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Scoring matrices (BLOSUM & PAM) in BLAST and other sequence-comparison programs
The Wikipedia page on BLAST states that:

The scores are created by comparing the word in the list in step 2* with all the 3-letter words. By using the scoring matrix (substitution matrix) to score the comparison of each residue pair, there are 203 possible match scores for a 3-letter word. For example, the score obtained by comparing PQG with PEG and PQA is 15 and 12, respectively with the BLOSUM62 weighting scheme.

I do not understand how they got a score of 15 for PQG v. PEG. What is a scoring matrix, how is it computed, and how is it used?

Step 2 on that page is Make a k-letter word list of the query sequence: “Take k=3 for example, we list the words of length 3 in the query protein sequence (k is usually 11 for a DNA sequence) sequentially, until the last letter of the query sequence is included”.

Hi Vandana - thanks for your question and Welcome to BiologySE! You may want to add some links to your question so that everyone can follow. The more descriptive you can be with the question the better the answer you may get from the community.

This has got nothing to do with BLAST per se. Read about BLOSUM and PAM matrices.

The two most common families of scoring matrices are BLOSUM and PAM. Each of them has a score for every possible alignment combination between the 20 standard amino acids1. They both do more or less the same job but have been derived using different approaches.
BLOSUM matrices

(image taken from Wikipedia)
The BLOSUM matrices are built from actual alignments between very conserved regions of protein families. The score for a given pair of amino acids aligning with each other is the log-odds score measuring how often this particular alignment is found and how often it would be expected to be found by chance:
$$ S_{ij} = \left ( \frac{1}{\lambda} \right ) \left ( \frac{p_{ij}}{q_i * q_j} \right )$$
Where $p_{ij}$ is the probability of finding the two amino acids $i$ and $j$ aligned to each other in a homologous sequence and $q_i$ and $q_j$ the background probability of finding the amino acids $i$ and $j$ in any protein sequence. The $\lambda$ is a scaling factor set to ensure that the matrix contains easily computable integer values.
In simple words, the BLOSUM matrices give you a score based on how often the alignment you observe in your sequences is found in alignments of similar sequences.
There are several BLOSUM matrices which have been computed using proteins of more or less sequence similarity. The most commonly used one is BLOSUM62 which was built using alignments between proteins of $\ge 62\%$ sequence identity. This is a nice middle ground and will do for most cases. If you are comparing proteins that are very closely related, you might want to use a matrix based on more similar sequences such as BLOSUM90 (built from sequences with $\ge 90\%$ sequence sequence identity) and for less conserved proteins, you might use something like BLOSUM45 ($\ge45\%$ sequence identity).
PAM matrices
The PAM matrices are built using a different approach. First, a global alignment (as opposed to the local ones used in BLOSUM) of of a set of sequences sharing 85% sequence identity is computed. Next, a score for the alignment of all possible pairs of amino acids is calculated based on its observed frequency in the aligned proteins. Then, the scores are extrapolated to alignments of different sequence similarity using mathematical tools. The PAM matrices assume a model of protein evolution and score the alignments based on that model.
The PAM-I matrix is the only one that was actually built from real alignments. The rest were obtained by  multiplying PAM-I by itself N times. In PAM, unlike in BLOSUM, the higher numbers correspond to greater evolutionary distances between proteins.

With all that in mind, the scoring matrices are used by BLAST to calculate the score of the alignment. You can think of this score as the sum of the scores of each individual pair of aligned amino acids in your BLAST result.
Useful references:

http://statgen.ncsu.edu/st590a/notes/76_ST590A_100509.pdf
https://en.wikipedia.org/wiki/Point_accepted_mutation
https://en.wikipedia.org/wiki/BLOSUM
http://www.ncbi.nlm.nih.gov/pubmed/21356840

1The non-standard amino acids Selenocysteine and Pyrrolysine are not included in any matrix I know of, probably because they are too rare for any reasonable conclusion to be drawn from statistic analyses.

A scoring matrix is used to compute a score for finding identical 3-letter words or similar 3-letter words that takes into account the liklihood of one being related to another. Although these matrices are empirical, they encompass factors like the number of mutations required (which is why there are different matrices for different extents of divergence) chemical/functional similarity, rarity etc. This produces a more accurate measure of relatedness than the naïve alternative of scoring all perfect matches the same and assigning no score to mismatches. Thus, it will allow better choice of the high-scoring segment pairs (HSPs), referred to in the article you cite.
As @WYSIWYG mentioned, such matrices are used generally in programs comparing sequences, not just BLAST, and there are two main matrices in use — the PAM matrix and the  BLOSSUM matrix — each well documented on-line.
Addendum: Blosum matrices
In response to an overlapping question that is likely to be marked as a duplicate I make two further remarks regarding the Blosum matrices.

There is a more extensive mathematical account of the derivation of the Blosum matrices in a set of slides from Columbia University. I suggest that one starts reading from the page starting “Henikoff and Henikfoff(1991)”.
The BLOSUM-45, BLOSUM-62 etc. matrices have been carefully prepared for sets of sequences with characteristics required by the approach. All one needs to do is decide which one is most appropriate to the sequences one is comparing — for example a higher number will be more appropriate for ‘mammalian v. mammalian’ than for ‘mammalian v. bacterial’. However in multiple sequence alignment (MSA) a position-specific dynamic scoring matrix is often used: after each sequence is aligned, the matrix is recalculated to take into account the actual matching pattern observed at each position. See, for example, this paper by Panchenko and Bryant.


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Full Sequence for Plasmid pMG101
I am trying to find the full plasmid sequence for pMG101. I have been looking through other papers that have sequenced this plasmid. The GenBank access numbers I got are the following: AY009372–AY009396, ASRI00000000. However, when I go on genbank it gives me a result saying it is not there..... I am stuck and not sure how I am suppose to find this full plasmid sequence. Does anyone know another way to find it?

Here it is: http://www.ncbi.nlm.nih.gov/nuccore/4206623?report=graph
This is the same plasmid as in E. Coli J53. This is the newest sequence.

Looks as if you'll have to do some reconstruction work building the full sequence from the information here and elsewhere in this paper:

Nucleotide sequence accession numbers.The DDBJ/EMBL/GenBank accession numbers for the sequences reported in this paper are AB031076(the SalI-XhoI 3.0-kb fragment of pMG101), D84187(rDNA for strain S55), D86354 (rDNA for USDA 4362), D86355 (rDNA for USDA 4377), AB031077 (plasmid pMG103), and AB031078 (plasmid pMG105).

--Sequence Analysis of the Cryptic Plasmid pMG101 from Rhodopseudomonas palustris and Construction of Stable Cloning Vectors

See I do not need the whole sequence, I just need the SilR SilS and SilE, but not as an individual protein, but all together. Also what do you mean my reconstruction work, like I need to sequence it again, or need to start putting the plasmid together based off of already sequenced parts?

Just from a quick skim of the paper, it seems like the information you need is all there, you just have to piece it together.

So I found this: http://www.ncbi.nlm.nih.gov/nuccore/AF067954.1. This is the part of the plasmid I am looking for, however, this plasmid pMG101 was not isolated from the same bacterial strain that I am using. I am going to be doing primer design, does this matter?

We have no way of telling.  Primers are cheap; if you have good controls downstream, consider making the primers and seeing if they work.

I just found out it is the same sequence. E. Coli J53's plasmid was derived from this bacterial plasmid.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


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Kinases that are ATP-sensitive at physiological conditions?
Phosphorylation is an ATP-dependent process performed by kinases. At physiological conditions it is generally assumed that ATP concentration is high enough so that ATP is not a limiting factor. Therefore the phosphorylation rate is independent of ATP concentration variations. At least this is the case in the examples I came across.
Are there known counterexample? A kinase that is sensitive to ATP concentration at physiological conditions?

Yes - AMP-activated protein kinase - or better known as AMPK. This kinase is sensitive to the ATP to AMP ratio with himself – search pubmed for any review on ANP kinase and you'll find more information.

Great, thanks! I would like to get other examples, I searched the literature with the keywords "ATP-sensitive kinase", or "ATP-regulated kinase" but couldn't find any. Maybe there are better keywords?

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


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How does mad cow disease evade immune system?
The mad cow disease is caused by prions right?
So how do prions avoid white blood cells and antibodies?

where have you looked for answers on this question? there is a lot of information that is easily accessible on the net.

Your question is a bit broad. There are many review articles written on prion infection and transmission. You can have a look at those and narrow down your question a little.

Prions are proteins that we produced but that are misfolded and affect the folding of other proteins. As we produce these proteins, we don't recognize them as antigens. If we were to recognize our own proteins as antigens, then the immune system would constantly be fighting against ourselves. This is what is called a autoimmune disease.
While this was a simple explanation, the reality on how the immune system interact with prions might be a little more complicated. Bradford and Mabbot (2012) might be a good place to start for further learning

Oh wait, i didn't mean how it avoids antigens. i meant how it avoids antibodies :P lol srry

I did not even notice the typo. It is fine, just edit your post to fix it.

thx :) but does antibodies and white blood cells ignore them in the same way?

antibodies are created kinda randomly and are retained only if they fail to match molecules from the body. Given that prions are produced by the body, any antibody that recognize the prion as an antigen will not be retained. (note btw, I am not an immunologist)

If you think I answered your question, then you can click on the checkmark. You might eventually want to wait for more answers and more peer-reviewing though.


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Plant cell question in age 12 science test
Can anyone help me answer the questions in the attachment about plant cells. It was a question in my 12 year olds science exam. I'm baffled as I think he has given a good knowledgable answer but it wasn't awarded a mark.
Kind Regards
Matthew

From a picture like this one cannot actually say whether "part-A" is a mitochondria or chloroplast. That could even be some random vesicles or, to think even crazier, assembling viruses.
The question is really bad and the kid isn't really incorrect. Mitochondria as a guess is pretty reasonable too. However, the second answer is incorrect. I don't know what the kid wants to imply by "to absorb photosynthesis"; it is unclear to me.

Hi You've confirmed what I thought but added even more to my knowledge regarding what part A represents. I'm not qualified in biology/teaching in any way but its disappointing when marks get dropped due to bad questions. Personally I think it deserved 1 mark out of 2. The kid wrote the part in green ink as they went over the questions after the teacher has marked the exam. There are some dodgy question s in this test which I'll be posting over the next few days/weeks and definitely appreciate your help. Before my kid goes back to school I'll review them all with him to reinforce his knowledge.

@MasterSQL  perhaps the kid deserved 1mark but don't get disappointed by such frivolous things. Happens all the time. Worry if this is consistent. I had read the entire cell biology book but I got a C grade because the teacher wanted me to match his way of thinking. I think this community, overall, doesn't appreciate a lot of questions like this. These are not of great use to others and doesn't fit very well with the scope and aim of the site. However, if you think the course content and the exams are not good then you can have a talk with the teacher or the principal or whoever is in charge.

Sorry to confuse here - I'm the dad but the test was done by my 12 year old :) I was hopeless at Biology at school but kids today tend to get a lot more support and do better (if their parents help them even if they don't like it - lol). I won't be going up to challenge the science teacher or anything like that - its partly for my own curiosity and to help my son out really.

@MasterSQL Not a problem. I was the one who got confused. However, I want to emphasize again that in this site we don't appreciate a lot of "is this book/exam assessment correct" sort of questions because they are not generally useful to the general public. You can, however, reword such questions such that it is about a scientific query, supported with some research from your side.


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What are "+" and "Ar" in consensus binding sequence of amino acids?
So I was reading this paper and found a figure as below:

I understand that [LEAM] means any of LEAM residues, pS is phosphoserine and X means any amino acid residue.
What is [+] here ? Is both R and Ar arginine itself?

Ar means aromatic and + means positively charged residues. However, this is not a standard code (as of now).
From the same paper:

Sequences closely matching these optimal binding motifs, R-X-[Ar/S]-[+]-pS-[LEAM]-P and R-[S/Ar]-[+]-pS-[LEAM]-P, denoted as mode 1 and mode 2 consensus sequences, were found to be present in many known 14-3-3 ligands ( Yaffe et al. 1997), where Ar denotes aromatic residues and + denotes basic residues.

From the mention of “aromatic residues” in the figure legend (in a different context) I assume Ar stands for aromatic residues. Ar is certainly not an abbreviation for arginine.
I would guess that [H/+] means either histidine or any positively-charged residue.
I think that the authors of the paper should have pointed this out in the figure legend, and that the referees should have insisted on it.


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Plant cell question in age 12 science test Part II
I'm a parent and I think the teacher had been a bit harsh with marking most of these questions but can someone help me answer the very last question on the paper please (where someone has written SP against it). Is the answer mitochondria?

As I already mentioned in the other post, questions like this are not generally useful for others because it is not really about a scientific query. The annotations/diagrams are not from a well known book/journal or other such published sources and therefore it is more about having an understanding with the teacher. Moreover, this would be considered a "homework" as per our site standards and such questions are expected to have some research effort from the asker.

what did the teacher say the answer was?

HI WYSIWYG I wasn't ignoring you - I didn't see your previous posts in time - I was too busy writing this one out :) But I won't post any more like this now - if anything I might post a question if I've tried many other avenues first together showing where I've checked.

To Vance I don't know as it was part of a test as I don't think the teacher went over all the answers.

No problem. You can even use the chat if you have quick questions.

I would grade alike. The subject might be considered advanced for 12 years old (I would assume the teacher is respecting the program) but the answers that are counted as wrong are quite obviously wrong.

The question is off-topic here as it is not about science but about teaching. If you happen to have doubts on how to deal with how the grade affects your kid, you might want to ask a question on parenting.SE.

I will decide what is off topic as I posted the original question I had trouble with.

The community decides what is off topic, not you @masterSQL

Or you either !!  Am I not the community as well then? Or does my opinion count for less or something?

@MasterSQL rg255 is right. You get to decided what is on topic in so much as you can post whatever you feel like posting. Higher rep users can go through questions and nominate questions for closing due to being off topic. If enough nominations are made, the question is closed (This is what rg255 means when they say "the community decides").

So, to go through the question in total:
(a) Part A nucleus is correct, but Part B ist the cytosol/cytoplasm, as the line does not stop at the border, but goes through it and ends in the gray part of the cell.
(b) For part C, it is the same problem as in your first question. Yes, the picture may be a plant cell, however, upon this drawing one cannot differentiate a mitochondrium from a chloroplast. In my opinion, a good teacher should have marked this answer as correct, even if he/she wanted to hear the other possibility. Part D is correct.
(c) 'Photosynthesis takes place here': Photosynthesis takes place in the chloroplasts. Mitochondria would have been correct, if the teacher would have asked for the respiratory chain or for the often in school simplified powerhouses of the cell.
'Many of the cell's chemical reactions take place here': I think, the teacher wanted to hear the cytosol as answer.

Hi SeRe I very appreciate your answer, thank you. I think if the very last question had said 'Jelly-like material surrounding the nucleus of a cell; chemical reactions take place here' then it would have given the pupils a better clue so yes the answer is cytoplasm. Thanks again.


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The mechanism of cancer metastasis
Generally, EMT, Epithelial to Mesenchymal Transition is thought to be involved in the mechanism in which cancer cells metastasize in the early stage. EMT is an process in which epithelial cells depolarize and lose their cell-to-cell contacts, and gain mesenchymal morphology. The mesenchymal cells is capable of reaching distant sites through the blood vessels. So, EMT is thought to be a necessary mechanism for metastasis.
However, I found a surprising report from Nature article indicating that EMT isn't required for metastasis:
Fischer, Kari R. et al. "EMT Is Not Required for Lung Metastasis but Contributes to Chemoresistance." Nature 527.7579 (2015): 472–476.
They established an EMT lineage-tracing system in mice with the mammary tumors to monitor metastasis of the epithelial cancer cells to lung through EMT using epithelial-specific and mesenchymal-specific markers. This report showed that a small proportion of cancer cells underwent EMT and lung metastasis mainly consisted of epithelial cells which didn't undergo EMT.
I think this report is innovative and overthrows the commonly accepted thought that EMT is necessary for metastasis,
However, some questions come to me.
How the epithelial cancer cells gain the motility and metastasize without undergoing EMT？

This is an extremely broad question – there are several new theories on cancer metastasis even within the last few years. Do you think you could narrow your question down a bit to ask about one specific question about cancer metastasis? For example, like why do certain cancers metastasize to a particular tissue – that's still broad but much less broad than your current question.

I don't know much the mechanisms of cancer metastasis. All I know about it is EMT. I think epithelial cancer cells can't metastasize because they contact with the basement membrane and are lacking in the motility. So, what I want to know is why epithelial cancer cells can metastasize keeping their epithelial morphology.

It might be possible due to certain exosome secretions that prepare "pre-metastatic" locations in lung tissue.

I don't know an exosome is involved in the mechanism of the cancer metastasis !! However, do the exosome secretions have to do with getting the motility of the epithelial cancer cells？

This paper describes the mechanism for a different cancer metastasis: http://www.nature.com/nm/journal/v18/n6/abs/nm.2753.html

Basically, the secreted exosomes reach certain locations and cause the tissue to become more of a "tumor fostering" microenvironment.


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Why our bees might have suddenly disappeared
We have a large garden in Bedfordshire, UK, next to woods and to arable fields currently planted with intensively farmed rape. We usually have many bees in the garden. Earlier this year, things were humming along as usual. A cotoneaster bush in flower had perhaps a hundred bees on it at once, of at least 6 different species.
Now, in July, we have lavender and clover in full bloom, normally swarming with bees. But, not now. This morning (overcast and warm) there were two bees on a lavender bush covering two square metres. I can walk for minutes in the garden without seeing a single bee. The leafcutter bees have left no holes in our rose leaves this year.
The nearest managed hives are about 800m away. It's not just a managed hive that has gone, the bumblebees that nest in our garden have gone too.
The rape flowers are long past. I don't know what might have been sprayed on the rape.  Our garden is organic.
Wasps are down too. This is the first year in the last twenty that there are no wasp nests in our outbuildings. There are, however, plenty of flies.
What might have caused such a sudden and unusual population change? Among multiple species of bee from multiple sources, between April and July?
Could it be our globally-warmed weather? June and July have been wetter and warmer than usual, although not exceptionally so.
Are UK farmers allowed to use an insecticide on rape that could kill most bees?
Or is a dramatic in-year population change in bees a routine, if uncommon, event?
Thanks!
Update August 17 2016
Our garden bees do seem to be gradually recovering - nothing like most years, but a few bees are coming back. Other nearby houses, at least 400m from the nearest rape field, have plenty of bees.

Welcome to BiologySE - thanks for your question... though I think there could be numerous reasons and it may be very difficult to answer in this format. Do you have any specific ideas that someone could address in an answer?

This does seem to be a global phenomenon. In Poland, I was recently surprised to find a beekeeper travel across half the country to pick up a colony from a tree in an orchard. Said there were very few this year. I'd say I've observed fewer yellowjackets, too, but I could be mistaken. See Remi.b's answer about CCD.

relevant article in today's PloS Pathogens, oddly enough: http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1005757

We call it Colony Collapse Disorder (CCD).
Consequences
The phenomenon is observed worldwide and is pretty serious. Northern Ireland lost 50% of its beehives for example. Between 1997 and 2003, 10 millions beehives were lost. Many cultivated crops are pollinated by bees and we don't quite have an alternative today. In 2005 a study showed that the worth of crops that are pollinated by bees is around 200 billions dollars.
Causes
Why? The short answer is "we don't know". There are a number of possible factors and the general consensus is to think that there is not a single factor that is causing the decline but it is a combination of different factors. Possible factors include:

Pesticides
Pathogens
Fungicides
Antibiotics
Miticides
Climate Change
migratory beekeeping
loss of genetic diversity through too intense selective breeeding
malnutrition
parasitic phlorid fly

More information
The wikipedia article for CCD is very complete. You should have a look at it!

I'm familiar with CCD, but can that affect all species of bees, multiple swarms of multiple species, in a small area, from a healthy population in spring to a low population in summer? Plus, I'm guessing that the population has dropped to a few percent of its usual value. Wouldn't that be extreme for CCD?

The first reference cited by the Wikipedia page (http://dx.doi.org/10.1371/journal.pbio.0050168) is a very accessible (though now slightly outdated) review of possible explanations for CCD. PloS Biology Unsolved Mysteries are a really interesting article format and mostly quite readable, even if you don't normally read primary scientific papers (and of course are all open access!).

Insecticides in the form of neonicotinoids (and possibly similar substances) can certainly be a factor, and they can affect a wide range of pollinating insects. It is also commonly used on rape seed. Have a look at this paper for some background:
Rundlöf et al. 2015. Seed coating with a neonicotinoid insecticide negatively affects wild bees. Nature (written partly by people from my department).
In it, they report that honey bees, solitary wild bees and bumble bees all are negatively effected by neonicotinoid-treated fields nearby, using paired fields in replicated landscapes. The effects could be seen in both population density, colony growth and reproductive success.
Much more has been written about this (check out references in paper above), and sorry for the short answer, but I don't have time for more at the moment. Other factors (weather, natural fluctuations etc) are certainly relevant as well. Also, from what I know, there is a neonicotinoid moratorium in the EU, so this might not be an issue where you live. I don't know if the ban is absolute, and to what extent it is enforced.

It's going to be hard to prove anything, but I am leaning towards this conclusion. These links: Independent, Nature show that neonicotinoids on rape are particularly harmful. Spraying this year seems to be illegal, but, who knows? Local bees about 800m distant from the nearest rape fields seem to be OK.

The causes are multi factorial. Sick bees usually leave the hive and this behaviour may explain some cases of CCD, where a small number of bees and the queen are found with all other colony members missing. A colony can also leave "en masse" if they are about to starve in a last resort to find better forage. Pollinators are no longer able to adapt rapidly to the numerous threats facing them in 2017.
The human activities listed in previous posts have caused the massive decline in all pollinators. Monoculture and pesticide useage being the main contributory factors. As a child I recall many dead insect on the car windscreen on weekend car journeys, this is a rare today.

as before - can you add some references so that others can read more about your answer and this topic in general?


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How are some people able to continue growing after reaching maturity?
This is technically a cross-post of a question posted last year concerning gigantism and how certain people are able to grow far past expectations after it's assumed they've reached maturity.
How are some people still able to grow after reaching adulthood? Someone gave the answer in the old post that epiphyseal growth plate closure is caused by testosterone and not growth hormones. Is it a lack of testosterone, or an excess of testosterone? If it's a lack, why are women usually shorter than men and stop growing sooner? If it's an excess, does that mean basketball players produce less testosterone than average height people?
There are a number of cases of pituitary gigantism out there, but these are the best examples of what I'm asking:

Väinö Myllyrinne was 2.22m at the age of 21 but is described as having "experienced a second phase of growth in his late thirties", attaining a height of 2.51m by the time of his death at 54.
Adam Rainer at the age of 18, he was only 1.22m. However, he had a growth spurt in his 20's, reaching a height of 2.18m at the age of 30 and 2.34m by the time of his death at age 49.

What could have caused these men to grow so much after modern medicine tells us our growth plates have closed? Is there a possibility of replicating their late growth for people who suffer from hereditary short stature or other growth-related problems? And would it be safe?
EDIT: Although my question is different in many ways, here is the original question.

Please [edit] your question and provide a link to the question you referenced in your first paragraph. Additionally, please provide links to verify the details you claimed about the two men in your post, preferably to reputable/scientific sources if possible.

Edited with information.

Usually the cause is 'acromegaly' but there are numerous possible causes.
It is impossible to start growing in length after your bones have matured too much. This is because of the 'Epiphyseal plate' this is a anatomical structure in bones that is necessary for length growth in bones and it degenerates at the start of adulthood.
The most common cause, although still not a common disease, for gigantism is acromegalia. It's cause is an abnormally high amount of growth hormone in the body which is most commonly caused by a hormone secreting tumor.
When the onset of this disease happens before the epiphyseal plates have degenerated it can cause them to stay active in which case the patient will continue growing.
Note: When the onset is after the degeneration of the disks it doesn't cause gigantism but it still causes a very recognizable change in appearance and the model for Shrek in the movie suffered from this illness.
Edit: Sorry, I didn't notice your subquestions initially. Yes, another possible cause in men is the lack of testosterone because this hormone is normally responsible for the degeneration of the plates in men.
Edit 2: In women estrogen is the hormone that is responsible for this, which explains why the length of men and women isn't dependent on testosterone in both cases

Please avoid having whole paragraphs bold, this is unpleasent to read and seen as yelling (as whole uppercase). Additionally: Most HTML commands do not work here, use the markup language of this page instead.

Thank you for the tips. How about just making the word edit bold?


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Which magnoliophyta groups are NOT pollinated by bees and why?
Considering the bees as the family Apidae which families of flowering plants are definitely not pollinated by them and what could be the reasons?
-Could you say that the relationship is preserved at the family level?
(Please suppose that both groups live in the same geographic context)

This is an interesting question, but it also sounds like a homework question (and a good one). What research have you done to try to answer it? Can you give us a few examples of why plants might not rely on bees for pollination?

Not a homework question. Actually is part of my PhD research.  I'm looking for putative ecological relations on taxonomic groups that co-occurre in the same place and nearby regions (less than 10km distance). I looked for the families of flowering plants that are always present every time a member of the family Apidae has been found.

The result is a long list of many families. I was wondering if there there is a family that it is very known that is not pollinated by bees (Apidae). That's why I did that question.

This is the list:

Amaryllidaceae
Iridaceae
Hypoxidaceae
Asparagaceae
Orchidaceae
Pontederiaceae
Commelinaceae
Smilacaceae
Melanthiaceae
Liliaceae
Eriocaulaceae
Poaceae
Cyperaceae
Juncaceae
Bromeliaceae
Arecaceae
Hydrocharitaceae
Juncaginaceae

Potamogetonaceae
Alismataceae
Dioscoreaceae
Musaceae
Lythraceae
Onagraceae
Myrtaceae
Melastomataceae
Cannabaceae
Rhamnaceae
Rosaceae
Moraceae
Urticaceae
Magnoliaceae
Zygophyllaceae
Krameriaceae
Begoniaceae
Cucurbitaceae
Resedaceae
Brassicaceae
Caricaceae
Cleomaceae
Piperaceae
Saururaceae
Aristolochiaceae
Simaroubaceae
Rutaceae

Anacardiaceae
Sapindaceae
Burseraceae
Meliaceae
Opiliaceae
Loranthaceae
Santalaceae
Schoepfiaceae
Hydrangeaceae
Cornaceae
Loasaceae
Berberidaceae
Papaveraceae
Ranunculaceae
Menispermaceae
Lauraceae
Convolvulaceae
Solanaceae
Hydroleaceae
Asteraceae
Campanulaceae
Polygalaceae

Fabaceae
Salicaceae
Hypericaceae
Linaceae
Passifloraceae
Euphorbiaceae
Malpighiaceae
Violaceae
Erythroxylaceae
Putranjivaceae
Picrodendraceae
Podostemaceae
Boraginaceae
Rubiaceae
Asclepiadaceae
Gentianaceae
Apocynaceae
Cistaceae
Malvaceae
Bixaceae
Talinaceae
Chenopodiaceae
Polygonaceae
Caryophyllaceae
Plumbaginaceae
Amaranthaceae
Nyctaginaceae
Cactaceae
Phytolaccaceae
Portulacaceae

Sorry! I think I should reformulate my question.. :(

Flowering plants evolved before bees, so clearly in the ~100 million years, they must have been pollinated by other methods. Some plants still retain this ancestral characteristic.
This paper shows a species Magnolia tamaulipana (Magnoliaceae) which is pollinated by beetles.

Thank you for your answer and the source! But, in this case, could you call the feature: "Not pollinated by apids (Apidae)" is an ancestral characteristic?


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Can anyone tell what kind of berry/currant this is?

I found this currant-like plant in Helsinki, Finland. It seems very similar to red currant but it has hairs on its fruits, and the fruits are pear-shaped. Can anyone please identify this plant? Many thanks!

Did you find it growing wild or did it seem cultivated?

@picapica It seemed to be growing wild, next to a street!

I am pretty sure this is a species of Ribes (Grossulariaceae, vernacular Finnish: herukat), and that it is not native to Finland.
I would guess that it might be a variety of R. rubrum L., but it also might be a species unrecorded in Finland so far. You might consider sending the photo to someone at Helsinki Botanical Garden, or at the Natural History Museum. (If you got a twitter account, you might just sent the link to this page to @Raino_Lampinen and ask on his opinion.)

Cool, thanks a lot! I should try out the Twitter :) I'll update it here when I get the answer!


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Why does dehydration lead to low blood pressure
I understand that the two leading causes of death from dehydration is imbalance in electrolytes and loss of blood pressure. I'm trying to understand what role water is playing in these cases and how the loss of it causes these imbalances, focusing for now on the blood pressure angle.
While I understand that blood is made up heavily of water, I'm still a little confused why dehydration so quickly leads to drop in blood pressure.  Why can't the body continue to pump the already existing blood through the body, where is it using the water to keep the blood pressure up and what vital function is no longer being performed that causes that pressure to drop?

Hmm.... So I can imagine, that because of a reduced water level in the blood, it becomes more sticky and is pumped harder through the vessels. This may decrease the blood pressure

May this article helps you, too :)
https://www.reddit.com/r/askscience/comments/31ini6/how_does_dehydration_cause_low_blood_pressure/

The blood pressure is the  exertion of force upon the blood vessels by the blood fluids. Thus having less fluids will results in decreased pressure.


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If we add only 1 primer in PCR
What would happen if we add only one primer, say forward primer, to PCR?
(Image Credits: Wikipedia) As it is clear from the image that we need both forward and reverse primers to get it working (Unless we have a sequence such that a single primer can work as both forward and reverse). I have read online here that including a single primer will result in linear amplification but I think there should be no amplification at all. Can you help me resolve my doubt?

Welcome to Biology Stack Exchange. However you need to do a little more research before asking questions like this one. Guesses are not enough. There are many resources on the web which describe PCR, and if you read them carefully — especially the diagrams — it will be obvious why two primers are needed. This is fundamental. Look at the diagram here, for example.

Hi @David! I have researched online before asking the question and also looked at the link you sent. My apologies as I didn't make it clear. I will edit the question to make it clear.

PCR with a single primer is similar to DNA sequencing, except you don't have labeled terminal monomers to stop the reaction.

I'm not sure why it has been put on hold as off-topic. It is not a question I'm getting grades for. I am not a student anymore. I study biology because of my interest. I was wondering what would happen if there is only one primer and I think theoretically there should be no amplification. I find contradictory views online and just wanted to know if I'm missing something.

I think the following should happen:
There would be no amplification but we will get n copies of single stranded DNA after n cycles and the only double stranded DNA with started with but with a new complementary strand.

Using 1 primer will results in amplifying the original sequence in each cycle in a linear fashion: the primer will guide a single run of the polymerase. In opposed to the "chain reaction" in PCR which is exponential. Therefore, with one primer you linear amplification of say x40 times the original number of molecules you started with, whie with two primers you get exponential (~240) amplification. You right that with one primer, the amplification is neglectable, almost invisible.

I don't think there would be no amplification at all. What will be present after 40 cycles are 40 single stranded DNAs and only one DNA of interest. Can you explain how would there be 40 more molecules?


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Can human be emotionless?
Is it possible that a person can't produce, like, dopamine, serotonin, and other emotion hormones? Or, a part of the brain can't function to make one feel something?

There are diseases, which are linked to suppressed hormone production or loss of the specific receptor. But completely emotionless? I don't think so, as this would mean, that all hormones or receptors are affected.

Yes Schizophrenia  is a disorder in which one suffers from lack of emotion and motivation.They are called negative symptoms.You can google it out

@SanjuktaGhose Even with negative schizophrenia symptoms, there is certainly not a complete lack of emotion, that doesn't seem to be the OPs question.


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What wasp like insect breeds in clay pots with dead spiders?
I found several small clay pots of oval/cigar shape roughly 2cm long in a rarely used window in the house, because a wasp like insect was flying into a small cavity of the window.
I removed one and found dead spiders inside.

I let the rest of the nest alone and closed the window again. I guess I don't have to bother them if they aren't bothering me.
I'm wondering what type of insect is that building such nests? It looked like a cross between a wasp and a hornet.
As far as I know, wasps and hornets build their nests from wood, which gives them a paper like material. This one however is made from soil/dirt.
I'm also not sure if spiders are the only food. But given the street lamps outside, I suspect that spiders are very available and easy to catch.
The region is central Europe.

You might be interested in the answer to my question: https://biology.stackexchange.com/questions/62724/which-organism-built-this-2-cm-long-sandy-tube

They are mud daubers. Rarely sting humans and hunt spiders. Seem like a pretty helpful hornet to me!!

It's some sort of potter wasp/mason wasp (Eumeninae). The spiders are paralyzed and brought there as food for its larvae.
Here is an example of an opened nest I found on Bugguide.net that looks similar to yours:

I don't know if it's possible to say what species it is from the nest.

Please note another family does similar things: the Sceliphron which is also common in Europe (some species are also invasive). After by the pictures and the victimology, I cannot say which type of family/genus/species.

Oh i didn't know their nests were so similar! Since the author of the question saw the animals, and described them as "like a cross between a wasp and a hornet" they should be able to tell of it was a potter wasp or Sceliphron since the latter is much more slender.


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Essential amino acids
Humans and the majority of animal species cannot synthesize essential amino acids (Info: Campbell biology 9th edition). However, meat, eggs, et cetera provide all required essential amino acids. And meat comes from animals.
Main question: So how do these animals we eat get their essential amino acids if they cannot synthesize them either?
My hypothesis: I know they can get it from their diet, but wouldn't it become a never-ending cycle of passing on essential amino acids?
Subquestion if hypothesis is proven: If that is the case, where did these essential amino acids come from?

Bacteria and plants are able to synthesize all amino acids, as they are capable of nitrogen fixation. If animals eat plants, they get the essential amino acids needed for their proteins. Humans get the essential amino acids by eating these animals or directly by consuming plants. So yes, it is a never-ending cycle of passing.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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Difference between pipette and pipettor
I've been translating a text listing some analytical laboratory equipment, and found that some fellow translators translate the Russian word "автоматическая пипетка" (avtomaticheskaya pipetka, which literally means "automatic pipette") as "pipettor".
I consulted the producer's website and found that the proper word for my particular model (thankfully the model code was mentioned) was indeed 'pipette'.
However, in case I come across a Russian 'pipetka' that really means "pipettor", how to distinguish between the two? Maybe the terms are largely synonymous?
Bear with me, I'm not a specialist in this sphere. I googled and found a discussion on Reddit that shed little light for me.

I think, that pipettes are handeled manually and pipettors are electrical like pipetboy and some steppers

In my mind, pipette and pipettor are generally* synonymous in the life sciences. Pipetman, which is actually a trademark, is also commonly used to refer to these instruments.

Gilson UK
That being said, there are some other things that you need to differentiate between. A pipette tip is the (usually plastic) thingy that goes on the end of the pipette, shown in the image above as clear white plastic on the left end. There are also serological pipettes

Argos Tech
and volumetric pipettes

Pro Lab Supply
together also referred to as transfer pipettes. These can be made of plastic or glass, and are used in conjunction with an electrical or mechanical pipettor, or a bulb (not your mouth!). Just to be confusing, sometimes lab personnel will refer to serological pipettes as just pipettes, even though they refer to the things pictured above in image 1 as pipettes as well.
Some people, such as SeRe above, distinguish between pipettes (the first image above) and pipettors, such as those used with serological pipettes:

Drummond
These are also known as Pipet-Aids or by other brand names.

However, in case I come across a Russian 'pipetka' that really means "pipettor", how to distinguish between the two? Maybe the terms are largely synonymous?

So yes, the two terms can be synonymous, so just be consistent, whichever you choose. I would stick with pipette unless it's clear from the text that the authors are transferring larger volumes than 1 ml, in which case they're probably using a pipettor in conjunction with a transfer pipette. If it's unclear, sticking with pipette should be good enough. If your readers are familiar with lab techniques, they'll understand what's going on.

You didn't include volumetric pipettes (similar to the serological (Mohr) pipettes, but only has the one volume mark, and may have a bulb to contain the fluid). https://en.wikipedia.org/wiki/Volumetric_pipette#:~:text=A%20volumetric%20pipette%2C%20bulb%20pipette,a%20fixed%20volume%20of%20liquid.

@LDC3 you are correct. Please see my edit above.

I look at the difference as being whether you are referring to the actual vessel that holds the fluid (the pipette no matter what its size) versus the pipettor, a device that allows for suction of air to draw liquid into the vessel (the pipette).
Pipet tips come into play when referring to very small volumes to be drawn into the vessel, but the device is still a pipettor or a micropipettor. Before real lab safety came along the human mouth was often the suction device, or the pipettor! We have tried to clarify this also for student lab manuals.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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Can 3% hydrogen peroxide be used as effective disinfectant and antiseptic?
I was curious to see whether 3% hydrogen peroxide can be used as antimicrobial and virucidal product for daily use in home. There are  several disinfecting products in the market claim that use of these wipes for some minutes can disinfect the hard surface. Also, there are quite a few ethyl alcohol based hand sanitizers. Can 3% hydrogen peroxide be used as effective disinfectant and antiseptic - similar efficacy with those of the commercial disinfecting products?
Website https://www.cdc.gov/hicpac/Disinfection_Sterilization/7_0formaldehyde.html discuss use of hydrogen peroxide against a wide range of pathogens. I found that the bottle of 3% hydrogen peroxide lists it as  antiseptic - to use for gargle etc. Can 3% hydrogen peroxide be used as a disinfectant for a broad spectrum of microbes?

Nope. Some microbes express high levels of catalase, in which case 3% HOOH does nothing to them.

If you need to disinfect regularly for medical reasons, it would be best to consult with your medical doctor. If there is no specific medical reason, and you are not particularly exposed to pathogens, the information of the "center of disease control and prevention", of the US government, which you refer to (and contains a detailed answer to your question) is more trustworthy than companies that have large budgets for advertisement to pull the money out of your pockets, with sub-perfect products, and with scaring people. If you are exposed to pathogens at work, consult your bio-safety officer.


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Why do people sing?
I was wondering the why people sing, but from a biological point of view.
Is it necessary for our body? If it is so, then why can't everyone sing well?
Is it in direct relation with neurotransmitter secretion, like the adrenaline? Or is it only a way to express our emotions?

is singing necessary for our bodies, No, but then neither is sex or making tools, That does not mean there is not an evolutionary advantage to doing them.

Nice question, I'll answer it in parts:

Is it necessary for our body?

Well, there can be many perspectives for why humans like singing. Let's talk about the evolutionary perspective first. I found three theories about why singing was evolutionarily beneficial for humans.

The Shakespearean theory, that music is at least one of the foods of love, has a strong claim to be true. The more mellifluous the singer, the more dexterous the harpist, the more mates he attracts. In simple words, whom would you like to marry: a singer + hunter or just a hunter?
A second idea that is widely touted is that music binds groups of people together. The resulting solidarity, its supporters suggest, might have helped bands of early humans to thrive at the expense of those that were less musical.
The third hypothesis, however, is that music is a cross between an accident and an invention. It is an accident because it is the consequence of abilities that evolved for other purposes. And it is an invention because, having thus come into existence, people have bent it to their will and made something they like from it.

Anither perspective is the biological one. According to a Chicago Tribune article people who sing live longer than those who do not. Why? Singing stimulates better blood flow by increasing the efficiency of chest wall muscles in air exchange. Whenever you'd have tried to sing a nice song, you must have felt that you need to regulate your breathing in order to get nice tones. At one moment, have a huge breath-in, and the very next moment, release it slowly. All these help in increasing blood flow and thus, if you keep singing when you grow old, you would live longer!

If it is so, then why isn't everyone able to sing?

This has a very simple answer. The element that makes people sing poorly is problems with pitch accuracy, which is also called intonation. (Pitch can be understood as the ‘sharpness’ of a voice; female voices are typically higher pitched than male voices.)
Why Does This Happen?
It all comes down to those tricky activities of the brain. The problem with the brain lies in not being able to adjust its activities against a particular target (which, in this case, is a particular tone). That may be a bit confusing, so let’s break it down a little further.
When you hear a tone, your brain has a perception of its various parameters, such as loudness, pitch, tone and so on. It turns out that human brains are pretty good at perceiving the right tone, which means that the possibility of an error in our brain’s perception of the tone is ruled out. Hence, the ‘input’ component in this case is alright; the problem occurs at the ‘output’. After hearing the tone, the brain maps out an output tone to match the one it heard, but sadly, it’s not in tune.
It’s not that you don’t realize when you are singing off-key; ears do register that you’re not quite producing the tone that you intended to, so the vocal cords ask for instructions from the brain. However, the brain still sends the same instructions, and you simply can’t get the tone right. It’s almost as though the vocal cords have locked themselves in a particular position to produce the same erroneous tone every time, even after knowing better!
source

Is it in direct relation with neurotransmitter secretion like adrenaline?

Let me clear out some things here first. First of all, adrenaline is not a neurotransmitter, its a hormone (unless you're talking about adrenergic neurons). You can see the differences between neurotransmitters and hormones here.
Second, singing is a complex process and cannot be totally dependent on neurotransmitter (though singing isn't even possible without neurotransmitters!).
Back to the question, serotonin might have an effect on singing. Serotonin is regarded by some researchers as a chemical that is responsible for maintaining mood balance, and that a deficit of serotonin leads to depression. However, its effect on singing is not known yet (at least I can't find a reference for such a study).
EDIT: Another neurotransmitter (which I forgot to mention ;) that plays some (if not all) role here is dopamine. Dopamine is considered as reward and pleasure chemical because it is released in areas of brain (like nucleus accumbens) to give a feeling of reward and pleasure. It has been suggested that dopamine, through the mesocorticolimbic pathway, gives a feeling of pleasure after singing. That is probably why we feel so nice when we hit the perfect tone in a song.

Mesocorticolimbic pathway: a dopaminergic pathway in the brain consisting of the mesolimbic and mesocortical pathways. The mesolimbic dopaminergic pathway originates in the ventral tegmental area (VTA) of the midbrain and connects to the limbic system via the nucleus accumbens (NAc), amygdala, the hippocampus, and medial prefrontal cortex; it plays a critical role in reward related behaviors and reinforcement learning. The closely related mesocortical dopaminergic pathway connects the VTA to the frontal lobes.

References:

Human evolution: why music?
Why do we sing?
Why some people just can't sing well, no matter how hard they try!
Neurotransmitters vs hormones
Serotonin: facts, what does serotonin do?
The neurochemistry of music; Mona Lisa Chanda and Daniel J. Levitin

Adrenaline (epinephrine) is a neurotransmitter. There are many adrenergic neurons.

I thought adrenergic neurons work only on noradrenaline & dopamine. Thanks for telling @WYSIWYG :)


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What might this animal be?
I have found two species of this strange looking animal on the Eastern shore of the Adriatic Sea and I was simply unable to recognise them.

This is probably a gastropod mollusc without (secondarily) shell, a sea slug (https://en.wikipedia.org/wiki/Sea_slug).

This looks like an Aplysia, or "sea hare", a marine gastropod. Some of them sometimes get stranded and look like fat violet/green/brown blobs, around 10cm diameter. In the water, they swim slowly. I've seen some in Brittany (France) and in Algarve (Portugal).

As bli said it is Aplysia more specifically Aplysia fasciata ,commonly called Sooty sea hare.
It is an Atlantic species of gastropod mollusc of the family Aplysiidae.

This sea hare occurs in the Western Atlantic from New Jersey to Brazil, and in the Eastern Atlantic including the Mediterranean and the West African coast.

Picture references:

From: ipaq

From: gbif.org


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How do the chemical components of these spices prevent fungal growth?
I am doing an EE on how spices affect fungal growth for the following spices -
oregano,
garlic,
cinnamon,
cumin and turmeric. Its been hard to find any sites that say why or how they affect fungal growth, as far as I can tell I am pretty sure they affect the Krebs (TCA) cycle and inhibit the production of ATP. It would be great if someone could help me explain why :)

What is the reason for your assumption that the inhibit ATP production?

What is EE? 2. Do you have any data/reference to say that these spices even have an effect on fungi? If you don't prove that first then the "how" makes no sense.

I have seen papers which talk about inhibiting ATP production, and that components of spice ( like curcuminoids and thymols etc ) can do that


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Venom Denaturing with Heat
My friend got stung by a stingray yesterday and the lifeguard quickly stuck her foot into hot water (she said the water burned slightly on contact) and remarkably, she was walking without pain in a hour. I have heard that rattlesnake's bites can be helped by applying heat to denature the proteins. I am assuming this is what happened here, please correct if wrong. Because I am often in areas where immediate help in cases of animal bites/stings is not available, this is important to me as a first response as I get the person to help.

What kinds of venom are susceptible to denaturing by heat? How do I know which the previous categories a given venom falls into?
Is there a rough temperature I should aim for to denature the venom?
How likely is it that I would end up doing more harm by applying heat out of ignorance than doing nothing till I get to help (could be a day or more depending on the location)?

Regarding snake venoms, they tested 28 snake venoms at 100'C: 19/28 of the venoms were still very dangerous after 5 minutes at 100'C.
"Heating all venoms led to the denaturation and loss of some proteins; however, most of the venoms retained a significant number of proteins. Seventeen venoms contained more than seven proteins after heating, whereas five venoms contained only one to three proteins. All but nine of the heated venoms had substantial hemorrhagic activity, and Agkistrodon piscivorus piscivorus venom had very high activity, almost four times that of the second most hemorrhagic venom from Crotalus viridis lutosus."
There is a good chance that land animals have higher heat tolerance spiders and snakes can experience a lot higher heat than marine organisms.
study of marine venoms and hot water says:
Sting ray venom is especially fast to denaturize in heat, and most fish spine venoms are. HWI hot wat immersion is recommended for fish spine stings by some organizations. They did tests to find that box jellyfish, sting rays and other sea creatures stings react significantly to HWI.
They tested that 122/138 marine envenomations were improved by HWI from a variety of surveys.
there are 50,000 marine stings a year from 2000 species and
about 5 million snake bites, 2mn envonomings and 20-125,000 deaths by snakes every year from 400 species out of 3000 species of snakes which are dangerous to humans.
Dangerous snake and spider bites are generally treated in hospital, and the only wise thing to do is not to not make your blood go around your body very fast by being active after a bite, stay calm and alert.

All venoms are proteins and proteins are chemicals whose shape is determined by the amino acids with the sequence of the protein coding gene. Applying UV radiation or heat can denature it by breaking the chemical interactions amongst the side chains inevitably resulting in a protein which cannot refold upon itself as it has been damaged and cannot cause harm.

Please add some references!

Hot water immersion is the best treatment for stings from marine fish, as the above paper says.
However, I  do not see that this paper claims the fish venoms denaturize in heat.
The above mentioned paper states that immersion of the stung part of the body in hot water alleviates the pain, swelling and other symptoms. It does not prove or offer the mechanism of this action.
That being said, venoms comprised of proteins should be more susceptible to denaturation.  The venom of Trachinus draco, dracotoxin has been characterized and it is a single polypeptide. It is also proven that it is sensitive to heat.
But, there is not much research done in fish venoms and not everything is so clear. For instance, from my own experience, I know that Trachinus Draco sting inflicts pain, that is not due to tissue damage alone, but due to some biological mechanism. It is said that this pain can grow so strong, that people far from the coast would sometimes amputate their fingers.
This pain quickly dissapears after immersion in hot water. But, all the research done on the Trachinus draco toxin so far says that this pain is not caused by the dracotoxin itself, but by some other, smaller molecule, that can be dialyzed. Paper from 1962. says it is due to  serotonin, but it remains an open question, particularly because all venom extractions so far were made by dissecting tissue around the venom glands, so it could contain parts not usually injected by the fish.

Welcome to Biology.SE! While anecdotes are potentially interesting, your answer is much more likely to receive a favorable response if you edit it to include supporting references (primary literature is best). ——— You may also want to take the [tour] and then consult the help pages for additional advice on [Answer] effectively on this site. Thanks!


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How specific are CRISPR-cas9 cuts?
CRISPR-cas9 uses a string of RNA that matches with DNA and makes a double stranded cut at that point.
If the RNA is just a few letters in length, the enzyme would cut DNA in many places. It would be unspecific. But if you can make the RNA string very long, it would only cut at the exact place where you want to cut.
So how long can you make the RNA sequences?
And is this enough to avoid unintended cuts?

The gRNA can be anywhere from ~17 to ~27 bases (not including the PAM site), with the average being about 20-23. See here for more info.

The problem of off-targets in CRISPR/Cas is often discussed. It was shown that the system allows mismatches up to five basepairs. For your question, if it is helpful to elongate the gRNA: it was shown that truncating the RNA enhances the specificity more than elongating (see also here).
So what can we do? Well, there are different methods to improve the specificity. The simplest may be the usage of lower dosages of the CRISPR/Cas system. Another method is to use altered PAM motifs.
A more complicated method is to convert the Cas9 into a nickase. In this strategy you would use two different gRNAs for two different target sites and introduce ssbreaks. A modification of this method is to completely knock-out the enzymatic activity of Cas9 and fuse it to a FokI nuclease which will cut the DNA only when it dimerizes.
There are several advantages in these methods, however, you may also loose on-target effects.
There is another method which, in my opinion, is really awesome. It is possible to alter the energetics of the DNA binding site resulting in high-fidelity variants of Cas9 (HF1 and HF2)
So, I hope I could help you. There are other and even more effective ways to increase CRISPR/Cas specificity instead of altering the gRNA. If you're interested, have a look on the references.


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What is the best way to analyze non-quantitative mass spec hits from an immunoprecipitation pull down?
I am studying a nuclear protein and want to come up with a list of potential proteins that it interacts with. From the nuclear fraction of 293T cells, I did an IP (immunoprecipitation) to pull down my protein and submitted whatever I pulled down for a mass spec analysis. I also did an IP with a non-specific antibody as a control. I got a huge list of hits, and I'm not sure how to prioritize them. I can manually remove the hits that also came down with the non-specific antibody, those are obviously just sticky proteins. I looked around Pubmed for ways to prioritize non-quantitative mass spec hits, but I'm not sure if any of them would work in my case. All of them require multiple mass spec repeats - I can do that if I need to, but would like a way to look at my initial data more intelligently.

The title refers to quantitative data but your question seems likely to be describing shotgun proteomics (where peptides are selected for MS/MS based on their intensity) which is not necessarily quantitative. Could you clarify this so that the question can be answered correctly? Also, the facility that has performed the analysis is likely to offer a basic consult on data interpretation.

@Michael_A its suppose to be quantitate. I apologies for the typo.

If they are available, talk to the people who analysed your data. Using their knowledge is intelligent.
I will assume two critical steps are completed. First that your results have been searched correctly. I will also assume that the peptide and protein identifications have been filtered to provide a false discovery rate of 1:100 at each level.
You can remove all the proteins that were identified in your affinity purification control. Another option is to use the Contaminant Repository for Affinity Purification (the CRAPome) which provides a formal framework for removing contaminant proteins. It is a nice resource if your data are compatible.
The remaining proteins are what you have to work with, this is the

list of potential proteins that [your protein] interacts with.

Prioritise these proteins based on the biology of your experimental system. If the list is small work through the function of each protein and assess how it fits with the biology you are researching.
To assess the potential functional links between the proteins you can create an in silico network. Markov clustering can highlight the presence of functionally distinct groups of proteins within a network. String, linked above, can do this. Centrality measures can indicate the presence of proteins with the potential to influence the behaviour of the network.
For larger lists you can also assess the function of the proteins in the list by performing a functional annotation enrichment analysis. There are many other things you could do but the primary goal is to keep biology at the forefront of your efforts.
Finally you mention that repeats are necessary. Analysing the data is time consuming. If this was a test run verify that the test was successful and then run the replicates. Time spent analysing incomplete data can be spent completing the data set or ensuring the right data is collected. Quantitative data can be very useful and with care shotgun proteomics approaches can provide quantitative data but the people who run the machine need to be consulted when quantitative data is required.

You can look for the most abundant proteins in your sample. Although, as you say, the LC-MS analysis of your IP was non-quantitative, you can still try to get some quantitative estimation. To elaborate, you can use for example sequence coverage, no. of PSMs for each protein, no. of peptides ID'ed for a protein, share of spectrum ID, etc, as proxies for abundance.
There exists rough correlation between abundance of a protein and all these quantities. If a protein is more abundant you are more likely to have more number of peptides ID'ed from it, more no. of PSMs assigned to it, it would have higher sequence coverage, etc. Different people use different things. I have often used no. of PSMs normalised by length of the protein as an estimation for the abundance of that protein.
As others mentioned, discuss with the people who analysed your data. As a rule of thumb, I would filter my data first on 1% FDR at the PSM level, then at the Peptide level and then at the protein level. Then I would throw out all the proteins that were not identified by at least two unique peptides. Then I would compare the proteins ID'ed in the negative control list and remove the common IDs. Then sort the remaining list on no. of PSM for each protein. This would give an estimate of the more abundant proteins in the IP sample. To give an example, your bait protein (protein against which you did the IP) should be the most abundant protein in your sample. Proteins after this could then be assumed to be interactors of your bait.
Do remember that this is not a proper quantitative way of measuring protein-protein interactions by affinity purification coupled to LC-MS. But, it is a useful start. I always used preliminary information from such an analysis to design better ones. Also, read about reciprocal IPs to confirm interactions.


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Why does the cloned cat, CC, exhibit mosaic fur color?
Since fur color in this cat is from a sex-dependent gene, I see how calico cats occur. However, I don't fully understand why it happens in cloned cats.
When the cat is cloned, the DNA is taken from a somatic cell in donor and put into the egg of a surrogate. Wouldn't the DNA from the donor already have one of the X chromosomes inactivated to a barr body? Since one of the X chromosomes are inactive, wouldn't there only be a single color expressed?

There are mechanisms through which the X-chromosome that has been turned into a Barr-body can be re-activated. This happens during cloning, but is also seen in some cells that turn into cancer cells. This paper discusses a lot of intriguing lessons we've learned from transplanting nuclei from one cell to another in frogs and mice.
Interestingly, though the succes rate of cloning is surprisingly low (see this paper), but it is equal for male and female clones. This implies that the failure to turn a Barr-body into an active X-chromosome does not contribute significantly to cloning failure.
Of course, if the Barr-body gets re-activated again and turns into a normal X-chromosome, that means that later in embryonic development it can get de-activated again (at random, as is normal in cats), leading to mosaic phenotypes such as the calico. The inherent randomness in this process (at least in some animals, such as cats) means that the calico pattern of the clone is highly unlikely to resemble the calico pattern of the original.


text:
Identification of an insect from Florida
Any entomologists or there that can identify this bug? I live in north Florida, found this guy in my bedroom and thought it was a bedbug but I think it was too big, about half an inch long.

It looks like a cockroach. Not sure which species

@bodonk agreed; definitely a cockroach.

It's a cockroach nymph. Unfortunately it's barely visible given the angle of the photo, but it looks like the pronotum (head shield) has a pale margin - which, coupled with the pale markings at the sides of the tergites, makes me think this is a late-instar nymph of the Australian cockroach (Periplaneta australasiae). This looks very similar to the American cockroach apart from the pale markings, and is found in the southern US as well as many greenhouses. Within the US, it is most abundant in Florida and the coastal southern states. It is found primarily outdoors, where it prefers to live under tree bark, in piles of firewood and other locations that are moist and sheltered, but it can also be found indoors (source). It is the most prevalent cockroach outdoors in south Florida.
It mostly eats vegetable matter but when it enters homes it may eat holes in clothing and feed upon book covers (source).

(image copyright J L Castner; source: University of Minnesota).

This looks like a nymph of the American cockroach, Periplaneta americana. The nymphs differ from the adults in that they do not have wings. The egg sac (leftmost object) is approx. 8mm long.

(source)
 (source)

Not sure about this - the abdominal markings look different and the abdomen itself appears more flattened in OP's post.

@arboviral I agree regarding the markings at the sides of the abdomen, but I feel that the flatness is probably an artifact of the example images being mounted cockroaches. I found another photo which shows less bright abdominal markings, which makes it likely that it was due to intra-species variance.

Could be; I agree it's difficult to tell. On a separate note, could you add a scale bar or something to your photo?

@arboviral Photos are not mine, but P. americana nymphs can range from 2mm-2cm long, which is within the range of ~1cm reported by OP.

Second photo certainly looks more convincing - good find!

Sorry for the poor picture quality, it was 1am and I was trying to sleep haha I freaked a bit because I thought it was a bad bug at first, it was more oval and flatter than I'm used to i, a cockroach, not to mention the white spots. So these nymphs are from Australia? Are they common in Florida?

@yaymuffins I've added some more detail on distribution and behaviour to my answer. Basically, they're the most common outdoor cockroach in south Florida but prefer to stay outdoors.

Thanks! Stack exchange is always a good bet for info because of people like you.


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Name of this flower?
i'd like to know the name of this flower.

where is this flower located? try to give us as much information as possible - will make it easier for someone to help you out.

It's a Dutchman's Pipe (aka Calico Flower); the genus has over 500 species, but I'm pretty sure this is it.


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Haploview command line: how to get tagSNP
I am trying to use Haploview command line software to compute haplotypes and extract tagSNP for those. When I use the standalone version on my local computer I tick the 'Show tags in blocks' option so that when I export my haplotypes I get the tagSNP to be marked with '!'.
I am trying to do the same thing with the command line version but can't find how to achieve that. My command is as follow (submitted to Linux running server):
java -XX:+UseParallelGC -XX:ParallelGCThreads=1 -jar haploview.jar -nogui \
                    -pedfile $pedfile \
                    -info $info \
                    -out $out  \
                    -maxDistance 100 \
                    -skipcheck \
                    -missingCutoff 0.5 \
                    -blockoutput GAB \
                    -dprime \
                    -log ${out}.log \
                    -memory 124000 \
                    -aggressiveTagging \
                    -aggressiveNumMarkers 3 \
                    -taglodcutoff 3 \
                    -tagrsqcounts \
                    -tagrsqcutoff 0.8 ;

I manually set arguments to the same value when using the standalone version so the only thing differing seems to be the 'Show tags in blocks' option.
Could you explain me how to get the tags to be marked in the *.GABRIELblocks files or how to do it myself using other output files ?
Thanks a bunch !


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Selectivity of anti-bacterial affect of oxygen
As far as I know, oxidizing agents (AKA reactive oxygen species or ROS) are potent antimicrobial agents that act on a broad range of bacteria and viruses, as well as inactivating certain toxins. Is this correct? How do ROS exert their effect on microbes? Do they inactivate certain toxins, and how?
Few quotes from this article:

Oxygen destroys pathogen.

Oxygen disrupts the integrity of the bacterial cell envelope through oxidation of the phospholipids and lipoproteins.

Aerobic organisms possess enzymes that deactivate oxygen so that reactive toxic molecules containing oxygen do not damage the cells.

Do ROS selectively kill pathogens but not non-pathogenic microbes or the multi-cellular organism's cells? If so, what causes ROS to only damage pathogens or damage them significantly more than it damages the organism's cells and non-pathogenic microbes?

The source you quote is a semi-literate advertising puff. What gives it away is the sort of anthropomorphic nonsense "But there are unicellular microorganisms that fear oxygen" which you used in your original title. This will not do on a scientific site. Microorganisms are unable to "fear", just as oxygen is unable to "know". I have modified your title and suggest you read about anaerobic bacteria.

First and foremost, the comments may be right that this question is being asked with the ulterior motive of promoting a product, but it is nevertheless true that hydrogen peroxide and other oxidants (AKA reactive oxygen species, or simply ROS) are potent antimicrobial agents, so I'm going to attempt to answer this question concisely.
I only study immunology tangentially, but my studies on aging usually overlap with immunology due to the role of reactive oxygen species (ROS) in diverse cellular pathways, including DNA damage, protein folding, and immunology.
The ROS produced by organisms (particularly hydrogen peroxide, peroxide radicals, and superoxide) aren't "selective" antimicrobial agents any more than bleach is. Both endogenous ROS and exogenous oxidants like bleach will attack (oxidize) any sufficiently strong electron donor:
https://en.wikipedia.org/wiki/Bleach#Antimicrobial_efficacy
ROS act both directly and indirectly to promote immunity, ROS are produced in many epithelial tissues constitutively (i.e. independent of infection) as well as in response to infection by pathogenic organisms. The detection of pathogenic organisms is cell-dependent, and immunological signaling pathways determine whether or not ROS production is appropriate; this is one mechanism by which ROS can be used "selectively" against microbes. On the other hand, innoculation with non-pathogenic microbes can be sensed through immunological signaling pathways at the cell/tissue level and can result in a reduction of extracellular ROS production below constitutive levels to allow colonization by symbiotic microbes:
Yang, H., Yang, M., Sun, J., Guo, F., Lan, J., Wang, X., & ... Wang, J. (2015). Full length article: Catalase eliminates reactive oxygen species and influences the intestinal microbiota of shrimp. Fish And Shellfish Immunology, 4763-73. doi:10.1016/j.fsi.2015.08.021
This article describes this phenomenon in detail, while giving a brief introduction to the other relationships between ROS and immunology that I mentioned. I should stress that this phenomenon is probably not the primary determinant of the effectiveness of ROS as an antimicrobial agent; your comment about microbes with negative reduction potentials is more relevant, although not precisely correct.
The net oxidation/reduction potential of an organism has less to do with the effects of ROS and more to do with their resistance to it. Even if there are plenty of reducing agents (AKA antioxidants) around (NADH-dependent enzymes, reduced glutathione, thioredoxin, etc.), proteins and lipids can be temporarily or permanently damaged by oxidation. Even if antioxidants are available, this damage can overload the cell's capacity to quickly reverse the damage, or even temporary damage can send pro-death signals by disrupting proteins/lipids involved in cellular signaling (see wiki article on bleach). See the following section of the wikipedia article on antioxidants (and its references) for a more thorough understanding of the interplay between a cell's antioxidant capabilities, it's production of ROS, the accumulation of oxidative damage, and the effects of oxidative damage:
https://en.wikipedia.org/wiki/Antioxidant#Oxidative_challenge_in_biology
Ultimately, a microbe's ability to tolerate temporary oxidative damage (a complex phenotype to explain) combined with its ability to rapidly reverse oxidative damage (based on expression of antioxidant enzymes, accumulation of glutathione, and cellular oxidative metabolism) are the primary determinants of a microbe's resistance to ROS - which is the more accurate way to describe the concept that ROS are (weakly) "selective" for certain kinds of microbes.


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What is this tiny insect?
I took this picture in central Mexico. The insect is about 1mm in size. I found lots of these dead on a desk, so many that at first I thought they were just dust. I assume they came from a plant that was above the desk.

Does anyone know what it might be?
EDIT:
I found the culprit walking nearby! I guess that verifies what others pointed out: It seems to be the molted cuticle of an aphid. (sorry for the poor quality of the pictures)
Thanks a lot!

Since you suggest they come from a plant, they might be dried aphids. These insects usually feed on plant sap, and I already noticed some tiny, white, and apparently dead ones on plants.
As suggested in the comments, these are actually not dead aphids, but only the cuticle they leave after moulting, or ecdysis.

Aphids shed skin, maybe this is simply an abandoned exoskeleton?

Agree with Alex that this is the shell of an aphid.  A quick search for aphid ecdysis returns this picture: http://footage.framepool.com/shotimg/qf/482460604-moulting-ecdysis-afid-varmint-skin.jpg


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How does having an empty stomach affect absorption of compounds?
From personal experience, compounds such as nicotine, caffeine and alchohol appear to absorb much quicker into the blood on an 'empty' stomach', or after extended periods of fasting. If this is the case, why would that occur?
Does time play a significant role in absorption in an average 'healthy' individual? Are there any srudies published on this phenomenon?

Welcome to BiologySE... have you looked anywhere in particular for the answer to this question? You may want to google drug absorption without or  with food. Different nutrients can affect the rate of gastric emptying (i.e. prolonged gastric emptying with fatty foods), though if you are strictly talking absorption from the stomach that may not matter (or could if you're taking about a highly lipophilic drug). Can you clarify if you are talking specifically about gastric specifically or overall GI absorption? Are you talking about "food compounds" or "drug compounds" or both?


text:
Do users of CRISPR/Cas iterate or parallelize to try multiple guide sequences?
I've read about on-target efficiency and off-target effects in use of CRISPR/Cas9, and about tools that suggest good guide sequences. I am wondering: how many guide sequences do typical CRISPR users try -- i.e. is there any iteration or parallelism involved?
I think the answer is yes for some use cases, but I am not sure:

Knocking out one particular locus: There are only a few possible guide sequences, so you can just make a library that includes all of those and run one experiment, without iteration. You would not know which guide sequence worked best, though, but users may not need this information.
Knocking out one gene, no matter at which loci: Since there are many possible loci for indels, the key is to choose a locus for which the guide sequence is effective and produces the last off-target effects elsewhere in the genome. This would mean iterating/trying several of the top suggested guide sequences individually. These could be tried in parallel across several experiments.
Knocking out multiple genes, aka multiplexing: The user would want to find good guide sequences for each gene separately to avoid any interactions. This would reduce to the previous example above.

Is my understanding above correct?

I usually do 2-3 parallel guides for a single gene, but I'm not sure on how common it is.

@MarchHo Thanks! Do you just use the 2-3 top guides from a guide selection tool like http://crispr.mit.edu/ in parallel, and then report whichever worked best?


text:
Is this some sort of fungus?
There is something strange growing straight out of the glass windows at work. They look like hairs, about half an inch long, and each have a white spot on the tip of them, slightly weighing them down. I first saw a few of them a week ago, and now there's about twice as many. They don't move, except when blown in the wind, etc.
Here's just a few of them, the first ones I discovered:

They haven't budged from this spot since I first discovered them, but more have appeared surrounding them. This is located in Louisville, KY, USA, and there has been some hot humid weather lately. This particular area where they're growing is in the shade and a partial roof, so these windows rarely ever get rained on.
A friend hinted that they might even be insect eggs.
What are these things? Fungus? If so, what kind?

Looks like a couple mold sporangia. I have no way of making an ID though.

@CMosychuk That makes sense (now that I look at pictures of them). Also since that area never gets any rain (but plenty of moisture in the air).

@CMosychuk But now that I look a bit more, I don't think so. A) None of these have any appearance of any sort of root or anything holding it on, and B) None of them are grouped together or growing two at once. They're all stand-alone.

I'm imagining some isolated spores blew in with the wind and attached. That would essentially illustrate how a colony gets started. Those fruiting bodies will eventually release spores of their own and you'll find more stalks over time (and eventually more features of a mold colony). I'd just use some bleach water and clean it off.

Now that I think about it, there is some field of fungus growing in the woodchips about 10 feet away. Those ones look a bit more developed, and look like light orange bubbles.

The ones growing a bit further away look like this: http://my.kwic.com/~pagodavista/schoolhouse/species/plants/pics/fungi3.jpg

This is definitely not fungus. See a related question here

These are lacewing eggs. Lacewings lay their eggs on stalks.
From wikipedia  :

can you add some sort of reference or other picture for confirmation? Thanks for your efforts.

From the linked article... "Eggs are deposited at night, singly or in small groups; one female produces some 100–200 eggs. Eggs are placed on plants, usually where aphids are present nearby in numbers. Each egg is hung on a slender stalk about 1 cm long, usually on the underside of a leaf."

Two differences - they weren't clustered like that, they were scattered - and also they were on windows, at least a few yards away from any vegetation.

this comment is a little late,but I read about this in a book,then another book,then Buggguide" i think


text:
Do the pH and other ions affect the hydrolysis of ATP
ATP hydrolizes to ADP and phosphate in a strongly exergonic reaction and is used for energy transfer and short-term storage in cells.
ATP is stable inside a cell, so a significant activation energy must be necessary for the reaction.
However, the English Wikipedia article implies that stability of ATP is not a given, but depends strongly on the properties of the surrouding solution:

"ATP is highly soluble in water and is quite stable in solutions between pH 6.8 and 7.4, but is rapidly hydrolysed at extreme pH." and
"ATP is an unstable molecule in unbuffered water, in which it hydrolyses to ADP and phosphate."

How does the pH affect the hydrolysis of ATP?
Why is it even relevant if the solution is buffered or not? (Do the ions stabilize the molecule somehow?)
Are there other effects that influence stability in animal cells?

Welcome to Biology SE. This is a reasonable question, although perhaps more chemistry than biology. However I have altered the title to include the key factor you are concerned about — pH. That will help others know what your question is about, and thus whether they feel they may be able to help you. It is also important for archiving purposes.

Actually, It seems that both the right ph and the existance of a buffer in the solution is required, so that needs clarification as well.
Sorry I asked two questions instead of one, but it might be related.
I did not ask at Chemistry SE, as there might be something else going on inside cells that might influence stability of ATP.

I guess alkaline hydolysis will happen via a mechanism similar to alkaline hydrolysis of phosphodiester bond in RNA.

I've changed the title to the more precise hydrolysis, because that's what the Wikipedia quotes refer to. I would imagine @WYSIWYG is right about alkaline hydrolysis. I don't know about acid hydrolysis.

I'm not sure how the activation energy would be affected by pH, but it is well known that the equilibrium is shifted by pH since the various phosphates have different pKa values. See for example http://www.jbc.org/content/193/1/425.citation

Stability of ATP is largely due to Mg2+. ATP in cell is actually Mg2ATP2-
The Mg ions stability the negative charges on the phosphates. pH is also important of course, but Mg is key, hence you see Mg2+ all the time in biochemical reactions where ATP is involved.

This is not an answer to the question. The question asked why extremes of pH affect the stability (the quote is for hydrolysis) of ATP. The fact that Mg ions interact with the phosphate negative charges has nothing to do with hydrolysis outside the range of pHs quoted.

@David. aside from the question " are there other effects that influence stability in animal cells.

Mg2+ is there as a counter-ion and is required so the ATP is in the right conformation to bind to the active site of enzymes. All this talk of "stability" is unscientific waffle. And the Wikipedia entry is of no relevance to biology talking about the need for buffers and suitable pH. That's the milieu of the cell. It's really the sort of thing a chemist would write about preparing solutions in the lab.

@ David: My question title was changed by a moderator. The answer matches my original question "Why is ATP stable in cells?".

@SciEnt: Thank you for your answer! Do you have any sources readily available?

@user25269 Any biochemistry textbook really. But one i have personally read. Lehninger Principles of Biochemistry. By Nelson & Cox 6th Ed.

@David: I'm no expert, but I don't see why Mg2+ cannot stabilize ATP in solution. Could you please elaborate?
Of course, ATP is (kinetically) stable in the milieu of the cell. However, it is unstable without a buffer and hydrolysis occurs without any enzyme or other catalyst.
I wanted to know which component/property of the cell milieu is responsible for ATP being stable in the cell, as the reason is not evident for me.
Also, please keep it civil.

@user25269 The only reason ATP would be "unstable" without a buffer is because when the free acid were  dissolved in water the solution would become acidic and (apparently) be hydrolysed. As the cellular milieu is buffered by a multitude of things ( especially bicarbonate) this problem does not arise. And stop talking about "stability". ATP does not undergo alkaline hydrolysis at cellular pH because it is only slightly alkaline and the concentration of hydroxyl ions is insufficient. You seem to be obsessed by a problem that doesn't exist.

The question is about pH. Your answer is about Mg. It basically qualifies as "insufficient explanation".

@TomD "I wonder how many of the downvoters to this answer realize the critical importance of Mg in all ATP-dependent biological reactions." I certainly do, but, as I have written, I regard it as irrelevant, because the question (not the title) was about the hydrolysis of ATP and something called its stability (degradation of the purine ring?). If you think Mg ions somehow prevent the hydrolysis or degradation of ATP, rather than just being the counter-ion required in enzymic reactions, please cite sources.

OK. Let’s answer the questions you pose:
How does the pH affect the hydrolysis of ATP?
High concentrations of hydrogen ions or hydroxyl ions (“extremes of pH” — as you quote) cause acid or alkaline hydrolysis. The mechanism of alkaline hydrolysis is presumably through a cyclic intermediate, as with the hydrolysis of RNA. Acid hydrolysis of ATP requires very low pH — for example it has been studied in 3M perchloric acid — and the mechanism is quite complex, according to work published by Hutchings et. al. in 1981.
Why is it even relevant if the solution is buffered or not?
In unbuffered solutions the pH may easily deviate from the physiological range. This is a practical consideration of work in vitro. Physiological and cellular systems are highly buffered by a variety of ions and even macromolecules so the problem does not arise.
Are there other effects that influence stability in animal cells?
You are mistaken in your assumption that there is a particular need to prevent hydrolysis of ATP within animal cells. This appears to be based on a misunderstanding of a Wikipedia entry which is more concerned with the chemistry of ATP rather than its situation in the cell.

@TomD — ATP is an important metabolite, and its generation and the coupling of its hydrolysis to chemical, electrochemical and mechanical processes is important. Whether it is “the basis of life” any more than DNA, RNA, proteins, lipids, NAD etc. is an irrelevant and fruitless question. What I maintain is that the problems Nature had to solve with respect to ATP were those already mentioned. Its activation energy and chemistry are such that there is no tendency for its spontaneous hydrolysis at physiological pH, so preventing this is not a problem and certainly not the “the basis of life”.


text:
How do antibiotics combined with a non-Western diet affect weight loss?
Wikipedia describes a Western diet as:

... higher intakes of red and processed meat, butter, high-fat dairy products, eggs, refined grains, white potatoes, french fries, and high-sugar drinks.

In the following article there is information about research done that suggests mice eating a high-fat diet while taking antibiotics become obese:
Scientific America: How Gut Bacteria Help Make Us Fat and Thin
I was wondering whether there has been any similar study to see what happens to obese mice or humans that take antibiotics while eating a non-western diet such as the Mediterranean diet, which this Guardian article suggests does not cause weight gain?:
The Guardian: High-fat Mediterranean diet does not cause weight gain

The Scientific American article states that food you are referring to was "high in fat and low in fruits, vegetables and fiber" but you refer to fat as the key.  It could be that the reduction of one of the other components is the cause.  For example, fiber is often prebiotic.  It could be the case that a high-fat, high-fiber diet would change the result.

Actually, on second look, your question actually misrepresents the study.  The mice on antibiotics gained much more weight on a normal diet but this effect could be eliminated by putting these mice in the same cage with those not treated with antibiotics.  The change in diet eliminated the cohabitation effect.

https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.6b00942 antibiotics in pigs and effect on plant lignan metabolites.

I don't believe elevated polyunsatured fatty acid consumption falls under the tendencies of the western diet, and may be more reminiscent of the Mediterranean diet, so hopefully this answers your question. This study took mice with elevated blood and tissue omega-3 levels, and were used to identify if high levels of omega-3's could prevent the deleterious effects of excessive antibiotic use on gut microbiota. Regarding microbiota diversity, antibiotics are known to create an imbalance between bacteroidetes (decreased) and firmucutes (increased) - this study evidenced that the omega-3 mice were able to rapidly recover their bacteroidetes composition and reduce the amount of firmucutes present in comparison to the control, which in short is good news, as this also prevented later-life obesity in the omega-3 mice in contrast to the obese controls.
For skeptics of microbiota-influenced weight loss (and I know there's many), there is quite a bit of literature out there describing the relationship between gut microbiota diversity and energy expenditure. The short description is that elevated bacteroidetes (in proportion to firmucutes) is associated with lean phenotypes, that diet is very much capable of modulating gut microbiota over short periods of time, and transplanting microbiota compositions into obese individuals has definitively shown an effect on metabolism. The only problem to a gung ho microbiota therapy is, no one knows the gold standard for microbiota composition.

Maybe what we need to do is go to one of these isolated communities where they still live on hunter gatherer diets and trade something for a turd specimen, preferably polished.

Although evidence of absence is not proof of absence, there are currently no published studies on PubMed which have mice/antibiotics/(Mediterranean diet) or (olive oil) in the abstract. But I guess such a study will be soon published as the question is fairly obvious and of high interest.

It's been well known in the poultry industry that giving birds antibiotics causes 'growth promotion'. Humans are obviously not birds but given that undisputed fact, it seems reasonable to consider that effect this might apply to other species.

There is no reason to think that taking antibotics is going to tweak your gut flora in a way that will make you lose weight for good.

I beg to differ. If antibiotics can increase weight gain through one type of diet, then is it that far off to reason that antibiotics with another type of diet may cause weight loss? The weight gain seems to indicate that antibiotics may help change gut flora.

Agreed with the comment above. Dysbiosis of the gut can radically change how your gut behaves. There are a number of studies now which have shown that antibiotics cause long lasting effects (e.g. https://www.ncbi.nlm.nih.gov/pubmed/29945240). Typically this has been tied to obesity rather than weight loss, but I suspect that's a Western research bias brought about by increased prevalence and relevance of obesity versus malnutrition.


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ID flying insect found in Belgium
I live in Belgium, and I've just witnessed a weird looking wasp/fly flying around in my room. Here's a picture:

So, what's this? It's still in my room, just chilling there. It zooms like a wasp, and flies VERY FAST. You can see white vertical stripes on his upper body, and then golden vertical patches. I couldn't get the camera to focus, so it's not really full-hd.
[Edit (better picture)]

Welcome to Biology.SE. You should add a descriptive of the size (or an object for size reference on the picture).

I have to disagree.  Horseflies are in the Tabanidae family, and I really suspect this is a hoverfly (the Syrphidae family).  Please see my answer below.

This is a hoverfly! Specifically in the genus Helophilus.  A lot of species of hoverflies exhibit Batesian mimicry of wasps/bees, as we see here, while they mainly feed on pollen and nectar.  So please, don't worry about it trying to bite you.
As far as species go, I think it is probably a Helophilus trivittatus.  I am basing that on location and a lot on the banding patterns on the thorax as well as the markings on the prominent terga.  Here is a picture below for you to compare.

It looks like a horse-fly

What is a horsfly?
Horse-flies (Tabanidae) represent a family in the order of Diptera that are distributed world-wide. They are large flies that fly quickly. Adults feed on nectar while females feed on mammals blood (including humans). When they sting, it hurts much more than a mosquito! You probably want to get rid of it before going to bed!
Wasps (Hymenoptera) vs flies
You thought about a wasp because you saw a pseudo-pattern of yellow bands on the abdomen I suppose. It is actually easy to tell it is a fly (Diptera) because (1) it has only two wings, (2) it has very big eye and (3) Hymenopterans have a thin waist while diptera don't. Another noticeable trait that should make you think of a horsefly is that it flies very fast. Note by the way that hoverflies have a very distinctive pattern of black and yellow bands but are flies and don't sting.
What species?
I don't know! But someone on this website will probably be able to find out.

As the OP noted, horseflies can indeed fly very fast. Actually, they are the fastest flying insect on earth! The speed of the male horsefly is attributed to Jerry Butler, an entomologist at the University of Florida, who once got a male Hybomitra to chase a plastic pellet fired from an air rifle; "Which it caught in midair and dropped," Butler says. From the speed of the pellet, he calculated the fly was going at least 90 miles per hour (145 km/h) at the beginning of female pursuit.

It's not a wasp. Wasps have a thin waist.
It's a fly, and flies can indeed be fast.
I would not bet on Tabanidae, but on Sarcophagidae instead, because your fly looks less hairy than what I'm used to for horseflies, and because of the striped pattern on the thorax, but it may well be some other family.