CharonY

Incidentally, one of my phDs is also working on T4P with a heavy focus on regulation, though.

Enjoy it, tis quite an interesting topic.

Any particular focus in your work (attachment, biofilm or motility?)?

You mean you want to visualize a protein in vivo? Usually that is done by marker fusion (e.g. GFP) of the protein in question. Other more error prone protocols involve the uptake of the ABs by endocytosis (in case of plants protoplasts are used). Overall specificity and efficiency can be worriesome, though.

I guess my main question are the limitations, right? Like if the eye can take on x amount of photons that's the limitation of how much visual information it can store, but is it possible to go beyond that limitation?

I don't quite understand your question. The photoreceptors react to incoming photons and hyperpolarize the cell (so light actually reduces the potential of the cell) in subsequent layers the information is already processed due to the way subsequen bipolar- and ganglia cells are connected (or more precisely, how they react to the secreted neurotransmitter).

So essentially the resolution is defined for one by the density of photoreceptors and how many of these are interconnected to produce signals.

Or, if you refer to how much information is stored in the retina or area I the answer is almost nothing. On the retina level adaptation to light intensities occur and the visual cortex apparently works as having some kind of short term cache of which the information has quickly transferred to the short term memory (otherwise it will get lost).

Regarding the visualization memories:

the primary visual cortex is indeed involved in the primary procession of visual information, however if you visualize something in your mind, you are first activating other areas which are involved in recreating memories. The precise areas depend on what you actually recall. For instance spatial information is recalled differently to, say, episodic memories. At least in dreams visual memories are then partly "reenacted" with the help of the visual cortex, and this might be also true in daydreams.

I posted too late yesterday. First a quick correction: I meant type IV secretion system, of course, not replication system (wouldn't make sense).

In general type IV pili are known to be involved in twitching motility rather than secretion. However part of the assembly system of type IV pili is closely related to type II secretion systems. So one could say that the apparatus for type IV pilus secretion is essentially a type II secretion system, but the type IV pilus is the substrate, not the means of the secretion.

(Or in short, type IV pili are not involved in type IV secretion mechanisms).

Also one have to add that some classifications of secretion systems are not that streamlined, mainly due to the different cell envelopes of Gram-negative and Gram-positive bacteria.

Some of the later experiments involved the use of synthetic trinucleotides, radioactive aminoacyl-tRNAs and incubate them with ribosomes. After filtering which will only retain ribosomes and everything bound to it, the radioactivity was screened.

Many bacteria possess extrachromosomal DNA in the form of plasmids. The Ti plasmids is one of such and is not produced per se but as is replicated like the main chromosome.

The DNA is tranferred into the plant cell with the means of a type IV replication system. Bacteria produce pili which in this case are used to "inject" the DNA into the plant.

not if the links are embedded in words within the main text...

Anyhow I got one diploma student who actually reads the papers I give em.

Yey!

Recently a colleague showed me the thesis of one of his diploma students. Several aspects indicate that large passages of the introduction were copied from wikipedia. Of course one could only detect them with the rigorous training of a scientific mind ... so these were top three hints:

-some passages showed a change of style and wording

-there was little coherence between certain passages

-the passages in question do not actually address the topic of the work

and finally:

- the girl/woman in question kept the fonts of the website (she used another throughout her work) and did not remove the links......

D'oh.

At the end of most articles, they have a references section, often refering to published journals.

And here is another problem. If there are references at all (not links) then they are only good in the most basic topics. And after browsing through some I also found serious misquotations.

That wouldn't be so bad if they wouldn't prefer wikipedia over pubmed, or rather reading a review and starting from there instead.

Also after some discussions with wikipedians apparently there are not that many experts there to do the serious clean ups. Or rather I would believe that there are not that many experts there having the time to do so.

While the precise connection to cancer is not clear, it is known that cancer and tumour cells in general usually have overactive telomerases as compared to normal somatic cells.

Also enlarging telomeres would be detrimental in general as different cells in your body must proliferate in a coordinated manner. Telomeres apparently also play a role in regulating this proliferation. A deregulation, even if not leading to cancer, is surely to be disadvantageous.

Finally, another widely acknowledge factor of aging, the oxidative stress, would not be addressed by this at all.

Equally sad is that a professor would be willing or compelled to let this slide. That person either isn't doing their job properly, or isn't being allowed to. The mention of faculty-wide rules indicates that at least some of this attitude is being dictated from above. Institutionalized lowering of the bar to keep allowing one to continue to declare "success" is disheartening.

Apparently it goes all the way up. The faculties get money in dependence on the amount of students. A professor fears that his reputation might suffer if his students get bad marks (although most profs are not that much directly involved in training students, at least not in direct lab-work). The guy in my case is even worse as he is not a full prof yet (tenure track). They fear that if students with bad marks leave his lab, he won't get enough to achieve full tenure.

And of course in the end the good students get to suffer. At the moment I am I have resolved to exclusively grade lab-performance as well as the ability to discuss their research with me (discussion with the PI doesn't help as he likes to make monologues instead). But unfortunately I have to do my own research as my position atm is limited, and as everyone has to get the same marks anyway...

Unfortunately this puts me under great stress as I really dislike this kind of injustice.

Just wanted to add that they are indeed stretch sensitive ion channels. AFAIK the precise mechanism of the way these channels react to the stretch is still unknown. There was something else involved by my memory is failing me now.

If you encounter the problem with copying from WP in diploma theses (it doesn´t clearly come out of your OP) then I think something is really going wrong with your supervision.

Well, if I didn't know it. However, they were not direct copies, but rather summaries of certain articles. I only found out because there were misconceptions similar to wikipedia articles and I subsequently queried them about it. I am still at a loss how to deal with that. I told them that they had to read original articles and provided some to them (and textbooks). But apparently they didn't read it.

So far I had only two instances of a direct copy/paste from wikipedia or a "Google" source and another one from a phD thesis. The latter one was in another ("non-elite") institute and the person in question got reprimanded. Here, at the moment I have to let it slip. In fact, I was told to rewrite the passage in question. Moreover, for tests there has been a new faculty-wide rule that the best test in any exam is supposed to count as 100% and any rating >=50% from that is supposed to be a pass.

And I have to add another thing, I have a few very good students, who feel being treated unfair, as they put much more work into it. In one on one discussion I explained the situation and most understood it. Yet, the overall mood in the lab is getting worse.

But then I might be leaving to another University soonish, anyway...

Well, there are few, but labs (or universities, or research institutes...) are usually hierarchically organized. Thus, if the group leader decides that he wants as many students graduating with an A there is not much you can do as a subordinate.

p-hydroxymercuribenzoate attacks unspecifically the thiol groups and is therefore a non-competitive inhibitor. This is also reflected by the fact that it is an inhibitor of a fairly large number of enzymes.

In case it wasn't a drone othe possibilities include dehydration (esp. in hot weather), malnourishment, or even disease. As insects have a comparatively simple body it can take a long time for them to die.

There are a lot of conjugates that one can use, with different advantages and disadvantages (e.g. dependent on application, throughput, detector and of course, price).

HRP is horseradish peroxidase and is used for enzymatic assays as compared to fluorescent dye conjugates.

Actually it is funny, as I was lamenting the use of wikipedia only recently.

Anyways, if the review is not enough and you got a decent library in your vicinity I'd pick up e.g. medical text books on inheritable diseases. Most of them are well written and well illustrated.

Ouch. Freethinker and fredrik already mentioned this but:

DNA is not entirely composed of amino acids. I know that for sure.

DNA is composed of something entirely different (desoxyribose+sugar) than amino acids. Period. Stating anything else is severely misleading.

What might be a bit confusing is that most of the effectors in a cell are proteins which in turn consist of peptide bound amino acids, but this has already been mentioned. Of course there are few other structural components necessary for enzymatic reactions, most notably rRNAs (which again are nucleic acids and not amino acids).

Just as a clarification:

However, tRNA tends to make the proteins by chaining and linking amino acids.

This is not correct. The tRNA only transports the amino acids to the ribosome (in which the "linking" occurs) and is responsible (via its anti codon) for the correct coupling of the genetic code.

At the same time I can understand students who use it within a college setting because everything is rushed...around mid-term things get chaotic...you got 6 classes and you have to write 10 papers...tests...presentations...

OK, this is understandable. Unfortunately much of the system is directed at short term lerning. It was a little bit better in Germany, when there was no Bachelor system. Now not anymore. Overall a good point though, as it could be that less students are actually interested in my particular field and thus deliver rush works. Judging from colleagues comments my described effect is a rather broad one, though. This should not apply to diploma and phd students, though, of course.

As far as your concerned, I wouldn't worry. A person who takes short-cuts will never benefit in the long run, People that take the time to do it correctly will come out with alot more, it will show.

Actually that is my concern. In academia it can take very long before it shows (if at all). If I gave all the students the same marks they will have equal chances of getting a phD position. There it might show, but by then it is far too late as it is very uncommon to fire a phD student.

Unfortunately the way students are graded are subject to not little amount of politics ins some cases.

Actually for simple taxonomy one usually do not use the whole genome. In fact this is atm still a bit limited for most eukaryotes and even not that common for prokarytes.

For taxonomic purposes it usally only takes a good marker that is very conseverd. Depending on application one often uses ribosomal genes or markers on mitochondria etc.

One possibility is thus to isolate your DNA, amplify conserved regions of the marker with pcr and sequence the products.

The chemicals are expensive but affordable, the most expensive stuff is the thermo-cycler (usually ~5k$ and up) for the PCR. Databases are available as well as free software for tree building. You usually need somewhat related sequences, though.

Yup that's precisely the reason. The seemingly missing neighbours are nothing more than the reverse complement of the given ones and read from the opposite strands they are identical to one of the "primary" ten neighbours.

Just as a preface: I do not intend to make a technology rant here, nor do I intend to succumb to

the old "in the olden times everything was better" notions. In addition, I think there was already a similar thread somewhere but

I could not dig it up. What I'd like to have is some input in the following thoughts:

Background:

At the moment I (still) work as a postdoc but due to various reasons I have a slightly higher than average workload regarding to creating and supervising both, theoretical and practical courses.

Due to the nature of the topics I teach, the practical courses alone are usually not a sufficient indicator of understanding the topic, thus I usually let the students present their results either as a talk, or a written report.

In addition I train students during their diploma or phD thesis in all aspects, but as I am not a full professor I am not allowed to directly grant titles or marks.

I am doing this for six to seven years now and I found that in a number of areas the quality of the test results, reports or diploma theses (only slightly in phD theses) appears to be detoriating. This is not a pure subjective feeling as the achieved marks were in deed detoriating over the las five years.

What I found in my tests is that the questions that require to give the correct "catchwords" and definitions were as good as five years ago, but those that require understandingwere lousy.

Identical tests that I gave five years ago scored consistenty better than today. I assume that a lot of parameteres are likely to be involved in this, however

in recent reports and theses I found that quite a lot of the information within was almost exclusively gathered by online sources like wikipedia.

While wikipedia (and encyclopedia in general) might be a good way to start or to get a rough overview but are certainly not sufficient to get in depth informations to write

good reports or even theses. The way theses sources are used range between pure copy/paste, slight rephrasings or summarizing it. These passages are often easily detected as they are often unconnected to their own work.While I often emphasize in the courses that this is not acceptable I found that less and less people are prepared to go to the library and check out original sources/journals. This is reflected in the reduced time students are spending on gathering information for the reports.

Earlier a good report took around one week, now I sometimes get some the next day. I am not saying that having to spend a lot of time to gather some information is a good thing (which is clearly not), but the accessability of online sources ( simply putting in key words into the google bar, or in wikipedia) apparently reduces the willingless of students to actually search for original literature or even reading textbooks in some depths.

In the beginning students came up with questions to papers they found, but now I get zero requests. After private questioning some students confessed that they feel inferior to their peers. It is their impression that everythin worth knowing is in the internet and being forced to ask ones mentor is perceived as a loss of face.

I started actually providing all papers in hard copy in the courses (something that I did earlier only in a limited fashion or for not easy available papers. I was told flat in the face that reading those was too much work and I again receive Wiki-like reports.

Now, I always held the belief that the internet would be a fascinating tool especially for students. At least I know that if the web (especially science resources and tools) was as available as now, I would not have been forced to waste that much time on the photocopier, or searching for articles in vain.

This overall situtation bothers me also because I cannot really sanction those that copy/paste their reports or even theses. The group leader is more interested in having as many students as possible (to improve his rankings) and I was told to let it happen. However, I find this very unfair to those that really do the work.

Now I wanted to ask the people here, both students and mentors, how you perceive this. Who else has similar (or differing) experiences, am I making too much of a fuss about it?

Maybe for clarification: a diploma is similar to a Master's degree and involves around 6-9 months of lab work (in theory conducting own experiments) and then writing the actual thesis.

Like trying to wipe puke in 0 g?

, if you are working in a scientist's lab, what would be your typical activities

Depends on your position (e.g. phD student, postdoc, PI, Prof, etc.) on your work ethics. In many labs your are free to setup your day (or nightwork) as it pleases you. Common to most labs are group meetings in which one should discuss ones results and, depending on your position and the institution you have to attend/give lectures and courses.

If I don't have teaching obligations I usually go to work in the mornig (~8:30 am) and start off with reading a couple of papers to stay informed (~30-90 minutes). After that its working in the lab or at the computer, usually according to some rough planning done the night before, 45 mins lunch some time after 1 pm and continue working until usually 9-10 pm, cleaning up and going home). This is interrupted by around 3 5 minutes breaks. No breaks while working on the computer, of course.

In addition this is frequently interrupted for tutoring master and phD students.

Overall, one migth agree that there is nothing like typical activities in the lab (unless in very specialized ones).