of multiple mutualism involve relationships in
which two of the partners are at the same organizational level—usually
two bacteria that might be interacting directly—but are both essential
for the survival of the host
— Entente cordiale: Multiple symbiosis illustrates the intricate interconnectivity of nature -Philip Hunter

For example, the glassy-winged sharpshooter (Homalodisca coagulata) primarily feeds on xylem-fluid which is low on organic nutrients…so it depends on 2 bacteria, Baumannia cicadellinicola and Sulcia muelleri. The sharpshooter provides these with raw carbon skeletons present in the xylem fluid, and those bacteria in return synthesizes vitamins, essential amino acids, etc. For more detailed study, see Wu et al, 2006.
However, there are also examples of three-way mutualistic symbioses in which all the partners are at different organizational levels. One known case involving a virus, a bacterium and an insect, see Moran NA, Degnan PH, Santos SR, Dunbar HE, Ochman H (2005) The players in a mutualistic symbiosis: insects, bacteria, viruses, and virulence genes. Proc Natl Acad Sci USA 102: 16919–16926
Anyway, the essence as stated by Andreas Brune, Professor of Biogeochemistry at the Max Planck Institute for Terrestrial Microbiology in Marburg, Germany:

Multiple symbiosis is probably more widespread than we think, especially in view of the symbiotic systems involving different organizational levels, for example between bacterium, nematode and insect, or bacterium, protozoan and insect.

@inf3rno , thank you for your appreciation...but would you mind , if I ask you to kindly remove the last link( http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1559669/#__ffn_sectitle )from your answer, which does not really is relevant to the topic of "human microbiom" you stressed upon & more importantly was originally posted in my article......thanks again...

It is relevant by this sentence: "Multipartite symbiosis is much more common in the nature than we previously thought." - I found it before reading your answer, but if that matters you...

@inf3rno , I'm really sorry, if inadvertantly I offended you...

The human body contains a few billion microbes (more than human cells), so we live in symbiosis with many different species. Some of them protect us from infections, some of them help in the digestion, and so on... So I think the human body fulfills your requirements.

wikipedia - human microbiome

Normally we don't live in sterile environment. So we depend on our microflora in order to protect us against pathogens by preventing them to colonize e.g. our intestines. So without a sterile environment we would die in the lack of our microflora e.g. in a C. difficile infection. In exchange we give our microbes shelter (e.g. we protect them from oxygen, UV radiation, temperature changes) and food (e.g. carbohydrates we cannot digest, for example xylitol). So the human-microbiome relationship is a mutualism. Some of these microbes are not detected outside of the (not necessary human) host, so these relationships can be obligate. These microbes do not only support us, but each other as well. E.g. they help each other to digest nutritients (syntrophy), so they can live in mutualism with each other as well. So multipartite symbiosis certainly exists in the human body, and it seems like much more common in the nature than we previously thought.

2013 - Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships
2003 - Honor thy symbionts
2014 - Cooperation, communication, and co-evolution: grand challenges in microbial symbiosis research
2007 - Interactions and competition within the microbial community of the human colon: links between diet and health
2005 - Host-Bacterial Mutualism in the Human Intestine
2013 - Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules
2013 - It Takes a Village: Ecological and Fitness Impacts of Multipartite Mutualism
2006 - Entente cordiale: Multiple symbiosis illustrates the intricate interconnectivity of nature

Hmm... I didn't think of this, and that is probably because I had in mind a relationship where all the agents were fully interdependent. I guess one could see the scenario you take as an example as an aggregation of 2-agent relationships? However, +1 for bringing this to the surface anyway.

I'm not entirely sure that this constitutes symbiosis. It's a very valid point and +1 but I wonder if someone working in the field would consider it so.

symbiosis is a kind of relationship between two (or more) individuals from different species benefiting to both individuals (unlike commensalism or predation/parasitism), so I think the human microbiome is a good example. From @Alex comment above, I guess that Alex might be interested in obligate symbiosis. Human are totally dependent on their microbiome. There might have at least two species of bacteria living in humans gut that can't live anywhere else and without which humans cannot live. If this is the case, the human microbiome, is again a good example.

@Remi.b Not just in the gut, e.g. on the skin, mouth, etc... Btw. I think this is the usual in nature, every larger organism has its own microbiome.

@Remi.b Thank you for the term obligate symbiosis, but I would rather say that I'm interested in examples where the symbiotic chain is in the form of a ring (or maybe a distributed) network, whereas I can only see the human/micro-organism as a star network (a bunch of 2-agent symbiotic relations with a common agent). I will update the question once again. And on a second note, are we even truly in an obligate symbiosis here? If we would eat omnipotent antibiotics for breakfast, would we actually eventually die from the lack of micro-organisms?

@Alex I don't think it is a "star network", afaik microbes in biofilms know of each other. It is not certain whether we would die, since nobody has omnipotent antibiotics. You can get e.g. C. difficile infection without proper microbiome, which can be lethal.

@inf3rno How do they know of each other? As in having a symbiotic relationship between themselves as well?

@Alex I am not certain of that. It might be so. I am trying to find studies about that.

@Alex http://www.pnas.org/content/100/18/10452.full "The results emphasize the contributions of symbionts to postnatal gut development and host physiology, as well as the remarkable strategies these microorganisms have evolved to sustain their alliances." Btw. pathogens can work this way as well, e.g. Staphylococcus and Streptococcus strains can help to each other during an infection.

Hmm that was just the abstract, and that sentence is ambiguous, so it might be about human-microbe relationship and not microbe-microbe relationship. I try to find that section, or another article.

@inf3rno Thanks, if they have symbiotic relationships between themselves as well it would definitely be more what I'm looking for.

Oh, and we have sterile mice in labs, right? I'd assume that that makes a good case that our symbiotic relation with our micro-flora is not obligatory from the human perspective, touching on that subject again.

@Alex Afaik. when sterile mice meet an intestinal pathogen, they die very soon, but I am not an expert of the topic... (Another thing that humans are not mices.)

@inf3rno Ah, right so the obligatoryness might be in that it guards against invading pathogenic, not that we directly can't live without them, thanks for making that point clear. And thanks for providing support that this seems to be what I call "bidirectional n-agent symbiosis" in my picture as well. Will keep this question open for a while though to see if there might be other examples and maybe even the "pure" 3-agent symbiotic ring.

@Alex "Bifidobacterium longum, has no SusC/D homologs but contains transporters that allow it to recover oligosaccharides generated from dietary polysaccharides by species such as B. thetaiotaomicron" - from the same article.", "The distinctive features of the B. thetaiotaomicron glycobiome suggest that a hierarchical and collaborative nutritional network is embedded in the intestinal microbiota." - from the same article. So I think they live in symbiosis with each other as well. This is a relatively old article: 2003. Newer articles would contain more about the details of these relationships.

@Alex Guarding against invading pathogens is just one role of the intestinal microbiome. It has direct effect on the immune system and probably on the development of the brain as well. It helps to digest food, it produces vitamins, etc...

I'll edit my answer, we have too many comments... :-)

I can think of an example for the 3rd picture in your image "Common Agent With Multiple Symbiotic Relationships."
We have: 1.) a species of parasitoid wasp 2.) a species of plant and 3.) a species of moth.
The moth provides pollination activity for the plant. The plant provides a place for the moth to lay its eggs, and a food source for caterpillars once they hatch. Once the plant begins undergoing herbivory it releases Volatile Organic Compounds (VOCs) which attract the wasp and inform it that there are potential hosts nearby. The parasitoid parasitizes either the eggs or the larvae (depending on the species of wasp) and helps the plant by limiting the damage it sustains due to herbivory (like a body guard).
Common example species could be:
1.) Wasps of the genus Cotesia (parasitize caterpillars) or of the genus Trichogramma (parasitize eggs).
2.) Plants of the family Solanaceae (Datura, tomatoes, or potatoes)
3.) Sphinx moths of the genus Manduca
There is a lot of literature on the subject of VOCs and parasitoids, but if you need a quick reference here is one: http://chemse.oxfordjournals.org/content/30/9/739.short.


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How to determine externally that a whale is a mammal?
Mammals have external qualifying characteristics like body hair, ear pinna, etc. But a whale has none of that. So, can it be identified as a mammal just by external observations?

Whales and dolphins have a few hairs on their snout that they usually shed just after birth, in addition to the warm-blooded thing and the live birth and the milk.

@JeremyKemball Only milk and hairs make them mammals. Warm-blooded and live birth are present outside of mammals.

Whales dont have gills.

@biogirl , I said 'external characteristics"...

Gills can easily be seen in a fish

A whale has a horizontal tail fin which is a typical feature of mammalian marine animals see link. Mammalian sea animals typically have a vertical movement of the tail fin for swimming. Fishes like sharks have a vertically oriented tail fin and move it side-ways for locomotion.

This is the answer. +1

Identification of an organism to a taxonomic rank (Class Mammalia) is not based only on morphological characteristics. It is a function of all characteristics that members of that rank share to the exclusion of others. Mammals have multiple features that have been mentioned before (the obvious ones are milk and hair) that they all share that are not present in other taxa. If you only based identification on external morphology you would risk grouping organisms based on convergent evolution (e.g., bats and birds would be in the same taxa).


text:
What proportion of salt in water would make it not dehydrate nor hydrate someone?
Drinking sea water can be deadly as it contains too much salt, basically de-hydrating the body. Normal tap water contains little salt and is good for re-hydration. My question: How much salt needs to be dissolved in water such that it does not hydrate nor de-hydrate? For instance, would a physiologic saline solution (9 grams of salt per liter of water) meet this criterion?

You are looking for physiological saline which is isotonic to most tissues. It is about 0.9% w/v, which equates to ~9g NaCl per liter water.

@kmm I thought isotonic solutions were often used in sports for rehydration?

There is no saline solution which will not either hydrate or dehydrate someone. Pure water hydrates, sea water dehydrates, and everything in between does one ot the other. You need to clarify your thinking on what constitutes "hydration".

@anongoodnurse Why do you say that? There are solutions that can be isosmotic with the cytoplasm. I agree that the cytoplasm can have small variations in osmolarity and you may not find a mathematically exact universal isotonic solution. Why do you think 0.9% saline won't be grossly isosmotic?

@AliceD The sports drinks are mostly for restoring electrolytes.

@anongoodnurse I disagree with your comment. Why would there be only two extremes and no middle ground?

@Nit - "everything in between does one ot the other." That's the middle ground. If you're not dehydrated, you cannot "hydrate" with a perfect imaginary solution. The body will remove the unnecessary salts of anything added. There is no magic solution.

@WYSIWYG - see above. The body doesn't keep solutes it doesn't need. There are isotonic solutions, but if a person is normally hydrated, the solutes of the solution will be removed, in effect reducing it to something close to water. There is no one answer for this question. It depends entirely on the state of "hydration".

@anongoodnurse That still makes no sense. What about solutions that are perfectly balanced between the body-needs-solutes and body-doesn't-need-solutes?

@anongoodnurse I still did not get it. I am talking in the sense of cells and tissues, not a human body. Isosmotic is not enough for excitable cells like neurons, for which the ions also have to be balanced; so lets assume PBS instead of normal saline.

@WYSIWYG - I didn't realize you were speaking about a cell; of course there are isotonic solutions. But the OP is asking about a human body (I presume), and my answer is unchanged for that question.

@anongoodnurse Perhaps you would want to write your point up as an answer (with references etc) on the other post. The comments do not explain the situation properly and are also confusing.

@Nit Oh sorry.. there was a confusion. I thought you asked anongoodnurse to read about loops of henle etc. Sorry. However you have to work on your other question- on terminologies and w.r.t addition of your own analysis on the issue.

I am closing this question as a dupe of this post since the latter has an answer.


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Phage base Biosensor
What kind of biosensor is made by Phages?
I need a list of published paper that used Phages for make LCR(inductance (L), capacitance (C), and resistance (R) of a component) biosensor for detection. for example detection of E.coli

If you are looking for the bacterial receptor that is used by phages then the following review may contain helpful info with respect to E.coli and the lambda phage. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3509688/

Hmm, No I am looking for application of these communication for making Biosensor for example immobilization a phage in a surface and use for detection a specific bacteria by attaching bacterial receptor to phage.

What is LCR? Ligase chain reaction? What is that? I suggest to elaborate your question, or at the very least explain (or better omit) acronyms.

@ChrisStronks An LCR meter is a piece of electronic test equipment used to measure the inductance (L), capacitance (C), and resistance (R) of a component.

So you want to immobilize phages on a surface, then use those to capture bacteria, then look for changes in electrical properties? Whole phages might not be necessary, antibodies against specific bacterial proteins might be easier to use.

This reminded me of something a friend of mine was working on, trying to attach antibodies to specific portions of a CD, then trying to detect protein binding with a standard CD drive. He hoped the proteins would change the reflection enough for the laser to be detect them, but I don't think he ever got it working. If it had worked he would have had a cheap way to detect lots of different proteins at once.

@user137 similar works about it has been worked and I want to use it to determine recombinant phage attachment quality to bacterial cell for treatment in most antibiotic resistant infections. and one more thing, I think your friend will made that.

@M007 That's his name, but I don't like giving out potentially identifying information on the internet. I'd ask you to say for me, but he wouldn't recognize my username.


text:
Do all Gram negative bacteria cause septic shock?
Do all Gram negative bacteria cause septic shock? If they don't could they if you attacked them with an antibiotic that could lyse the cell? For example any antibiotic that attacks the cell wall, although I suppose that could be difficult with the gram negative wall, not to many gram negatives are susceptible to a wall attack.

all Gram negative bacteria can potentially cause septic shock, but septic shock is not limited to Gram negative cell wall lipopolysaccharides. Any infectious agent can cause septic shock, including gram positive and gram negative bacteria, fungi and even viruses (this is quite evident in the recent Ebola outbreak).[1]
The causative agents for sepsis/septic shock have evolved. Originally strongly considered to be related to Gram-negative bacteria, that is no longer the case. About 25 years ago, sepsis was considered to be a response to endotoxin thought to be relatively specific for Gram-negative bacteria. That Gram-negative bacteria were the most common causes of sepsis[2] resulted in trials that focused on  specific therapies for G negative endotoxins.
It is now recognized that sepsis may occur from bacterial, fungal and viral organisms. More recent epidemiology studies reveal that Gram-positive bacteria have become the most common cause of sepsis in the past 25 years. According to the most recent estimates in sepsis, there are approximately 200,000 cases of Gram-positive sepsis each year, compared with approximately 150,000 cases of Gram-negative sepsis.[3]
Fungal causes of sepsis have also grown at a rapid pace. Why this occurs may be two-fold: a general increase in nosocomial (hospital acquired) cases of sepsis, and more effective treatment of bacterial infections, thus promoting fungal infections to a more leading role. The increase of fungal nosocomial infections has also shifted away from the common Candida albicans organism to the more recalcitrant torulopsis, glabrata and krusei subspecies.[4]
So while the Gram negative Lipopolysaccharide or “endotoxin” is unique to Gram negative bacteria, cell components of Gram positive bacteria have been identified that appear to be biologically equivalent to endotoxin in stimulating the inflammatory response associated with sepsis and septic shock. These include a peptidoglycan layer outside the cell membrane of Gram positive bacteria as well as non-peptidoglycan polymers (such as the teichoic acids). They have been shown to stimulate the release of cytokines, specifically tumor necrosis factor and interleukin-1.[5]
[1] How Ebola Kills You: It's Not The Virus
[2] Septic shock in humans. Advances in the understanding of pathogenesis, cardiovascular dysfunction, and therapy
[3] The epidemiology of sepsis in the United States from 1979 through 2000.
[4] Nosocomial bloodstream infections. Secular trends in rates, mortality, and contribution to total hospital deaths.
[5] Sepsis and Septic Shock
Sepsis, severe sepsis and septic shock: changes in incidence, pathogens and outcomes

Regarding your connection to Ebola: As far as I remember the clinic in Hamburg decribed that the main problem with sepsis came from bacteria which leaked from the gut into the blood stream, causing problems. But this is most likely due to effects that the virus caused, so this is a bit of a hen and egg problem.

Without directly addressing your comment's content, I can say that a common misconception about septic shock is that it is a result of pathogens in the bloodstream. It's not. Septic shock in Ebola is due to a cytokine storm. Ebola virus appears to trigger a release of pro-inflammatory cytokines with subsequent vascular leak and impairment of clotting ultimately resulting in multi-organ failure and shock. The gut stuff is the result of GI end-organ failure.

Ok, this was an unclear formulation. Viable bacteria in the blood stream can be considered as one of the ultimate dangers. But still substances like LPS (which can cause septic shock) will find an entry route here.

@Chris - That's a good point. If you're interested in the medical side of this, here is some very interesting reading: Approaches to Clinical Management for Patients with Ebola Treated in U.S. Hospitals. It goes through everything we know about Ebola in the US-treated patients (except from Dallas). I didn't see any mention of positive blood cultures even in the patient requiring ventilatory support and dialysis (so very close to death).

The major factor defining Gram-negative (vs. Gram-positive) bacteria is the structure of the cell wall, outer membranes, and the moieties that extend out into the environment:

http://en.wikipedia.org/w/index.php?title=File:Gram-Cell-wall.svg
Gram+ bacteria have an inner plasma membrane and an outer, thick layer of peptidoglycans. This is what takes up Gram's stain. Gram-, on the other hand, have a plasma membrane, a thinner peptidoglycan wall, then an outer membrane consisting of lipopolysaccharides (also known as LPS or endotoxin) anchored into the membrane's phospholipids, along with various proteins within the membrane:

https://commons.wikimedia.org/wiki/File:Gram_negative_cell_wall.svg
Sepsis, a systemic inflammatory response syndrom (SIRS) can be caused by both Gram-positive and -negative bacteria, as well as viruses and fungi. In the case of Gram-negatives, the immune system is activated in response to the presence of LPS from extracellular lysed and intracellular antigen-processed bacteria, through the Toll-like receptor TLR4/CD14/MD-2 pathway. One can have a local infection, and still not develop sepsis. However, if the infection becomes large enough or the bacteria enter the blood stream in significant numbers, sepsis can occur. Not all patients with sepsis develop septic shock, which is characterized not only by a microorganism-caused SIRS and organ dysfunction/hypoperfusion, but also by chronic hypotension (low blood pressure) even after administration of IV fluids.
Structurally, LPS contains the highly-conserved Lipid A, which anchors the molecule into the outer membrane, a core oligosaccharide, and the outer O-antigen:

https://commons.wikimedia.org/wiki/File:LPS.svg
Lipid A is actually the most toxic segment of LPS (the portion recognized by TLR4 and MD-2), and while it is generally highly-conserved among different bacterial strains and species, studies have shown that different human-pathogenic species of bacteria have altered Lipid A from the "canonical" structure derived from E. coli. This can cause variations in the downstream signaling from TLR4 to NF-κB, potentially leading to immune system evasion.
So, to directly address your question:

Do all Gram negative bacteria cause septic shock?

They can, if present in sufficient quantities, but not necessarily through the same mechanisms. The immune system recognizes many different pathogen-associated molecular patterns (PAMPs) through a variety of TLRs and other pattern recognition receptors (PRRs) like C-type lectin receptors, Nod1 and Nod-like receptors, etc. Some work on intact bacteria, others recognize intracellular epitopes. Therefore, sepsis and, in severe cases, septic shock, can be caused by Gram-negative bacteria through LPS-independent pathways. While it's possible that lysing these bacteria chemically by antibiotics could potentially enhance the immune response, cells like macrophages are very good at recognizing foreign invaders and lysing them on their own, giving plenty of substrates to the various receptors. Also, keep in mind that dead cells may auto-lyse, so the antibiotics need not necessarily attack the cell wall itself, just kill the bacteria.


text:
At which temperature is the Tick-Borne Encephalitis Virus destroyed?
At which temperature is the Tick-Borne Encephalitis Virus destroyed? If there is no data specifically for TBEV, is there any data for typical temperatures at which other Flaviviruses / Flaviviridae / other similar viruses are destroyed? (Or if there's nothing specific at all, then viruses in general?)

A very basic model of virus inactivation is exponential decay.
You can describe exponential decay with the $N(t) = N_0e^{-\lambda t}$ equation, of if you want to use half-time, then with the $N(t) = N_02^{-t/t_{1/2}}$, where $N$ is the value which reduces by time, $t$ is the time, $\lambda$ is the exponential decay constant and $t_{1/2}$ is the half-life (the time required to reduce the actual value to its half).
Exponential decay looks like this on diagrams:

Figure 1 - exponential decay

Figure 2 - exponential decay on log scale is linear

In the case of your TBEV virus, the $N_0$ will be the initial virus titer, the $N(t)$ will be the virus titer by a specific time, the $t$ will be the time and the $t_{1/2}$ will be the half-life, which depends on many things; TBEV strain, temperature, dry/moist heat, pH, etc...
Now real life logarithmic diagrams of TBEV thermal inactivation are linear only by the first 30 mins or so (the inactivation is exponential during that period) as you can see on Figure 3.

Figure 3 - virus inactivation at 60°C
2004 - West Nile virus: recent experience with the model virus approach.
where $TCID_50$ is the tissue culture infective dose

By virus inactivation most of the articles like to use log 10 reduction factors. For example $3 lg$ or $3 log 10$ means in this context, that lowering the initial value to $10^3 = 1000$ fold.
According to this article most of the checked TBEV strains has an inactivation index (the reduction factor difference between two temperatures) around 1.7lg between 50°C and 37°C for 15 mins. So you need 15 mins at 50°C to reduce them at least $10^{1.7}=50$ fold. The reduction factor by this study was around 4lg by 37°C for 15mins (so the virus count reduces certainly not just because the heat, but other environmental factors).

Thermoresistance (Т50) of TBEV strains was tested by Ovchinnikova et
  al. method [17] using 24-hour cell culture grown in 96-hole plates at
  the presence of СО2. The thermoresistance was determined by
  inactivation index – difference in lg of titers of virus samples
  heated at 50°С during 15 minutes or unheated (4°С). In case of titers
  difference equal or less than 2.0 lg the strain was characterized as
  Т50+, from 2.1 to 3.0 lg – as medium, equal or more than 3.1 lg – as
  Т50-.
The values of lgTCD50/ml at 37ºС varied from 3.5 to 8.26. According to
  the thermoresistanse feature all tested strains were divided into
  three group: thermostable (Т50+) - nine strains; thermolabile (Т50-) –
  one strain; strains with medium thermoresistance – three strains. It
  should be noted that all strains isolated from I. persulcatus ticks
  collected in Krasnochikoiskiy district of Transbaikalia were
  thermostable.

2013 - Genetic and Biological Properties of Original TBEV Strains Group Circulating in Eastern Siberia

According to another study TBEV required 6 hours of moist heat at 60°C for inactivation of 6.6 lg.

Vapor heating of a FVII concentrate in another study (which used
  lyophilization, followed by adding water to achieve homogenous
  moistening, then heating at 60°C for 10 hours, followed by heating at
  80°C for one hour in an airtight container under nitrogen gas
  atmosphere) was evaluated for its ability to inactivate HAV, HIV-1,
  TBEV, PRV, and MVM. HAV was readily inactivated within one hour at
  60°C (5.9 log 10 ). TBEV required six hours of this treatment for
  inactivation of 6.6 log 10 , and three hours were required to
  inactivate
  6.2 log 10 of HIV-1 and 6.9 log 10 of PRV.

2002 - Part 3a, Plasma and Plasma Products - Heat and Solvent/Detergent Treatments

According to this study TBEV is considered not heat resistant, so if you are worried for example about raw milk pasteurization, then I think boiling the milk for a few minutes is enough.

Due to the lipid envelope, TBEV is readily inactivated by heat
  treatment, detergents and organic solvents. Even though a viremic
  phase is common during a TBEV infection in several animal species,
  foodborne infection via contaminated meat or organs is unlikely due to
  the fast virus inactivation at elevated temperatures.

2011 - Scientific Opinion on an update on the present knowledge on the
occurrence and control of foodborne viruses

Thanks! This is very interesting, definitely very relevant and I'll certainly  upvote, but it doesn't quite answer my question... The "thermostable" strains are able to survive 50ºС, but how high does the temperature need to be to destroy them? The paper doesn't seem to have any data beyond  50ºС. Basically, I am looking for the minimum temperature at which it would be safe to assume that TBEV has been destroyed, regardless of strain.

@EugeneO I don't think you get the basic idea behind heat inactivation... I'll edit my answer.

Thanks for adding all this detail - I now realize I haven't made my question precise enough. I understand the concept of half-life / exponential decay. I guess the question I'm really trying to answer is, for a reasonably large reduction (let's say 3lg), and the most thermoresistant strain I'm likely to encounter, at what temperature do I have to treat it (given some reasonable fixed treatment time, e.g. 15min or 60min) to ensure that 3lg reduction will happen?

... And to add to that, I might as well ask the layman's question I'm really trying to answer. If I come back from a hike in the woods in Siberia with potentially live ticks on my clothes, and put the clothes through a wash cycle (e.g. 30min at 60 deg C), can I be reasonably assured that whatever viral particles that remain won't be enough to infect me? Is there any setting on a commercially-available washing machine (temperature, length of cycle) that will give that assurance?

(Actually, just noticed the part about "detergents" in the last article you linked, this may be my answer... But more details would be nice, this is not a theoretical question, I actually do go for hikes in the woods of Siberia so having additional data would certainly be reassuring :)

@EugeneO According to the linked articles, 3lg seems like achievable with 60°C, 30mins by every TBEV strain. Yes, detergents will boost the inactivation as well. Most laundry detergents contain e.g. proteolytic enzymes, which can help too...


text:
C.elegans and antioxidants
How would you test the effect of antioxidants on C.elegans lifespan?
Is this done through feeding E.coli with antioxidants and then C.elegans with E.coli, or is there another method?

base on a article they do the test of nano-Pt, kind of SOD, and they do the experiment in several steps, first choose C. elegans strains and growth conditions, meanwhile prepare the nano-pt. then, do the lifespan assay. thired is Oxidative stress resistance. the last step is Fluorescence microscopy. in the mictoscopy they do several steps, include Measurement of lipofuscin accumulation, Detection of ROS, Measurement of SOD/catalase activit, Thermotolerance and Effects of dietary restriction

You can simply add the molecule of interest in the NGM or Liquid medium.
From this paper.

The worms were bleach-synchronized as follows: 2 mL of 6% NaOCl were
  mixed with 1 mL of 5 M NaOH per 7.5 mL of concentrated worm
  suspension, and shaken for 4–7 minutes until the carcasses dissolved
  as monitored by direct observation. The remaining eggs were then
  washed 3 times by pelleting at ~1150 g for 2 minutes at room
  temperature, followed by aspiration of the supernatant and
  resuspension in 50 mL of 0.1 M NaCl. A final pellet of eggs was
  obtained by centrifugation at ~1150 g for 2 minutes at room
  temperature, followed by aspiration of the supernatant. Eggs were then
  added to a 250 mL liquid culture, as described above. For experiments
  without RNAi treatment, bacteria were heat killed at 80°C for 60
  minutes. The worms were cultured at 20°C and monitored until they
  reached adulthood (~72 h), at which time FUdR was added to a final
  concentration of 400 µM. Worm viability was scored every two days by
  taking ten 10 µL drops (initially ~20 worms per drop) of the culture
  and counting the living worms under a microscope. The average number
  of living worms was then calculated. S medium or deionized water
containing 10 mM malate, succinate, or fumarate was added back every
  three days to compensate for metabolism of the compounds and
  evaporation, and S medium containing FUdR and bacteria was replaced
  every 6 days. At least two replicates of each experiment were
  performed.


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

Welcome to biology SE! Could you elaborate your question? For example, it is not clear if you are talking about keeping the organs fit for transplantation after the donor has passed away, or whether you are asking whether organs have to be transplanted before the donor reaches a certain age while alive.

@ChrisStronks I am asking about does the organs age, or is it possible to transplant organs indefinitely from donor to donor. See my edit please.

I took the liberty to edit your question - I hope it accurately reflects your question.

First of all, it will be practically impossible to make an estimation of how long a transplanted organ will live and how many times it could be transplanted. However, it is relatively safe to say that it will not live forever.
To be able to receive an organ transplantation, the HLA MHC-complexes of donor and receiver need to be matched very carefully, to limit the host-vs-graft reaction. This limits the number of possible donor-receiver patient pars drastically. So to be able to do a "row transplantation" (one receiver to the next and so on), they need to have matching MHC-complexes.
Otherwise the immune system of the receiver turns against the transplanted organ and will eventually destroy it. To avoid this reaction, transplantation patients also receive drugs, which severely suppress their immune system, thus making other infections potentially dangerous. This reaction will still take place, since you cannot shut down the immune system of the receiver completely (for obvious reasons), though it happens at a much slower rate. Transplanted organs will only live for a certain time (see estimates from a number of transplantations below) and it is possible that people need to receive transplants twice in their life.
For this reason, no doctor will put their patient at risk by giving them an organ which might have a reduced lifetime. The risk of the operation itself is also substantial.  Additionally, the original receiver needs to be dead to do this, as he would otherise need another organ in exchange.
What we can do is to take the average number of a lot of transplantations together and calculate some average life-years for a transplant. According to table 2 in this paper ("The Life-Years Saved by a Deceased Organ Donor") the "average benefit by type of transplant (life-years)" is:

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

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

The table you cite refers to average number of years a person on a transplant waiting list will live after receiving a donated organ, i.e. the expected lifetime of the recipient. This is unrelated to the maxium or average lifespan of the transplanted organ, which is what the OP is asking about. It's an outlandish question but this doesn't answer it.

No, you are wrong. What I cite here partly is table 2 from the article which describes "Table 2.  Average expected gain in life-years for wait-listed patients from an extra deceased organ donor".

As I understand the article, the numbers cited in the table represents the average number of years by which a single donated organ will extend the life of a person on the donor waiting list for that particular organ. So if one "extra" liver was made available for donation it would be transplanted into a recipient who would then go on to live for an additional 16.9 years. The 16.9 years refers to the expected remaining lifetime of the recipient, not the transplanted organ. Theoretically the organ could be once again transplanted upon the death of the first recipient. [ctd]

Of course this is incredibly unlikely for the exact reason you specify: it will have been damaged by the recipient's immune system. Regardless, the OP is asking how long or how often such an organ could be transplanted in a functioning state, which you did not directly address.

What they did was to calculate the additional livetime gained by a transplated organ which they calculated from a large number of organs. So if you are on the transplantation waiting list or a liver and get a transplantation before you die, this can result in up to 16.9 years.

Even if the numbers listed here are not for the lifetime of the organ, an organ can't be used forever, I suspect the lifetime of an organ can't be much longer than the lifetime of the average person in ideal conditions. Add in stress from immune rejection, lifestyle, infections, and multiple surgeries and the organ lifetime will be even shorter.

@user137 Agreed, but that's precisely what the OP is asking. Ideally this answer would state that explicitly, provide a source for the claim that organs are (almost) never retransplanted and then the table is a good indicator of the practical lifetime of a transplanted organ.

@Chris Apparently we both understand what that table means perfectly, but my point is that it's not actually the number the OP is looking for, unless you preface it as being the average limit to an organ's lifetime in practice (see above comment to user137).

@Lilienthal I have edited the answer, is this clearer now?

@Chris Perfect. Thanks for clearing it up and nice find on the article itself. +1

The median lifetime of an organ transplant is some 5 to 10 years mainly due to chronic rejection mediated by host-versus-graft immune responses.  Hence long-term transplants definitely have a limited half life. However, this graft rejection is relatively slow and early explantation and re-implantation in a new host may actually "reset" this process? With re-setting I mean that the new host's immune system must start the slow graft rejection process (immunization) all over again, including antigen recognition and build up of the humoral and cellular immunity (see wiki on graft rejection). So in theory the organ-lifetime may actually surpass the recipient lifetime as mentioned earlier when grafts are explanted and re-implanted. As this scenario has never been tried as far as I am aware - due to the obvious risks associated with repeated complex surgeries - it becomes speculative at this point.

I don't understand, is it possible or not, or unknown?

@matthew he is saying its unknown.

I tried to improve the clarity of my answer - but indeed it is unknown what happens with repeated re-implantation

It really depends on the primary disease of the transplant recipient and the organ transplanted. Some diseases cause organ failure and will do damage to the transplanted organ and shorten its survival. There are rejection process in the host that will do all sorts of damage to the graft. There is also surgical complications when trying to ex-plant a transplanted organ and re-implant it into another recipient. However, if you want to know the record of how long an transplanted organ has survived please check this out:
http://www.bbc.co.uk/news/uk-england-tyne-37025389


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What is the biological basis of "energy" that extraverted humans draw from social engagements and introverts expend?
This question is related to this question about introverts becoming exhausted after extended social events on cognitive sciences stack exchange.
As I read more on the topic of human extraversion-introversion, I keep seeing the mention of "energy" which extraverts draw from social engagements and introverts expend in such engagements.

When energy is drained, the state can be called "exhaustion", depletion, being drained
When enough energy is accumulated, the state can be called "elation", being energized

The idea makes sense, and I see many diverse writers use it, but nobody defines what this energy is in a biological sense.
What is the biological mechanism behind "energy" spent/gained in social interactions - what is it in brain terms? I'm looking for an answer like: Dopamine in X part of the brain? Mirror neuron activation? Amygdala overreacting?
I found a quote from this article on introversion, although it does not seem to have any sources listed

Research has shown that the mind of an introvert works differently
  than the mind of an extrovert. Introverts have more pronounced
  activity in the parts of the brain that deal with long term memory,
  planning, complex thinking and organizing. Our introverted mind is
  always turning and running and because of this, we need very little
  outside stimulation. The extrovert's brain has more pronounced
  activity in the areas associated with sensing and processing
  information from the outside. That's why extroverts seek outside
  stimulation

What are the scientific names of the brain regions described in the quote above?

You are probably asking this question 50 years too soon. If we don't know how sleep works then I doubt we know how psychic energy works.

A completely anecdotal observation: extraverted people are more physically active in social situations and use more gestures/movement. They would be moving more than introverted people (who are more likely to just sit and listen), thus extraverts may benefit from improved blood circulation, thus sustaining higher levels of engagement for longer. An introvert who's engaged in an interesting conversation moves/gestures just as much as an ordinary extravert, and thus feels less fatigue from social situations.

Another observation: Both extraverts and introverts would be fatigued by an extended "sit here and listen to me talk" kind of meeting that runs for 2 hours.

Why do we like movies then?


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How to identify genes required for biofilm formation
This is just a homework question:
Q: Let’s assume that there is an unknown set of E. coli genes that are required for biofilm formation. Describe a genetic experiment you could perform to try to identify those genes.
The one idea that I can think of is:

Compare strains that produce biofilm against strains that do not produce biofilm. Sequence genes, find differences, interrupt genes in biofilm producing strains and confirm biofilm ability is impaired.

Is there a better approach than this?

You could do different things: First you could, as you say yourself, sequence the complete genomes of the strains from a biofilm and compare these with some, which do not form biofilms. This may give you an idea which genes are involved when they are present in the "biofilm genome" but not in the other. The proof would be to disrupt these genes either by removing or mutating them or by gene silencing techniques and see what the outcome is.
It is also possible that only a mutation in a gene which exists in the sample and the control genome makes the difference. Then site-directed mutagenesis would help to identify the important genes.
The second possibility is that there is no real difference in the sample and the control genome and the difference for developing a biofilm "simply" lies in the difference of gene expression. Then the isolation of RNA (either total or mRNA only) would help to find involved genes. If the environment makes the difference for the development of a biofilm, then the biofilm and the control cells should have show no (or almost no) difference in their gene expression profiles when they are cultivated under identical conditions. You then need to test the gene expression for different environmental conditions (including those that favor the development of biofilms) to find genes which are involved.
This comparison of the different conditions will then deliver genes which are uniquely or more highly expressed in the biofilm group, a lot of genes which are comparable in expression to the control sample, and some genes which have a lower expression than the control. It is now worth looking at the higher (or unique) and lower expressed genes, find out their function and then start mutating them to check their function for the formation of a biofilm.
Additionally there is the chance that the gene(s) which is necessary for the biofilm formation is located on an extra-chromosomal plasmid. I would also check the plasmids present in the biofilm and the control sample, sequence them (if present) and see which genes they express. The function for the biofilm formation can easily be tested with a simple transformation.

Nice answer! :-)

In the second possibility, the difference isn't genes, but expression of genes, then there must be some environmental trigger, right? So if both strains are cultured under the same conditions, they should both produce or not produce biofilm, right? In that case, you would figure out which environmental conditions triggers the difference and compare RNA expression to see which gene is affected. Is this correct?

@clay Yes, you are right. If it is really the environment which makes the difference, then there should be no (or almost no) difference in the gene expression profiles. Then you need to test different environmental conditions. Good point, I will add this to the answer.

Addition to Chris' answer.
If you do not have a strain that doesn't produce biofilm then you would have to screen for the genes that are involved in biofilm production (this goes for any phenotype).
In earlier times people used to do this by random mutagenesis with mutagens such as EMS (Ethyl Methanesulphonate) or UV. Nowadays it is possible to build a library of targeted mutagens against each gene for e.g. Library of CRISPR-Cas nucleases.


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Are Purkinje Action Potentials Neuronal and Cardiac?
I first thought that action potentials of His-bundle i.e. Purkinje fibers are Cardiac.
However, I started to think that this is not enough.
I think now that they are neuronal and cardiac.
My conjecture. They have first short-acting neuronal part and then long-acting cardiac part.
Are Purkinje Action Potentials Neuronal and Cardiac?

The His-Purkinje fiber system is a network of one type of specialized conducting cardiac cells that carry an action potential in the heart. There are other cells which perform this function in different parts of the heart. The initiation time, shape, and duration of the action potential are distinctive for different parts of the heart, reflecting their different functions. These distinctions arise because the myocytes in each region of the heart have a characteristic set of channels and anatomy. You can completely dissociate the nervous system from the heart, and the heart will still pace itself. Think of what happens with heart transplants. This completely eliminates neuronal influence. See the following brief excerpt which explains one type of cells conduction method. Please note there is no reference to neurons.

The positive charge that enters cell A not only depolarizes cell A but also produces a flow of positive charge to cell B—intracellular current. This flow of positive charge discharges the membrane capacitance of cell B, thereby depolarizing cell B and releasing extracellular positive charges that had been associated with the membrane. The movement of this extracellular positive charge from around cell B toward the extracellular region around cell A constitutes the extracellular current. The flow of intracellular current from cell A to cell B and the flow of extracellular current from around cell B to around cell A are equal and opposite. It is the flow of this extracellular current in the heart that gives rise to an instantaneous electrical vector, which changes with time. Each point on an electrocardiogram (ECG) is the sum of the many such electrical vectors, generated by the many cells of the heart.

This has been extensively studied, so much so that cardiac electrophysiologists can pinpoint the location of a small group of cells that are misfiring by the nature of the impulse they are giving off. The annual median salary for an electrophysiologist in the US is $480,000. :-( There is a lot of grant money in this area. It's a big deal.
For in-depth study of electrophysiology of cardiac cells, please see Electrophysiology of Cardiac Cells or any other of a number of reliable sources.

Thank you for your answer! The case study does not cancel out my conjuncture. One reason why those neurons have not been found is that they are extremely small. They give signals of very little energy with the same frequency as Purkinje fiber. Other reason is that they are entangled to the Purkinje network together and difficult to separate them when you do not know where to look and how. It would be interesting to study the small group of cells misfiring. I am trying to get a research place in this area so I can start to research better. My options are Norway's research laboratories and USA.

@Masi - If I understand correctly, it is your contention that neuronal cells exist in cardiac muscle but they just haven't been found yet? How do you explain heart transplantation? Are there neurons that exist apart from the nervous system?

I do not know how these neuronal cells exists along cardiac muscle (in, out, near) but I have a clue that they work very closely together. And the only way to do so they should coexist, I think. I have only clues about this coexistent in Purkinje fibers. Person can live without this system some time. These neurons seem to exist in a link with the nervous system. I have not studied any heart transplantation patient. To process such an data (AAMI) similarly would tell me if similar regulation exist. It would be interesting to get such an data to understand your last case better.

Well, Hassall studied this in guinea pigs in the 80's and 90's. I found conflicting studies about it starting in the 2000's on. I don't know much about that. Clearly the nervous system has an effect on the heart. It would be interesting to study the differences in heart transplant patients vs. normal.

Thank you for your excellent comment! I sent requests of data for MIT-BIH's creator (George Moody), my close link of signal processing in Finnish Academy and my Baltic research fellows. The problem has been to get AAMI standard data. Only George's data has passed my validation at this point, although officially, many data are verified so by their AAMI devices.

Can you, please, point me to those conflicting studies from 2000's. I am making an application to my universities for request of data in heart transplant patients for this study.

On the wiki they are called cardiac action potentials. As the generation of the action potentials in the sinoatrial node is mediated by muscle cells, as is the conduction of the action potentials through the purkinje network (see wiki), the action potentials are not neural in nature, but cardiac.


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Why are there no marine birds?
Walking  by the lake and watching the ducks the other day a thought struck me; there are lots of aquatic birds but all remain at least somewhat terrestrial, nesting on land.
Why is it that no birds have taken the evolutionary route of the dolphins and whales and returned to the sea?
Is there something in avian biology that means this is not possible?

Feathers require a lot of maintenance with fats to be waterproof, which would be quite impractical for a bird which constantly lives in the water.

Penguins are probably one of the farthest along the evolutionary path you describe, as they spend a large amount of time in the water, not just on the water.

egg laying in general makes it harder, placental mammals have a much easier time going back to the ocean since they carry their young internally. cetaceans had a much easier time of it then aquatic birds and reptiles.

Apart from one isolated group of birds in Australia (i.e., mound nesters found in Australia that use external heat for incubation - see link), all birds incubate their eggs (see link). All species that returned from land to sea have retained their reproductive cycle (marine mammals still give live birth and suckle their young) and still rely on air for oxygen intake. Extrapolating this mammalian evolution to birds would result in a creature that returns to sea, with all ties to land cut off, but that still has to incubate their eggs under water. As they would still rely on air, this is not very feasible as they would need to go up often to breath. This would leave the eggs vulnerable to predation. Even worse, it would leave the eggs at the mercy of a relatively cold ocean cooling them down quickly. Incubation means that the eggs are pretty much kept at body temperature which is difficult in the sea regardless of breathing parents. In all, while there may be certain benefits of underwater life for birds, it will require some drastic evolutionary changes in terms of the reproductive cycle. A more parsimonious way of colonizing the sea is to go back to land once and a while to lay eggs, incubate them, and raise the young until they are sea-worthy, like penguins do as @MattDMo mentioned.

All birds incubate their eggs? You forgot the cuckoo!

I think that sea snakes have returned from land to sea and have altered their reproduction to fit that. Sea snakes are truly vivipare, they give birth to live babies. This is an adaptation necessary for them to remain in the water. For laying eggs, the snake would have to go on land.

This is a quite old question (more than 3 years now), and chances are OP will never read this. However, I'd like to give my contribution:
The issue here is not if birds incubate or not their eggs (see the other answer). Even if we suppose that no bird incubate its eggs, that is, that all birds lay their eggs and just walk away and that the eggs develop normally at cold temperatures, even so there could be no "marine bird" the way OP asks, like a dolphin. And the answer is in the egg itself.
The amniotic egg
Birds, which are a group of dinosaurs, together with the other reptiles and the mammals show an outstanding evolutionary innovation: the amniotic egg.
The amniotic egg allowed our Amniota ancestor to leave the water and to complete the whole reproductive cycle on land. It was a great evolutionary achievement, which allowed the tetrapod "conquest" of dry land.

An amniotic egg (tortoise)
However, there is a catch: that amniotic egg, which allowed our ancestors to be independent of water for reproduction, cannot be laid on water. Due to several reasons, mainly the (lack of) gas exchange through its shell, the embryo will not develop if the amniotic egg is laid on water.
That's why marine turtles have to leave the water to lay eggs, slowly crawling on the sand in a very exhausting task which will some time later put their very babies in danger. It would be preferable laying the eggs in the water, where they are already... but they can't.
Evolutionary solution: Viviparity
So, how could some mammals take that evolutionary route? Because (most of) mammals don't lay amniotic eggs: they developed viviparity instead. And that viviparity allowed mammals such as whales and dolphins to spend their whole life in the water, never coming to the land.
A very interesting proof of this evolutionary explanation is the case of the ichthysaurs. This extinct group of marine reptiles spent all their reproductive cycle in the water, never returning to the land. How is that possible with an amniotic egg? The answer is that ichthyosaurs didn't lay eggs: just as mammals, they were viviparous. That viviparity allowed them to be truly aquatic.

Artistic representation of an ichthyosaur with its viviparous embryo
This now famous image (Motani et al., 2014) shows a very rare — and tragic, since they died — fossil, a pelvis of a Chaohusaurus mother with three embryos, one of them clearly visible:

So, we can only speculate that, the day some bird develop viviparity (or radical changes in the amniotic egg structure and physiology), then we can have a truly marine bird.

Source: Motani, R., Jiang, D., Tintori, A., Rieppel, O. and Chen, G. (2014). Terrestrial Origin of Viviparity in Mesozoic Marine Reptiles Indicated by Early Triassic Embryonic Fossils. PLoS ONE, 9(2), p.e88640.

But WRT birds, viviparity would seriously restrict flying ability due to the extra weight.  You might get it in a non-flying, bird-descended creature akin to a penguin, but (IMHO, anyway) it'd be arguable whether such creatures should still be considered birds, and not an entirely new branch of the tree of life.

Phylogenetically It doesn't matter: any organism descending from a species belonging to a given clade x also belongs to that clade x, without exception. That's a basic phylogenetic rule. If a given bird evolves to an organism with fur and teeth, that organism is obligatorily a bird.

there are ovoviviparous sea snakes (Hydrophiinae), they do not need to come back onto land to lay eggs, but the derived hard shelled avian egg is ill suited for ovoviviparity.

@Gerardo Furtado: So by that logic, everything with a backbone is a fish :-)

@jamesqf Yes, we are fishes indeed! That's a very famous concept in Phylogenetic Systematics. Have a look here, Campbell's biology: https://books.google.com.au/books?id=5t6aBQAAQBAJ&pg=PA742&lpg=PA742&dq=osteichthyes+phylogenetic+systematics&source=bl&ots=uqb-cjxiAE&sig=7dnF7ljffqheSmwYhCOr27nbvqY&hl=en&sa=X&ved=0ahUKEwic8LHdx9jYAhVDgLwKHbnmBHcQ6AEIYzAK#v=onepage&q=osteichthyes%20phylogenetic%20systematics&f=false The text says: "Systematics today include tetrapods along with the bony fishes in the clade Osteichthyes".

If you don't include humans, dogs and parrots in the Osteichthyes (bony fishes), the group becomes paraphyletic, which is wrong.

@Gerardo Furtado: So humans, dogs, and parrots are fish?  Perhaps it is Phylogenetic Systematics which is wrong, or at least being extended far beyond its usefulness?  See https://en.wikipedia.org/wiki/Reductio_ad_absurdum

No, that's not a reductio ad absurdum at all, it's a very simple and basic concept, widely accepted. That's the same reason birds are dinosaurs, and reptiles, and tetrapods, and fishes. That's the concept of clade. Anyway, feel free to think that Phylogenetic Systematics is wrong...