How do cellular waste products enter arterial blood? I recently learned that blood in renal arteries contains waste materials, which is filtered via nephrons in the kidneys.

My question is, how are these waste materials getting into the arterial blood? I believe arterial blood is pure and devoid of waste (since all the waste from cells and tissues must enter veins).

Arterial blood isn't "pure". It is simply in one part of a complex circuit which carries varying degrees of oxygen, nutrients, and waste products, etc., to varyious parts of the circuit.

  ...how are these waste materials getting into the arterial blood?

The most simple and direct (but teleological) answer to this is that toxins need to get into arterial blood to ever get to the kidneys to be filtered. The arteries carry blood to every part of the body, detoxifying organs included. Veins carry blood away. If there were no waste products in arterial blood, the kidney would be superfluous.

Waste is produced in all tissue. Blood carries oxygen and nutrients to the tissue (where some of it is used), and via the venous side (all over the body) blood carries the waste products (as well as unused oxygen and nutrients) away toward the heart. The blood carrying waste products collects in increasingly larger veins until it is dumped into the right side of the heart and pumped into the lungs, where a major waste product (CO2) is partially removed. Things that need to be removed by the kidney are all still there. Blood carrying these toxic products is dumped into the left side of the heart, and thus enter the arterial blood supply. The kidney then can remove waste products partially or completely when it reaches them.


Are all dipeptides synthesizable? Probably a basic question, but are all possible dipeptides synthesizable?
For 20 amino acids, there should be in principle 190 dipeptides; do they
all exist or is there chemistry that makes some combinations unstable?
A straight forward generalization would be to ask what percentage of
peptides (or proteins) are synthesizable (in the lab or in cells).

I see no reason why not. Just to make sure, I decided to test. I ran a search on all human proteins (using the UniProt flat file) for all possible dipeptide combinations of the 20 standard amino acids (selenocysteine is also present in humans but only in 22--or so, depending on how you count them--proteins, so I wouldn't expect all possible sec-containing dipeptides to be present) .

As expected, each of the 400 possible dipeptides were indeed present in at least one human protein. In case anyone wants to repeat this, the "protocol" is as follows:

Download the human flat file from Expassy.
Extract the peptide sequences

perl -ne 'if(s/^\s+//){s/\s+//g;print}' human.flat > human.pep

Generate the list of possible dipeptides:

AA
AC
AD
AE
AF
AG
AH
AI
AK
AL
AM
AN
AP
AQ
AR
AS
AT
AV
AW
AY
CA
CC
CD
CE
CF
CG
CH
CI
CK
CL
CM
CN
CP
CQ
CR
CS
CT
CV
CW
CY
DA
DC
DD
DE
DF
DG
DH
DI
DK
DL
DM
DN
DP
DQ
DR
DS
DT
DV
DW
DY
EA
EC
ED
EE
EF
EG
EH
EI
EK
EL
EM
EN
EP
EQ
ER
ES
ET
EV
EW
EY
FA
FC
FD
FE
FF
FG
FH
FI
FK
FL
FM
FN
FP
FQ
FR
FS
FT
FV
FW
FY
GA
GC
GD
GE
GF
GG
GH
GI
GK
GL
GM
GN
GP
GQ
GR
GS
GT
GV
GW
GY
HA
HC
HD
HE
HF
HG
HH
HI
HK
HL
HM
HN
HP
HQ
HR
HS
HT
HV
HW
HY
IA
IC
ID
IE
IF
IG
IH
II
IK
IL
IM
IN
IP
IQ
IR
IS
IT
IV
IW
IY
KA
KC
KD
KE
KF
KG
KH
KI
KK
KL
KM
KN
KP
KQ
KR
KS
KT
KV
KW
KY
LA
LC
LD
LE
LF
LG
LH
LI
LK
LL
LM
LN
LP
LQ
LR
LS
LT
LV
LW
LY
MA
MC
MD
ME
MF
MG
MH
MI
MK
ML
MM
MN
MP
MQ
MR
MS
MT
MV
MW
MY
NA
NC
ND
NE
NF
NG
NH
NI
NK
NL
NM
NN
NP
NQ
NR
NS
NT
NV
NW
NY
PA
PC
PD
PE
PF
PG
PH
PI
PK
PL
PM
PN
PP
PQ
PR
PS
PT
PV
PW
PY
QA
QC
QD
QE
QF
QG
QH
QI
QK
QL
QM
QN
QP
QQ
QR
QS
QT
QV
QW
QY
RA
RC
RD
RE
RF
RG
RH
RI
RK
RL
RM
RN
RP
RQ
RR
RS
RT
RV
RW
RY
SA
SC
SD
SE
SF
SG
SH
SI
SK
SL
SM
SN
SP
SQ
SR
SS
ST
SV
SW
SY
TA
TC
TD
TE
TF
TG
TH
TI
TK
TL
TM
TN
TP
TQ
TR
TS
TT
TV
TW
TY
VA
VC
VD
VE
VF
VG
VH
VI
VK
VL
VM
VN
VP
VQ
VR
VS
VT
VV
VW
VY
WA
WC
WD
WE
WF
WG
WH
WI
WK
WL
WM
WN
WP
WQ
WR
WS
WT
WV
WW
WY
YA
YC
YD
YE
YF
YG
YH
YI
YK
YL
YM
YN
YP
YQ
YR
YS
YT
YV
YW
YY

Save that list as dip.txt.
Use that file to search the protein sequences:

perl -ne 'BEGIN{open(A,"human.pep"); while(<A>){chomp; $k.=$_}}; chomp; print "$_\n" if $k=~/$_/  ' dip.txt

The script above will print each dipeptide that was found in at least one protein. Since all were printed, all dipeptides exist in the human proteome.


Structure of proteins Regarding the secondary structure of proteins, I know that there are 3 main types. The beta sheet formation is made up of beta strands stabilized by hydrogen bonds to form an anti parallel or a parallel structure. I learned that these beta strands are a zigzag sequence of amino acids, but what traits of beta strands differentiate it from the primary structure? Or are the beta strands just primary structures that link together to make beta sheets?

primary structure
focus = peptide bonds (because these link the amino acids
The sequence of amino acids, for example AGGVHIL..

secondary structure
focus = H-bonds between the parts of the backbone
 There are several different types of secondary structure (α-helices, β-sheets, etc.). However the most import thing to remember is that the secondary structure refers to the the patterns of hydrogen bonds formed between amine hydrogen and carbonyl oxygen atoms contained in the backbone peptide bonds of the protein

your confusion
You are partly correct from a very simple perspective you can see the secondary structure of β-Sheets just as connected primary structures. However when talking about a piece of secondary structure you have to take the hydrogen bonding into consideration as this is what connects your primary structure parts (β-strands) to form a β-sheet.


What’s wrong with a shriveled cell? When you place a cell into a hypotonic solution, water rushes into it and it bursts/lyses. Thus, the cell dies.

However, when you place a cell into a hypertonic solution, water rushes out of it and it shrivels. The membrane is still in tact and all the organelles are still held inside. Why is having a shriveled cell a problem then?

Plant Cell

In the case of plants, shriveled cells are a huge problem. When plant cells are put in a hypertonic solution, the cell wall remains turgid and stays that way but the plasma membrane doesn't, it shrinks as you already know with the other organelles as well. This is known as plasmolysis. If this situation continues it causes death.

Shrivelling  causes the plant to wilt too.

Animal Cells

Well it does have affects overall and at cellular level

It changes the RMP(resting membrane potential) across the cell because of change of sodium ions outside the cell
-It decreases rate of metabolism


Multiplication of bacillus subtilis I have a supplement for use in horticulture.  It is a powder that contains mostly subtilis with smaller amounts of a few other strains.

Prior to horticultural application I would like to "multiply" them so as to get to most out of the product.

Is water and a drop of molasses sufficient? (that seems to be accepted in cannabis culture)

How fast do these guys replicate? Without high tech lab equipment is there anyway I can tell that they are in fact multiplying?

I am basing my answer on this document issued by one of the departments of the Ludwig Maximilian University of Munich.

Bacillus subtilis:

Doubling time: 30 minutes
Incubation temperature: 37°C
Growth conditions: strictly aerobe

Recommended media:

Luria-Bertani (LB) broth/plates - (for everyday use)
Difco Sporulation    Medium (DSM) - (for long-term storage)

You can find the formulations for the aforementioned media by following the link above.

With regards to the latter part of your question, the easiest way to tell (and doesn't require any "high-tech" lab equipment) whether your cells are multiplying or not is to inoculate a broth and see whether there is turbidity after a certain time of incubation. However, please be aware that you may have cross-contaminated your broth so unless you do further testing you cannot know for certain if it is Bacillus subtilis in your broth.


How to map the Gene name to its Gene Symbol? I am learning in Gene data lately so I apologize for the silly questions in advance. I read a paper for a cancer on human which found some important genes. For example, the paper listed one of genes in its name as

gene1:    chromosome 12 open reading frame 52

May I know how I can find its corresponding gene symbol as

C12orf52

Is there a mapping table or  tool I can use ?

Thank you very much,

Unfortunately, protein and gene name mapping is one of the most annoying problems in modern computational biology. There is no surefire way of doing this. Especially from hopeless gene names as the one in the paper you cite. Here are a few services you can try though:

General, text search, useful if you have a gene description (as in the case described in your question):

NCBI Entrez,
UniProt search

Mapping servers, useful if you have an actual gene/protein symbol/name (e.g. P53_HUMAN, AF240684, NP_001119585 etc)

UniProt ID Mapping
DAVID Gene ID Conversion Tool


How many Type II restrictions enzymes are currently available (commercially) How many Type II restrictions enzymes are currently available (commercially) for purchase as of the date of this posting (September 1, 2014)

The Restriction Enzymes section at Biocompare is likely not comprehensive, but short of contacting every single molecular biology company and merging all their inventories into a master list, it's probably the best you can do on short notice. They currently list 289 uniquely-named enzymes, but I'm not enough of an expert to say how many are similar in activity/recognition sequence, or whether they might also be known by other names not currently listed. For your purposes, however, it'd probably be enough to tell your students that there are on the order of 300 common commercially-available enzymes. Hope this helps.


When does weak selection produce qualitatively different results from strong selection? In evolutionary game theory, it is typical to model organisms as having a base fitness that is modified slightly by the game interaction. The ratio of the game effect versus the base fitness determines the strength of selection, with weak selection meaning the game modifies overall fitness only slightly, and strong selection meaning that the game payoff is a big part of the overall fitness of the organism.

Most analytic models like to assume weak selection because it allows the authors to Taylor expand the selection function and linearize it by dropping terms that are higher order in the stength of selection. However, it is unclear that results derived for weak selection would necessarily hold under strong selection. Are there mathematical (or computational) models where weak and strong selection produce qualitatively different results? If not, is there an argument as to why weak and strong selection should produce the same results?

I've also seen this discussion come up outside of evolutionary game theory, in a more general biological setting. In particular, with respect to inclusive fitness. The take away message I got was that in the regime of weak selection relatedness means what you expect it to mean, but for strong selection the concept becomes very slippery and counter-intuitive. What does inclusive fitness theory tell us about going from weak to strong selection? Again, I prefer arguments supported by clean mathematical or computational models over ones based on intuition and words alone.

It has been shown that predictions based on weak selection can be different from that on strong selection.
In fact, for rare mutations, each strategy has stationary distribution at the mutation selection equilibrium. The rank of the component depicts the relative prevalence of the available strategies. Yet the rank of the components of this distribution can change with the selection intensity. Thus results obtained under weak selection can not generally carry over to strong selection.

For more details, please refer to Fig. 1 in [1] and Fig. 2 in the supplementary information of [2].

1 Julián García and Arne Traulsen, (2012), Journal of Theoretical Biology, Leaving the loners alone: Evolution of cooperation in the presence of antisocial punishment

2 Christoph Hauert, Arne Traulsen, Hannelore Brandt, Martin A. Nowak and Karl Sigmund, (2007), Science, Via freedom to coercion: the emergence of costly punishment


Is there an "Adam and Eve" for each new trait during (not just human) evolution? Do new beneficial mutation evolve simultaneously and independently with several individuals of the same specie or only with one specimen who then transfers it to all of the specie?
In other words, when we talks about common ancestor we usually mean a specie, so for example, all earth dwelling reptiles, birds and mammals are the descendants of Tiktaalik (to the best of my knowledge), and we know that Tiktaalik was the first (or one of the first) species to come to land, but was there a first individual Tiktaalik who went to the land, like Tim Minchin's Tony the fish.

Imagine being the first dude ever to have feet...
Imagine you're a fish, and you are swimming in the ocean ... and suddenly out of nowhere Tony just goes "I'm getting out, I'm freezing, I'm just gonna pop out for a bit, maybe lie on my towel, I'll bring you an ice cream"
-"Don't bother ,Tony, you are a freak! Tony is a freak, let's go, let's ostracize him for being different"

It seems to me that from the same species of ancestors there are several descending distinct species, so it seems to me that that that there was a species of reptiles that at some point some individual of that group developed Dinosaur features and traits and whose descendants became Dinosaurs and then Birds, and another individual of that specie or a descending specie (not necessarily at the same time) developed mammary glands whose descendants became mammals, and other individuals who didn't mate with those two whose descendants remained reptiles.
Was there ever a first dinosaur with feathers who is the father or mother of all birds, or the first fish with lungs, the first monkey with opposable thumbs from whom all apes descend, or the first mammal that decided to go for a swim and all dolphins, whale and seals are his direct descendant of that first swimming mammal?
And also for traits that don't lead to speciation, was there a first human who was lactose tolerant, and all the lactose tolerant people on the world are his/her descendants, or the first person with no wisdom teeth, the first person with slanted eyes, and the first person with red/blond hair?
*- If there are gross inaccuracies and/or over-simplification in my understanding of the evolutionary process, this is because I'm not a biologist, and I would accept happily any correction.

For most traits, there is no clear line where the trait is present or not. Exceptions are traits that occur with a single mutation, like lactose tolerance. So to pick one example, you had a population of fish that had a lung-like organ, and that by genetic drift that organ got more lung-like in a sub-population. So for most traits, you have a combination of mutations that lead to the traits, and these mutations need not occur in a direct line of ancestors. (I.e., a descendant will combine independent mutations from its parents.)

So there is no "Adam and Eve" in the sense that these are the only ancestors of all living individuals of a species. This would be a terrible genetic bottleneck! See this illustration, which comes with the estimate that the population size of the chimp-human ancestor was around 100,000.

You ask for "a first dinosaur with feathers who is the father or mother of all birds". It's possible that feathers arose multiple times from the same feather-like structures, or only once. But it is clear that this first dinosaur is only one of many dinosaurs that lived at the same time, and who are also ancestors of all birds.

Further reading: Lactose tolerance evolved several times independently (see "Convergent adaptation of human lactase persistence in Africa and Europe.").


Function and Characterization of poly(T) and (AT) I came across three terms; "poly(T)45", "poly(A)45" and "(AT)15". Can anyone explain what they are? I know the number refers to strand length, possibly poly-T is a strand of thymine monomers and that ss(AT)15 refers to a 30-base (dAdT). I assume this refers to a single that looks like this;
dAdT-dAdT-dAdT...repeated 15 times.
In that case, what is the d?

Poly(T) is an oligonucleotide with only repeating thymine residues. These are generally used as primers in Reverse Transcription PCR, as mature eukaryotic mRNAs have a Poly(A) [adenosine] tail added to them as a post transcriptional modification in order to protect against mRNA degradation. You would also sometimes see this referred to as an oligo dT. It could also be the primer for some paired end adapters used in next-generation sequencing (NGS)

The 45 generally would indicate the number of residues in the oligonucleotide.

Poly(A) could be a primer for a paired end adapter for NGS, however I would need to see the context of where you saw the terms to be sure.

d = Deoxyribonucleotide, in other words you are dealing with a DNA oligonucleotide (though Thymine is also an indication). Technically the d refers to the 2' Carbon on ribose having a hydrogen instead of a hydroxyl attached to it making it deoxyribose.

Without the d it is a Ribonucleotide, indicating that you are looking at an RNA molecule and that the 2' Carbon on ribose has a hydroxyl group.

You will sometimes also see ddN (N for any base). This indicates a chain terminating dideoxynucleotide which has a hydrogen on both the 2' and 3' Carbon instead of hydroxyl groups. The reason this molecule is chain terminating is because you need the 3' hydroxyl in order to link to a 5' phosphate group to form a phosphodiester bond, which is needed to continue the elongation of the nucleic acid molecule.

As for the ss(AT)15, I think you are correct in saying that this is a 15 pair repeat of AT so a 30 nucleotide oligonucleotide. Though it didn't say dAdT, you are likely correct that they are deoxyribonucleotides as they use thymine instead of uracil as the base.

Just in case, the ss stands for single-stranded, which is often the case for oligonucleotide primers for PCR reactions.


How to extract oxygen from grow chamber I have been developing LED grow lights for a year or so and one of the things I am trying to do is to build a grow chamber where I can control temperature, humidity, light intensity and quality and levels of $\ce{CO2}$ and $\ce{O2}$.
I don't have any problems with most of the variables except the gases. I can inject $\ce{CO2}$ and monitor the gas, but as the chamber is hermetically sealed, how do I get rid of excess oxygen produced by the plants? Is there something similar to the $\ce{CO2}$ scrubbers used in aquariums? As a matter of fact, plants also need oxygen for their metabolic processes occurring during darkness, but they produce oxygen in excess of this requirement during the day. It is the excess of oxygen the one I want to extract, and not the whole amount of oxygen in the air of the chamber.
The whole idea is that through the chamber, I can adjust light conditions to each crop based on performance. Gas exchange is an important proxy for Chlorophyll fluorescence and has shown a good correlation with performance.
Any ideas?

Absolutely, this is actually looking more as an engineering problem rather than a biology one.
In any case, I think I have found a satisfactory answer on a paper from the 1997 Proceedings of the Sixth European Symposium on Space Environmental Control Systems. The article is called: Oxygen Scrubbing and Sensing in Plant Growth Chambers using Solid Oxide Electrolyzers.
Basically, a disk of non-porous yttria stabilised zirconia (YSZ) is sandwiched between platinum electrodes and inserted in the chamber half-way, with the other half enclosed in whatever will store the extracted oxygen. The electrodes must be porous to allow gas diffusion. The only problem is, that sort of electrolysis cell needs to be maintained at an elevated temperature (800 to 1000 Celsius) in order to work.
By means of electrocatalysis and thermal dissociation the oxygen molecule dissociates to form two oxygen atoms, these in turn pick up two electrons from the cathode and become ions. The ion is then transported by the electrolyte (YSZ) by means of electron vacancies located in the crystal lattice (basically a similar process to that of a N-doped semiconductor whereby impurities create electron holes).
I think I am satisfied with the above explanation. Doable at home? No way, but it does answer the core question.


Identify this insect with a big "face" pattern on its brown fuzzy wings Hiking in low mountains in northern Taiwan in early May I noticed that something seemed to be looking at me from the ground, and it turned out to be the pattern on an insect's wings.

The wings are fuzzy like a moth or butterfly but they fold back.

There is also a striking face-like pattern on the wings, one "eye" with heavy upper eyelid on each and a "mouth" across both, and it has very long black (or blue?) and white densely-striped antennae or feelers which project straight forward, and it's legs were also black with several white bands. The length from head to wingtips (not counting antennae) was about 2 or 2.5 cm.

I also got the distinct impression that its orientation was not flat (parallel to the leaf's surface) but oriented with its rear high, so that something in front of it could see the "face". I don't have a photo from the side but based on judging things from what is and isn't in focus I think it's pretty clear.

Question: Is it possible to identify this insect with a big “face” pattern on its brown fuzzy wings? Is it also possible to know if the pattern has some underlying structural function within the wings, or is it only for appearance?

I fully admit that I am not an expert on Asian insects but having trawled through various species identification keys and collections I am fairly certain that the insect you observed was:

Deltoplastis commatopa

I lifted the following species description from Wikipedia and I think it matches your description & photo rather well:

  Deltoplastis commatopa is a moth in the family Lecithoceridae. It is
  found in Taiwan and the provinces of Jiangxi, Hunan, Hubei and Sichuan
  in China.

  The wingspan is 16–22 mm. The forewings are light lilac-fuscous with
  blackish-fuscous markings, edged ochreous-whitish. There is a large
  subtriangular antemedian blotch from the dorsum nearly reaching the
  costa, connected with costa by an angulated mark. There is a large
  triangular postmedian blotch, its base posterior, reaching the costa
  and the dorsum, its apex cut off by ochreous-whitish to form a
  tadpole-shaped mark. The terminal area beyond this irrorated
  (speckled) ochreous-whitish, a blackish marginal line round it. The
  hindwings are fuscous, darker posteriorly.

Here is a screenshot of the entry in the Global Biodiversity Information Facility:

You can see from the entry that several occurrences have been reported (with images) by people in Taiwan.

I also found this Taiwanese biodiversity website (in Traditional Chinese) and thought I would include it here (although I have to admit that I am not able to read Traditional Chinese).


How to design a permanent vaccine to cholera using CRISPR? I know that Vibrio Cholerae infects the body through the GM1 ganglioside. So, would it be possible to engineer a CRISPR gene editing tool to prevent Vibrio Cholerae from getting into our cells?

Specifically, would it be possible to insert a piece of DNA into our genes that allow the synthesis of cholera toxin-suspressing protein shown  here (Pubmed link).

The reason I ask this question is that there are obvious benefits to being immune to cholera from birth. While I'm definitely not planning on being the next He Jiankui, I find the prospect of such a vaccine highly intriguing.

Edit: changed link because I posted the wrong link.

So, would it be possible to engineer a CRISPR gene editing tool to
  prevent Vibrio Cholerae from getting into our cells?

Vibrio Cholerae doesn't get into our cells.

Did you observe that your paper has no in vitro experiments?

It's going to be tough to get a cell to transcribe and translate something so small, and will the peptide work if it needs a leader sequence to be exported out of the cell?

Its much much easier to break a gene in every cell than to add a new gene and have just a small subset of cell types make large quantities of that gene product.


Cyanobacteria: Gram negative or Gram positive? My (school) textbook states that cyanobacteria ("blue-green algae") are Gram positive (no references provided). They mention this at several points over the chapter we're doing so it doesn't look like a typo.

However, this Wikipedia article on "Gram staining" (under "Gram negative bacteria") states:

  Gram-negative bacteria generally possess a thin layer of peptidoglycan between two membranes (diderms). Most bacterial phyla are gram-negative, including the cyanobacteria, spirochaetes, and green sulfur bacteria, and most Proteobacteria (exceptions being some members of the Rickettsiales and the insect-endosymbionts of the Enterobacteriales).

   Emphasis, mine.

There is no mention of cyanobacteria under the section "Gram positive bacteria".

I understand that there is a possibility that some cyanobacteria stain positive, and other stain negative (owing to the lack of a very sharp definition for "cyanobacteria", as well as the limitations of Gram-staining).

So what I want to know:

1) Are cyanobacteria generally Gram positive or Gram negative?

2) Are there exceptions to that general trend? If so, what are they?

Cyanobacteria are clearly didermic (two membranes, inner and outer) bacteria, normally classified as Gram-negative bacteria. If your textbook says several times that they are Gram-positive, instead of a typo, you have a plain mistake.

However, things are not that simple.

According to Hoiczyk and Hansel (2000), this traditional classification of the prokaryotic envelope doesn't work well with cyanobacteria, whose cells show a combination of the features of Gram-positive and Gram-negative bacteria:

  The multilayered peptidoglycan of gram-positive bacteria, with a thickness ranging from 20 to 40 nm, usually forms a physical barrier for the dye. In gram-negative bacteria, however, with their relatively thin sacculus of 2 to 6 nm, the stain can easily be washed out. Together with other characteristics, such as the occurrence of accessory cell wall polymers or the presence of an outer membrane, the peptidoglycan architecture largely determines the different properties of the two cell wall types in terms of mechanical stability, permeability, and resistance toward chemical substances. Although this classification is generally useful, it oversimplifies the concept of bacterial cell walls. It also ignores, for example, that the largest and perhaps most diverse group of bacteria, the cyanobacteria, possess cell envelopes with a combination of these features. (emphasis mine)

Here is an image (ibid.) comparing a Gram-negative cyanobacteria with Escherichia coli:

Electron microscopical comparison of the gram-negative cell envelopes of the cyanobacterium P. uncinatum (A) and E. coli (B). Both bacteria were identically processed using cryosubstitution procedures. Note the combination of gram-positive and gram-negative features present in the cyanobacterial cell wall, like the thick peptidoglycan layer and the outer membrane, respectively.

Hoiczyk and Hansel (2000) add that...

  ... Despite their overall gram-negative structure, the peptidoglycan layer found in cyanobacteria is considerably thicker than that of most gram-negative bacteria. (emphasis mine)

In conclusion, cyanobacteria are Gram-negative bacteria. However, their envelope show some features os Gram-positive bacteria. Besides that, there is variation withing the group.

Source:

Hoiczyk, E. and Hansel, A. (2000). Cyanobacterial Cell Walls: News from an Unusual Prokaryotic Envelope. Journal of Bacteriology, 182(5), pp.1191-1199.


How do prions transmit their conformation to other proteins? I was reading about prions and many sources say something to this effect:

"Prions may propagate by transmitting their misfolded protein state: When a prion enters a healthy organism, it induces existing, properly folded proteins to convert into the misfolded prion form. In this way, the prion acts as a template to guide the misfolding of more proteins into prion form." (Wikipedia)

How can/does a prion cause another protein to change its shape to match the prion's?

It is thought that infectious prions exist as clusters forming a crystalline structure. When a protein with the same primary structure is encountered but with a different tertiary structure, the normal protein undergoes a conformational change in order to integrate into the cluster. Presumably there are molecular forces involved that induce the conformational change.

http://www.rsc.org/chemistryworld/Issues/2005/October/prions.asp


Would a person live longer, if such a person lived in a planet with lower gravity? (say, Mars) I was wondering: some companies plan to colonize Mars, many of us know.

But if one were to live on Mars, would this person live longer?

It seems to me that a lower gravity would mean less overall damage to the body cells, so they could last longer: resulting in a longer lifespan.

Or maybe lack of gravity = lack of exercise = lesser lifespan?

I'd like the opinion of some expert in the matter. Thanks.

Probably not. There's a thing called Hayflick limit, which is basically a limit of life expectancy caused by a shortening of telomeres with every cell division. And since most of our cells complete cycles more based on time (life cycle of RBC 100 days), and not due to damages to a cell, our telomeres would still shorten at the same rate. Of course the gravity could play a small part once organs have started failing, but there are many other factors that affect how long it takes for everything to completely deteriorate, and wouldn't have a big role. In fact, it could even shorten life expectancy, seeing as how our bodies are currently built to live in our current gravitational field. Without gravity, our muscles could become weak, causing other problems, which is why people at the space stations have frequent dedicated times to workout, to keep their muscles fit.


What is a bacterial biofilm? Bacteria produce something called a biofilm.

I have found a few definitions; some say it is a complex of live and dead bacteria and others say it is a layer on cell wall.

What is it made of?
What is its purpose?
How do we combat biofilms when we encounter them?

Aside from the actual microbial cells themselves, biofilms are a slime matrix made of a variety of substances, including DNA, lipids, proteins, and other signaling molecules, but the major component is something called extracellular polymeric substance (EPS), also known as exopolysaccharides.

Succinoglycan from Sinorhizobium meliloti

These are high molecular weight extracellular (exo) polymers (poly) of sugars (saccharides) linked together into long linear or branched chains, which can be modified by moieties such as phosphate, sulfate, acetate, and succinate. As the biofilm forms (below), channels can form in the EPS to facilitate nutrient uptake and distribution, hydration, and inter-cellular signaling such as quorum sensing. Biofilms are often composed of multiple species of microorganisms, from bacteria and archaea to fungi and algae, with the social (and physical) structure dependent on the species that compose it.


The role of antibodies interacting with cancer I'm learning about antibodies. As I understand it, antibodies detect stranger cells/bacterial/viruses by the molecules present in their membranes. In cancer cells, the cancer cell have produce some unknown protein, so why antibody cannot detect that molecule and kill them?

Is it that the cancer cell is surrounded by a normal cell?

Or is the protein it produces is not obvious in the cell membrane?

Or that the protein can bypass antibody? if so, why?

This article on the University of Kentucky website is pretty good, it seems the cancer cells hide because they do not express CD80, a co-stimulating molecule. Co-stimulating molecules are often necessary for an effective immune response.

This is a big part of the article and I think they do a good job of explaining it so I'll just quote:

  "People once thought that cancer occurred because of a weakness in the
  body's immune system," says Yannelli, "but we have known for years
  that overall that is not the case. The immune system in cancer
  patients actually works quite well. Otherwise, they could not survive
  the disease for long periods of time nor could they fight off other
  viruses, which they routinely do. The problem is not that the immune
  system doesn't work; it is that the immune system doesn't recognize
  the tumor."

  According to Yannelli, for the body's defense system to work properly,
  key antigens must be presented in a specific way to lymphocytes, the
  cellular mediators of the immune system, which then kill the cancerous
  cells. Normally, antigens are tipped off by co-stimulating molecules.
  When the co-stimulating molecules are not present, the immune system
  does not "see" the cancer cell, and therefore does not act to destroy
  it.

  Scientists have discovered that lymphocytes have very narrow job
  descriptions, each one designed to attack only a specific molecule.
  The researchers have also discovered a wide range of co-stimulating
  molecules. A critical co-simulating molecule is CD80. Because cancer
  cells do not express CD80, they are invisible to the lymphocytes
  responsible for destroying them.

This paper has more on the function and mechanism of CD80.

Thanks to @Nico for pointing out that not all cancers are the same so the generalization discussed in this answer may not be true of all cancers.


Can one use a hemocytometer on a compound upright microscope? I'm posting this as a follow-up on What to look for when buying a light microscope?. The answerer states that you would need to use a an inverted microscope to count cell in the hemocytometer(counting chamber).

I've read, partly, a book on lab diagnostics tests and it was not written that there. Moreover, they mentioned things about microscopes featuring a compound upright microscope both in words and picture.

Yes it can. You will want to use a thin hemocytometer and the working distance of the objective (20x) needs to be long enough to focus both the cells under the cover glass and the grid under the hemocytometer. Because you are looking at it from the top it would be helpful probably to have some phase on the scope to increase your contrast so that you can more clearly see the grid.

Hemocytometers are most commonly used with inverted microscopes because inverted microscopes are the most convenient microscope for performing tissue culture, and 's a commonly used to count cells when passaging or setting up an experiment etc, as they allow you to view cells in a culture plate. Upright microscopes require that you make a slide.


Why do humans have digestive system present at front and kidneys back? Outlet of digestive system is present at back of the body but its digestive system at front.

Outlet of urinary system is present at front of the body but its system present at back.

Why do humans have digestive system present at front and kidneys back?

I don't claim to have the full answer to why these organs are located in the way they are, but I think these factors have an influence on the anatomy:

1- The urinary system's link with the reproductive system in male mammals: The male reproductive system outlet needs to be located as far to the front as possible in a 4 legged mammal to facilitate sexual function, forcing the urinary system to follow

2- The kidneys are very fragile and need to be protected by the thick back muscles and partly under the rib cage. They would be too vulnerable at the front

3- The urinary system is generally sterile of bacteria, and so is the reproductive system in males, and partially in females. The digestive system isn't sterile in both. The outlet of the digestive system can't be in the front of the genitals in a male as this will increase the risk of urinary infections overall and also genital infections after mating. It can't be in between the urinary and reproductive outlets for the same reason, so it has to be located behind both to cause the least interference with their functions


Does the use of UV light beam lead to poorer contrast in optical microscopy of cells than the higher wavelengths visible light? I am reading about "diffraction-limited system" on Wikipedia, which mentioned

  "To increase the resolution, shorter wavelengths can be used, such as UV and X-ray microscopes. These techniques offer better resolution but are expensive, suffer from lack of contrast in biological samples and may damage the sample."

without giving a more detailed explanation for why the higher energy EM waves might lead to poor contrast. I have tried to search on Google, but still can't find a satisfying answer. Can anyone here kindly refer me to more detailed discussion on this question? Thank you.

Contrast in optical microscopy typically depends on different substances having different absorption spectra. Practically everything absorbs UV light, so there tends to be less contrast in that range than in the visible spectrum where there is a bit more selectivity.  All of this changes when there are contrast-enhancing substances added.  For example, molecules that absorb in one wavelength and emit at a different wavelength via fluorescence, attached to antibodies that bind selectively to specific cell components, can provide very high contrast.  E.g., see [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2156041/].

An alternative optical microscopy technique is phase-contrast microscopy which does not use absorption at all.  Instead, it measures the effective optical path length through the sample, which depends on local refractive index of the sample.

Yet another alternative is x-ray fluorescence microscopy, which can identify specific elements in the composition of a sample.  See, for example,[https://www.americanlaboratory.com/913-Technical-Articles/18833-Three-Dimensional-Elemental-Imaging-Using-a-Confocal-X-Ray-Fluorescence-Microscope/].


What is this plant with white-spotted thorny leaves from Morocco? What is this plant with white-spotted thorny leaves from Morocco? Photographed in spring.

The distinctive leaves identify the plant as Silybum marianum. It is a member of the plant family Asteraceae. It is commonly called "milk thistle". Originating in the Mediterranean region, it has now spread to many places around the world.  The plant in your photo is immature at ground level. These links will give a better idea of the mature plant.

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

https://www.google.com/search?q=silybum+marianum&source=lnms&tbm=isch&sa=X&ved=0ahUKEwiG46Kj6L7aAhWvpFkKHfYjA0AQ_AUICigB&biw=1097&bih=642


How can cane sugar sucrose be different from beet sugar in regard to carbon-13 content? According to an article in SCIENZA IN CUCINA, by Dario Bressanini, le Scienze Blog content of $^{13}C$ differs in sucrose in beet sugar compared to cane sugar. What is this due to? Are there any similar examples?
Is the difference in synthesis enough to explain the difference?
One could guess that the weight of the carbon molecule is more critical in one of the synthesis chains.

The differential uptake of different isotopes of carbon is covered well at:
https://en.m.wikipedia.org/wiki/Fractionation_of_carbon_isotopes_in_oxygenic_photosynthesis
Plants have a lower proportion of C-13 than atmospheric CO2.
The two mechanisms that cause this are the reduced diffusion speed of the heavier C-13, and an energetic difference in the chemical reactions that favours C-12.
In sugar cane (C4 photosynthesis) the carbon dioxide is captured in an additional step compared with sugar beet (C3 plant).
This capture step in C4 plants (using phosphoenolpyruvate carboxylase) is less exclusive toward C-13, so the carbon in these plants has detectably more C-13 than C3 plants.
This subsequently affects the isotopic proportion of all the carbon in the plant


What happens to bones that do not heal? I would like to know the steps the body takes to heal a broken bone and what happens if it cannot heal properly.  I am not looking for advice or explanations on resting and not doing activity, I am genuinely interested in understanding the outcome if activity is not stopped

Here is the scenario:

A rock climber develops a pain in the lower part of their middle finger.  The pain is not so bad so the climber continues to climb for four weeks, but the pain has not gone away.  The climber decides to go to the doctor fearing they have an A2 Pulley tear.

To their surprise the Doctors tests show no A2 pulley tear but rather a minor stress fracture of the Proximal Phalanx.  The doctor says stop climbing, however the climber has several trips planned and does not experience any pain while climbing nor a loss of strength or power while climbing.  The only time pain is felt is when the lower part of the middle finger is squeezed.  Because of this the climber decides to continue climbing as they just love it so much.

Question:  What will happen to a stress fracture in the finger if adequate rest is not given?

I understand the first thing the body does is try to stabilize the break and then starts to repair.  What happens if it is continually used and not given the chance to properly heal?  Will the climber just have a sore spot on their finger for the rest of their life or will it progressively get worse and worse?

Fracture healing occurrs in several steps:

haemorrhage: blood and surrounding cells fill the space created by the fracture.
fibrous callus: chondrocytes colonize the fracture space, with neovascularization.
bony callus: osteocytes colonize the fracture space and rearrange in woven bone
remodelling: in long bones, woven bone is remodelled into lamellar bone and creates a new haversian system

If the fracture is not immobilized enough (not enough rest), several things can happen that are mutually exclusive:

normal healing: luckily, the bone is not too much mobilized and is able to heal normally
fracture displacement: the bone heals, but in an incorrect alignment. This gets partially corrected over time, but the correction mechanism is limited, especially in adults.
pseudarthrosis: the worst case. instead of normal healing, cartilage grows to protect the bony extremities that are mobilized and prevents further healing. This causes pain, and will require surgery in most cases.


Why is flash light harmful to what aquatic life forms? When visiting an aquarium, it's often not allowed to take photographs with a flashlight on. It is said that the flash light with very high intensity is harmful to the displayed life forms.

I respect that and try to capture images without flash.

I'd still like to know how flash light interacts with the animals (or even the plants) in an undesirable way? Is it harmful because they are not used to it?

The light emitted from the arc of a welder for example is so intense, that it destroys the human eye. Laser is another example. Technology is so advanced that we can produce harmful light sources that not even the winking reflex can protect us against. Maybe a flashlight used for photography is the welding arc for aquatic life?

Additional light can increase growth of algae, which would in turn influence the (very little) ecosystem in an aquarium. On the other hand, I don't think the short bursts of light from photographic flashes introduce enough light to have an impact. Or do they?

The motivation for this question is not to be knowledgeable about what creatures are not harmed by flash in order to fry them in light. Advancements in camera technology make it unnecessary to add more light to the scene in the form of flash light. What made me curious about it is that except for the industrial light sources mentioned above, we rarely consider single bursts of light to be dangerous for us humans. We are much more concerned about the continuous sunlight.

I am sure the main reason is that flash lights, certainly in a dark aquarium, are very frightening and might cause temporary blindness for the animals. If someone flashes in your eyes, you can't see for a few seconds as well. That will cause distress for the animals and distressed animals live considerably shorter.

The total amount of light is indeed much to small to cause algal growth and real blindness is not likely from camera flashes.

EDIT:
I've found this article that will certainly be of interest to your question.


Isolating a specific gene (specifically TRAV* series of genes) for sequencing I'm trying to figure out (for pedagogical purposes) the right way to isolate and PCR the regions coding the T-Cell receptor.

My understanding is that I would need to use restriction enzymes that target regions near the start and end of the gene. I was looking at a bunch of different restriction enzymes on this site: https://www.addgene.org/mol-bio-reference/restriction-enzymes/

What I'm not sure about is: how do you pick the combination that will specifically cut out that gene and not any of the other ones? It seems like the restriction enzymes only consist of a few base pairs, and I would guess they can slice at many many sites.

Furthermore once it is cut, how do I isolate just the DNA for the gene I want to sequence as opposed to the rest of the junk DNA?

Restriction enzymes are usually only used when you do molecular cloning using plasmids or other forms of shorter DNA moleclues, since - like you said - using them on genomic DNA would cut it into much more than thousands of pieces.

Instead what you can do is perform your PCR directly on the genomic DNA (or potentially cDNA, if you want to get rid of introns).
Doing PCR on genomic DNA is often a bit tricky (i.e. you'll likely have to try different conditions to get a product), but generally possible. If you want to analyse the whole coding region it might be better to extract mRNA instead of DNA and reverse transcribe it, so that can amplify the coding region as one block, that doesn't contain Introns - PCR on cDNA is also easier than on genomic DNA.

Another thing you need to look out for is that T-Cell-Receptors (similar to antibodies) are different in every T-Cell. This means that you can't use Sanger sequencing, which will only give you a proper result if you input has the exact same sequence. To get the sequences of a mix of T-cells you would need to use next-gen sequencing.


How do diving marine mammals avoid decompression sickness? How do marine mammals, whose very survival depends on regular diving, manage to avoid decompression sickness or "the bends?" Do they, indeed, avoid it?

I think I got the answer....

  The primary anatomical adaptations for pressure of a deep-diving mammal such as the sperm whale center on air-containing spaces and the prevention of tissue barotrauma. Air cavities, when present, are lined with venous plexuses, which are thought to fill at depth, obliterate the air space, and prevent "the squeeze." The lungs collapse, which prevents lung rupture and (important with regard to physiology) blocks gas exchange in the lung. Lack of nitrogen absorption at depth prevents the development of nitrogen narcosis and decompression sickness.

Source: Scientific American


What is the proper quick freezing /snap freezing protocol for pancreatic tissue? I would like to do a quick freeze on pancreas from mice. I want to then make sections (30 µm thick).  The idea is to preserve a fluorescent staining done in vivo.

I do not know if I should place my fresh tissue directly into liquid nitrogen, then embed the tissue in OCT, and then freeze everything in cold isopentane?

Or do I have to embed the fresh tissue in OCT first, prior to putting everything in nitrogen?

Or is there another protocol to do quick freezing in order to do sectioning?

Embed the tissue in OCT first (roughly cut to remove everything what is not needed) and the flash freeze it. Then you can cut your sections.

The first protocol describes it in detail, the second gives some additional information:

Protocol for Preparation of Frozen Tissues for Sectioning
Tissue freezing methods for cryostat sectioning


Can RNA be extracted from tissue suspended in formalin? There are two tumor samples floating in a 10% formaldehyde solution (i.e formalin). Is there a protocol for RNA extraction under these circumstances? I am concerned that using the protocol for Formalin Fixed Paraffin Embedded (FFPE) tissue will damage the RNA, since there is no paraffin for the xylene to remove.

If I were to use the FFPE protocol without xylene, should I homogenize the tissue before removing the formalin, or after?

Formaldehyde forms adducts with RNA and can also make it more susceptible to degradation. It can also cause crosslinks to form between RNA and proteins (or possibly other RNAs). For all these reasons extraction of high quality RNA from formaldehyde fixed samples is very difficult and the yields are low (Howat and Wilson, 2014).

Have a look at this article by Evers et al. (2011) which explores optimal conditions for removal of the formaldehyde adducts. However, this study does not involve actual RNA extraction from fixed tissues, which would be even more difficult.

RNeasy FFPE Kit from Qiagen claims to be specially designed for RNA extraction from formaldehyde fixed samples. The product description says that the lysis buffer contains substances that reverse the modifications formed because of formaldehyde. There is a similar kit from Thermo-Fisher. Russel et al. (2013), report that the RNA yield was similar between fixed (using Qiagen RNeasy FFPE kit) and unfixed samples (using Qiagen RNeasy Plus mini Total RNA extraction kit).

  should I homogenize the tissue before removing the formalin, or after?

Homogenize after removing formalin. Since the tissues are already brittle because of formaldehyde fixation, you need not use harsh homogenization procedures. Pipette gently. You can use proteinase-K and DNAse to remove proteins and DNA respectively (RNeasy kit involves these steps).

For future experiments, you can store the tissues in RNAlater solution (Thermo-Fisher; or similar formulations from other vendors/lab). Store one part of tissue in formaldehyde for IHC/ISH and the other in RNAlater for RNA/DNA extraction.


Distribution of synapses of CA1 neurons In the Wikipedia article on dendritic spikes I read:

  In the hippocampus, the CA1 neurons contain two distinctive regions
  that receive excitatory synaptic inputs: the perforant path (PP)
  through the apical dendritic tuft (500-750 μm from soma) and the
  Schaffer-collateral (SC) through the basal and apical dendrites
  (250-500 μm from soma).

I wonder how the distinctiveness of these two regions does appear when plotting the number of synapses as a function of the distance to the soma:

More like the gray, or more like the red, or more like the green curve? Or which other?

One source for this estimate is Megias et al. 2001, an electron microscopy study in CA1 of the rat hippocampus.

I plot their data from Table 3 in the following graph.

The X-axis is not in micrometers. Rather it represents dendritic subclasses. $Ori$ stands for Stratum Oriens, $Rad$ for S. Radiatum, $L-M$ for Lacunosum-Moleculare, $T$ for thick dendrites, $t$ for thin dendrites, $prox/med/dist$ for proximal, medial, and distal, respectively. Stratum Oriens represents basal dendrites that are close to the cell body, stratum Radiatum apical trunks, and stratum Lacunosum-Moleculare the apical tufts. The approximate locations of the layers in reference to the cell body are (in micrometers): $Ori = (-100, 0)$, $Rad = (100, 350)$, $L-M = (350,550)$. The Y-axis represents the total number of synapses, both excitatory and inhibitory.


What is the best way to express two proteins in a mammalian cell? I have two proteins and I will be preparing a vector with both genes for stable transfection. Each protein will have their own promoter and I will use piggyBac vector to insert a single cassette with both genes in it into the chromosomes. My questions are:

If I use the same promoter (CMV, SV40 or an inducible one) for both genes how would this affect the expression levels? I read in some papers that one of the genes might get expressed lower than the other. If you have first-hand experience I will be grateful if you share it.
If I use the same promoter for both, but put them far away (i.e. ends of the cassette) would the expression levels get affected again? It sounds simple enough but I think people would have published something if they had a good result with that.
If I use different promoters for each gene (e.g. CMV for one and Tet-inducible for the other) how would it work? I couldn't find a paper which used this and I would like to continue with this approach; therefore, if you have any experience I will be really grateful for any help.

I don't want to use IRES or 2A-peptide. I would like to be able to control this experiment in transcription stage.

You can use a bidirectional promoter. The problem that you mentioned about proteins not expressed in same level happens because of competition for polymerase. But there are well optimized parts and also commercially available vectors that work fine.

You can clone genes in a serial order. It won't be a problem. Just leave a 100bp linker after the polyA signal of previous gene. If your cassette becomes too huge, then insertion becomes slightly difficult. That's why people use IRES or TA-peptides, etc.

Retroviral based insertions work quite decently, but you can't control copy number variation between different cells.

You can use two different promoters. The dynamics will depend on the promoter strength and concentration of inducer.


Why do I see purple stripes when moving a small source of light (flashlight) quickly in a dark room? I was playing with my phone's flashlight (white) in a dark room, Just moving it around quickly when I noticed that I could see thin stripes of purple in the same shape as my hand moved, they didn't disappear instantly rather I could see them like a net of thin purple strips, but vanished when I looked at them for more than 2 seconds. I don't understand why it happened and was curious.

This phenomenon is called afterimage and happens because of adaptations of the photoreceptors in the retina of your eye to the stimulation by light and adaptations by your neurons in the visual processing in your brain.


RMSD during conformational transition in proteins When I was investigating the differences between protein structures obtained by X-ray crystallography and NMR spectroscopy, I found the paper [1] compairing structures of several proteins resolved both with X-ray and NMR. The average root-mean-square deviation (RMSD) between NMR and Xray structures is 1.4Å (max. 3.6Å), and the average RMSD between different NMR structures for same protein is 0.4Å (max. 1.3Å). I've checked some proteins studied in this paper, and they are mostly within 100–200 residues long.

However, there are plenty of papers (e.g. [2], [3], dealing with similarly sized proteins) that base their statements about conformational transitions on structures with RMSD difference 1–2Å.

I wonder what is considered reliable RMSD between two structures to draw any solid conlusions about conformational transitions (e.g. upon ligand binding) as opposed to simple thermal fluctuations or perturbance caused by the method to obtain structure?

Of course, the best way (at least in my opinion) to distinguish actual conformational transition from thermal fluctuations is to measure its lifetime, but it is often not an option.

 Andrec M, Snyder DA, Zhou Z, Young J, Montelione GT, Levy RM. 2007. A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing. Proteins 69: 449–65.
 Grant BJ, Gorfe AA, McCammon JA. 2009. Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics. PLoS Computational Biology 5(3): e1000325.
 Kumaraswami M, Newberry KJ, Brennan RG. 2010. Conformational plasticity of the coiled-coil domain of BmrR is required for bmr operator binding: the structure of unliganded BmrR. Journal of Molecular Biology 398: 264–75.

The best way to distinguish "actual conformational transition from thermal fluctuations" in a protein is to (determine and) compare atomic-resolution structures of the ligand-free and ligand-bound protein.

http://www.rcsb.org/pdb/home/home.do


How come large herbivores have such thin legs? Edit:
This question is very similar to this and related to this one (though the latter focuses on homology instead of scaling laws). However, the answer to this question is far more comprehensive, in particular it offers a plausible explanation why horse legs evolved as they did (vs human or even rhino legs).

Large grazing mammals such as horses, moose, and cows tend to have relatively thin legs despite being up to ~1000kg. For example, this rider's and her horse's legs appear to have about the same cross-sectional area both for below and above the "knee":

If this horse is 500 kg (a mid-range mass for horses), each leg would have to support 125 kg, compared to only 37.5 kg for a 75 kg adult. Why don't we see a corresponding difference in cross-section?

Elephant, rhinoceros, &c all have much thicker legs in proportion.  The answer, I think, lies in the fact that the animals you mention all evolved as cursorial animals (that is, they run to escape predators).  Less mass in the lower leg means it swings easier, so the animal can run faster.

There are two things you're apparently not noticing in that picture.  First, the the horse's lower leg is almost entirely bone (and some tendon), and it's bone that does the supporting.  The propulsive power comes from the large muscles of the hip, thighs, and shoulders.

Second, the lower part of the leg (with the white wrappings) is not anatomically equivalent to the human's lower leg, but to the bones of the hand and foot.  You can see this if you look closely at the rear leg in that picture.  The femur, equivalent to the human's thigh, ends at the knee just above the belly line.  Then the tibia extends about halfway down, ending at another joint which you might think is the knee, but which is called the 'hock' in horse-speak.  The white-wrapped part is a metatarsal, equivalent to human foot bones, then there pastern bones equivalent to human toe bones, ending in the hoof/toenail.

So consider that you can, if reasonably fit, walk around on tiptoe without crushing your foot and toe bones, then imagine the end result of your ancestors having done this for the last several tens of millions of years :-)

PS: With horses, there is some effect from human selection, too.  Racing & show breeds tend to have thin lower legs, draft horses & working breeds have proportionately thicker ones.  My first horse, a thorobred/arab mix, had legs about as thick as my wrists (granted, I'm a fairly muscular guy); my current mustang, about the same height & weight, has legs about twice as thick.


Connectivity of the Superior Colliculus Does anyone know anything about the connectivity of the superior colliculus? Or know of any straightforward published literature?

I've got that the superficial layers receive input from the visual system and the deep layers have multi-sensory inputs, but I'm finding conflicting information about the specifics.

I've read one source that suggests inputs are from magno and konio cellular retinal ganglion cells. But as I understand it, these are cell types in the lateral geniculate nucleus, so it's not clear if the inputs are from the LGN, or the retina.

Edit: Figure 2  here, shows "koniocellular" ganglion cells. Which I can't tell if they're meant to come from the LGN, or retina.

This article discusses some of the connectivity, but only with regards to eye fixation, rather than a general overview.

(About the tectospinal tract) the tectospinales fibers originate in the superior colliculus, its axons pass ventromedially by the central gray matter and cross in the posterior tegmental decussation. The upper colliculus receives visual information, and the tectospinal tract is believed to act as a mediator of reflex eye movements in response to visual stimuli (Neuroanatomy of Crossman and Neary pg 81).

A relatively small number of fibers leave the optic tract, before reaching the dorsal nucleus of the lateral geniculate body, to terminate in the pretectal area and superior colliculus (fibers involved in pupillary reflex mediation) (Neuroanatomy of Crossman and Neary pg 157).


Which of the following lacks DNA? a) An Enucleated ovum
b) Mature RBC
c) A mature spermatozoan
d) Hair root

According to me, there can be 2 answers, a and b because an ovum whose nucleus has been removed lacks DNA. And also, initially RBC has a nucleus but as it matures it's nucleus disappears. So, mature RBC should also lack DNA. Then which one will be a more appropriate answer ?

There are two answers if the question refers to genomic DNA (neither enucleated ova nor mature RBCs have genomic DNA).  However, since the question doesn't specify genomic DNA, we can exclude enucleated ova, which would still have mitochondria and therefore mitochondrial genomic DNA.  Mature RBCS (at least in most mammals) do not have mitochondria, so the safest answer is probably b) Mature RBC.


Will salting the ground kill insects and spiders? I want to kill the insects and spiders living in my egress using something non-toxic to humans, dogs. I was thinking copious amounts of salt would kill earth dwelling bugs and what appears to be ground spiders with funnel like webs. The insects seem to be majorly silverfish. I am in Missoula Montana.

I think the bugs are coming from the egress. Here's an internet photo similar to my egress. The ground at the bottom is the area in question.

Dusting the area with a diatomaceous earth based insecticide ought to do the trick, while being essentially non-toxic. If you want to prevent plant growth there too then of course salt the earth.

See Efficacy of modified diatomaceous earth on different cockroach species (Orthoptera, Blattellidae) and silverfish (Thysanura, Lepismatidae)


Why do some vegetables taste bitter? Bitter gourd, cucumber, etc. are bitter to taste. Which chemical causes bitterness in them?

I found these when I searched online: this says that it is because of calcium, while this and this talk about physical effects.

Nice question! Many vegetables taste bitter because they contain compounds known as phytonutrients (Greek phyto = "plant"). There are more than 2500 phytonutrients known, and the most important (and common) ones are categorized as1:

Carotenoids: they are the ones that give red/orange/yellow color to some vegetables. They are mainly antioxidants, but some of them, like $\beta$-carotene and $\beta$-cryptoxanthin, are good for eyes as they can be converted into vitamin-A, whose derivative forms a part of phototransduction cascade.
Ellagic acid: it is found in a number of berries, such as strawberries, raspberries, pomegranates, etc. and has been shown in vitro to be helpful in slowing the growth of cancer cells and aid liver in neutralizing cancer-causing chemicals.
Flavonoids: they are found in a large variety of plants and constitute a large number of phytonutrients. Some flavonoids, like catechins, hesperidin and quercetin are very good for health. For example, see this answer for effects of catechins on the body.
Resveratrol: it is found in grapes, red wine, etc. and shows antioxidant and anti-inflammatory effects. Some researches have also concluded that it may reduce risk of heart disease and certain cancers.
Glucosinolates: these are found in cruciferous vegetables, like sprouts, cabbage, etc. and help checking formation and growth of cancer. This is the one we're talking about, so I'll continue about this below.
Phytoestrogens: they can exert estrogen-like effects on the body because of their structure, and even block body's natural supply of estrogen. Isoflavones can also reduce risk of endometrial cancer and bone loss in women. They are also found in a large number of plants, including soybeans, oats, barley, rice, apples, carrots, etc. (see full list here).

Another category, alkaloids, has been discussed by @WYSIWYG in their answer. These are all made naturally by plants as a part of their defense mechanism against insects and pests. This, in part, explains why they are bitter.

Coming to main point, glucosinolates are organic compounds that are responsible for bitter taste and pungent smell of many cruciferous vegetables. They are derived from glucose and amino acid, and contain sulfur and nitrogen as constituents. When they are cooked, chewed, or otherwise damaged, an enzyme myrosinase cleaves the glucose molecule, while the remaining molecule converts into isothiocyanate, thiocyanate and nitrile2, which cause the bitter taste and pungent smell (think of the isocyanide test you performed in grade XI and the smell it produced ;) The reaction looks like this:

source

A special glucosinolate, sinigrin, has been shown as responsible for the bitterness of Brussels sprouts and cauliflower3. Also, high concentration of glucosinolates are toxic to humans as well as other animals, though tolerance levels vary even within the same genera (Acomys cahirinus and Acomys russatus)4. So, that partly explains why these compounds are bitter.

Talking about the anti-cancer properties of glucosinolates (going a bit off-topic just so that you know why these are good for you), two of the main compounds that are responsible for such effects are sulforaphane and indole-3-carbinol. Sulforaphane (in which R- becomes C5H11OS- in R-NCS), for example, is derived by the action of myrosinase on glucoraphanin (again, a glucosinolate). It has been shown to have anti-cancer properties. For example, Li et al, 2010 have shown that sulforaphane prevents breast cancer by inhibiting breast cancer stem cells and downregulating the Wnt/$\beta$-catenin pathway (yeah, there is something like cancer stem cell!). In another research, Hsu et al, 2011 showed that sulforaphane prevents prostate cancer by inhibiting HDACs (histone deacetylases, which interfere with normal functioning of tumor suppressor genes) and DNA methylation. This example was just to mention about the anti-cancer properties of glucosinolates in general.

Another class of compounds, called cucurbitacins, are produced in plants of Cucurbitaceae family. Unlike phytonutrients, cucurbitacins are considered a type of steroid since they are derived from cucurbitane and stored as glycosides5. Their derivatives are also found in other families like Rubiaceae, Rosaceae and even some marine mollusks, and, much like glucosinolates, they are also produced for defense against herbivores.

However, it is not sure whether only glucosinolates are the only compounds responsible for bitterness of vegetables. A study suggests that increased levels of calcium can also be responsible for bitterness of vegetables6, although its evolutionary cause and mechanism of action are unknown yet. Also, it may even depend on the person(!). If you are a supertaster (which has high chances to be true if you're woman or from Asia, South America or Africa), you will tend to be highly sensitive to bitterness of Brassica oleracca cultivars, such as kale, Brussels sprouts or cabbage7,8. Sensitivity to coffee, green tea, mushrooms, etc. is also known to increase. You can view a full list on Wikipedia.

References:

 1. Phytonutrients - WebMD

 2. Burow, M; Bergner, A; Gershenzon, J; Wittstock, U (2007). "Glucosinolate hydrolysis in Lepidium sativum--identification of the thiocyanate-forming protein.". Plant molecular biology. 63 (1): 49–61.

 3. Van Doorn, Hans E; Van Der Kruk, Gert C; Van Holst, Gerrit-Jan; Raaijmakers-Ruijs, Natasja C M E; Postma, Erik; Groeneweg, Bas; Jongen, Wim H F (1998). "The glucosinolates sinigrin and progoitrin are important determinants for taste preference and bitterness of Brussels sprouts". Journal of the Science of Food and Agriculture. 78: 30–38.

 4. Samuni Blank, M; Arad, Z; Dearing, MD; Gerchman, Y; Karasov, WH; Izhaki, I (2013). "Friend or foe? Disparate plant–animal interactions of two congeneric rodents". Evolutionary Ecology. 27 (6): 1069–1080.

 5. Jian Chao Chen, Ming Hua Chiu, Rui Lin Nie, Geoffrey A. Cordell and Samuel X. Qiu (2005), "Cucurbitacins and cucurbitane glycosides: structures and biological activities" Natural Product Reports, volume 22, pages 386-399

 6. Tordoff MG, Sandell MA. Vegetable Bitterness is Related to Calcium Content. Appetite. 2009;52(2):498-504. doi:10.1016/j.appet.2009.01.002.

 7. Dinehart, M.E.; Hayes, J.E.; Bartoshuk, L.M.; Lanier, S.L.; Duffy, V.B. (2006). "Bitter taste markers explain variability in vegetable sweetness, bitterness, and intake". Physiology & Behavior. 87 (2): 304–13.

 8. Drewnowski, Adam; Henderson, Susan Ahlstrom; Levine, Alisa; Hann, Clayton (2007). "Taste and food preferences as predictors of dietary practices in young women". Public Health Nutrition. 2 (4).

 9. Li Y, Zhang T, Korkaya H, et al. Sulforaphane, a Dietary Component of Broccoli/Broccoli Sprouts, Inhibits Breast Cancer Stem Cells. Clinical cancer research : an official journal of the American Association for Cancer Research. 2010;16(9):2580-2590. doi:10.1158/1078-0432.CCR-09-2937.


Possibility and feasibility of producing designed antibodies with bacteria As stated here it is possible to produce fragments of antibodies in bacteria and harvest them (from the medium, I guess, but I don't have access to the full article).
As it is possible to design antibodies, would it be possible and feasible to produce important antibodies large scale through bacteria like it is done for example with insulin?

I'll preface this by saying that I'm talking about antibodies of mammalian/human origin, consisting of two identical heavy and two identical light chains disulfide-bonded into the classic antibody structure:

It is possible to produce antibody-like molecules known as single-chain antibodies, including single-chain variable fragments (scFv) in bacteria and viruses, where it is also known as phage display. These hosts can also produce a modified Fab fragment that is engineered as a single polypeptide chain, and multiple other single-chain antibody-like molecules as shown below. In the past, this has primarily been done in E. coli, as they are a common tool used in protein expression, and have many advantages as an experimental system in general. However, single-chain antibody production in E. coli is hampered by the fact that these exogenous proteins tend to form inclusion bodies instead of being secreted into the medium, where they can be collected and purified much more easily, without the need for lysing the host cells. The paper you linked to describes a method for producing scFvs in the Gram-positive bacterium Bacillus megaterium, which is becoming more common for the production of recombinant proteins.

So, it is possible to produce antibody-like molecules in bacteria. However, unlike insulin, full-length antibodies are made up of multiple polypeptide chains, and are both glycosylated and disulfide-bonded. While there is evidence that bacteria can accomplish both of these biochemical tasks, the processes seem to require additional chaperone, trafficking, and regulatory proteins that bacteria do not possess, and as far as I know scientists have so far not been successful in producing full "proper" antibody molecules in prokaryotes.

However, there are many mammalian/human expression systems for producing fully functional recombinant antibodies in very high yield, and a number of FDA-approved monoclonal antibody drugs are now on the market, with many more in various stages of development and clinical trials.


What kind of shiny bronze beetle is this? Lots of these on my rosemary bush

About 7mm long

The plant helped identifying the beetle: This is a rosemary beetle (Chrysolina americana), which feeds on rosemary,  lavender and thyme. See here and here for some more information.


Identification of fuzzy insect in Pennsylvania I live in south eastern Pennsylvania, USA. About a month ago I came across this very peculiar insect. Its body was about an inch long, it was fuzzy, and it had a long proboscis(?) and long orange legs.  I've been wondering about it ever since. Can anyone identify it?

This is the nymph of a bug (Hemiptera) from the Genus Arilus, probably Arilus cristatus, also known as "wheel bug".

Here is another image of it, for comparison:

Source: http://bugguide.net/node/view/288330

And here is the adult:

Source: https://en.wikipedia.org/wiki/Wheel_bug


What's the difference between male and female? As long as we only look at humans the differences are clear: males have chromosomes XY, produce sperm and don't get pregnant. Females have chromosomes XX, produce egg cells and bear babies. But when you consider other species, things are more complicated: in birds, it's females who carry the Y chromosomes. In pipefish and sea horses, it's the males who get pregnant. So maybe the only reliable criterion to tell if an animal is a male or a female is looking at its reproductive cells, and decide if they look like spermatozoa or egg cells. But then there are male and female plants, where none of the methods above applies.

So how do you tell, in general, who's male and who's female in a species? Or is the distinction arbitrary?

Sexes (male and female) are generally defined in terms of Anisogamy, which means that there are size differences between the gametes (i.e. the reproductive cells that fuse at fertilization). The sex with smaller gametes is defined as male and the sex with larger gametes is defined as female, and individuals that can produce both types of gametes are called hermaphrodites. This is the case in both animals and plants (plants have pollen vs. ovules and microsporangia vs. megasporangia), and the definition of sexes is therefore not dependent on chromosomal makeup as such or which sex that carries the young. Actual sex determiniation in a particular species is often based on chromosomal inheritance though, but other systems also exists (e.g. environmental cues or sequential hermaphroditism). Anisogamy also comes in several different types, where animals generally have Oogamy, where males have small mobile spermatozoa and females large stationary egg cells.

More generally, Anisogamy is a special case of mating types in sexually reproducing organisms, where fertilization (on syngamy) generally can only occur between gametes of different mating types. In for instance fungi, gametes of different mating types are of the same size (isogamous) and they are therefore only labelled as mating types (e.g +/-) and not different sexes. Functionally, if we are simplifying the issue, male gametes can be viewed only as carriers of genetic information, while female gametes also contain the nutrients necessary for the early development of a newly formed embryo.


Why are fearful stimuli more powerful at night? For example, horror movies appear to be scarier when viewed at night than during broad day light.

Does light have any role in this phenomenon?

Are there changes in hormones at night versus during the day that makes fear stronger?

Short answer
The increased fear responses during the night are believed to be mediated by elevated corticotropin-releasing hormone (CRH) levels in the brain that drive the fear responses in the amygdala.

Background
Fear responses can be experimentally assessed by recording the startle reflex. For example, loud noises can evoke gross startle responses in rodents (whole-body startles) and more subtle responses in humans (eye blinks).

In nocturnal animals, it has been shown that startles are facilitated by bright light. In contrast, fear responses in humans, a diurnal species, have been shown to be stronger in the dark (Grillon et al., 2007).

In the rat, the light-enhanced startle is has been associated with the hypothalamic–pituitary–adrenal axis (Fig. 1). Specifically, light exposure has been shown fear mediated by corticotropin-releasing hormone (CRH) (Grillon et al., 2007).

Fig. 1. HPA axis. source: Wikipedia

The HPA-axis is affected by the circadian clock and therefore exhibits a pronounced daily rhythmicity. The HPA axis is activated by hypothalamic release of CRH, which stimulates the secretion of adrenocorticotropic hormone (ACH) from the anterior pituitary. ACH triggers the production of cortisol by the adrenal glands. Cortisol, in turn, provides negative feedback and shuts down HPA-axis activity by binding to corticosteroid receptors in various HPA-axis structures, e.g.the hypothalamus (Fig. 1). As a result, cortisol levels show a robust diurnal rhythm that runs in opposite phase with CRH. Cortisol in humans peaks at the time of awakening and drops to its lowest levels around bedtime, whereas the opposite is true for CRH (Miller & Gronfier, 2001).

The startle reflex shows a diurnal variation roughly opposite to the rhythm of corticosterone and in phase with CRH. Specifically, startle responses in nocturnal animals such as rats are highest during daytime (their passive phase) when CRH is peaking, and corticosterone is at its lowest. Conversely, startles are lowest during the night (their active phase) when CRH levels are lowest, and corticosterone levels are high. In man, a diurnal species, exactly the opposite pattern is observed. Hence, startle responses are thought to be endogenously modulated by the circadian system, most likely via effectors of the central pacemaker such as the HPA-axis (Miller & Gronfier, 2001).

In rats, administration of exogenous CRH enhances the startle reflex and blocking of the glucocorticoid receptors which produces a blockade of negative feedback, also increases startles. Conversely, blocking CRH receptors decreases the startle response, as does corticosterone administration (Miller & Gronfier, 2001).

CRH receptors are expressed at various brain centers, including the amygdala. The amygdala is a key structure in the limbic system, the emotional control center of the brain. The amygdala is specifically associated with anxiety and fear responses. Indeed, it is thought that CRH receptors in the amygdala are responsible for the fear-promoting actions of CRH (Grillon et al., 2015).

Hence, it is not darkness or light per se that mediate fear responses. Instead, it is the circadian control of the HPA axis that controls the daily variations in fear responses.

References
- Grillon et al., Biol Psych (2007); 62(10): 1183–6
- Grillon et al., Neuropsychopharmacol (2015); 40: 1064–71
- Miller & Gronfier, Psychophysiol (2006); 43(3): 297–301


Simple protein graphics software for stick models Anybody know of a good free molecular graphics system that allows PDB file input? I prefer that it does not use Java. I also prefer that it is online, although I would consider recommended software with a simple download process.

I am looking into trying to display a stick version of one of the chains of a protein, and want a program that can help me easily do this.

I have tried using FirstGlance and Protein Workshop, but FirstGlance is difficult to navigate through and the Protein Workshop doesn’t do stick models.

This is an answer simply because I can't fit it all in a comment, or several...

To install and run PyMOL, you'll need a few extras. They are all free and open-source:

Python 2.7.10: Make sure you choose to install pip during the setup process, and also choose to add Python to your PATH, if that option is given. Also, note whether you installed the 32-bit version (x86 MSI installer) or the 64-bit one (x86_64). Which you choose depends on your operating system - if you have a 32-bit OS, you only have one choice. If you have 64-bit Windows, you can do either one - there's no real difference to the casual user. I like 64-bit, but I'm a nerd :)
The numpy+mkl package: I'd get version 1.9.2, as 1.10.0b1 is a beta version. Make sure it's not one of the "unoptimized" builds! You want the cp27 (stands for CPython 2.7) package, either 32- or 64-bit, matching your choice above.
From the same page, the PMW package (choose the py2 version).
Finally, PyMOL itself (both pymol and pymol_launcher packages for cp27).

Once you have everything downloaded and Python installed, open the command prompt by hitting WinR, typing cmd into the box, and hitting Enter. Use the cd command to change to the directory where you downloaded the .whl files (paths with spaces in them should be completely enclosed in double quotes: cd "C:\Users\John Smith\Downloads"). Next, type pip -V to ensure pip works. If it doesn't, just use the whole path: C:\Python27\Scripts\pip -V. Once you get the version statement, you're good to go. For each filename, type pip install really_long_filename.whl to install it. Remember that you can start typing a long name, then hit Tab to complete it. Do this for all four wheels - numpy+mkl, pmw, pymol, and pymol_launcher - in that order.

Once you do that, you should be all set. I'm not on Windows at the moment, so I can't tell you whether you'll get an icon or not, but if you don't, then open Windows Explorer and browse to the C:\Python27\Scripts directory - there may be a PyMOL script there you can run.

If you have any questions, please ask on Stack Overflow, tagging the question with [python] and [pymol]. People are generally very quick with comments and/or answers, so please stick around on the question's page for 5 or 10 minutes to assist those who would help you.

Good luck!


Does a bigger breast give creamier milk? It is fairly common for a woman to have one breast larger than the other.  I have also heard that, for a breastfeeding mother it is common for one of the breasts to yield a creamier milk whilst the other is more watery and has less nutritional value.
Is there any correlation between the larger of the two breasts and the one which yields the fattier milk?

Because mammary glands define us (mammals), the genetics of the ability to make milk has been of interest.[1] Because we consume milk, we have a dairy industry. Because the industry places a monetary value to certain milk constituents, the genetics of milk component production has been a viable area of study[2]. Since you are talking of cream production, we'll stick to that.

The effect of nutrition and the environment (e.g. temperature) on milk fat production has long been known, and the ability to selectively breed for higher fat content has been exercised for decades if not longer[3][4], But the molecular genetics of milk fat production is only recently starting to be understood.

Mammals with the highest fat content are those in cold environments where an insulating layer of fat is required, such as gray seal milk (53.2% fat), whale milk (34.8%), and polar bear (31%). Humans and cows have approximately the same milk fat percentage (~4.5% fat).[5]  The gene most studied to date is the DTAG1 allele[6] on chromosome 14.[7]

It is very clear that genetically milkfat production is under the governance of part of chromosome 14.[7][8] Since this chromosome is identical in both breasts, genetically one breast cannot make milk with a higher fat content than the other. Environmental and nutritional factors affect both breasts equally, so those can be ruled out as a source of fat percentage differences. The only factors left that can be variables are 1) fat content of one breast over the other, and 2) demand from one breast over the other.

In cows, more frequent milking increased milk production but decreased fat percentage; in the end, the effect on fat in milk was the least influenced by frequency of milking (significance questionable).[9]

Triglycerides in milk are synthesized in the smooth endoplasmic reticulum of the mammary alveolar cell from precursor fatty acids and glycerol (obtained from blood nutrients), and while other cell types are involved in milk let down, etc., there is no known function of interstitial adipocytes (fat cells).[10]

That was the long answer. The short answer is: no[11].

[1] The origin and evolution of lactation
[2] Milk Components: Understanding the Causes and Importance of Milk Fat and Protein Variation in Your Dairy Herd
[3] A review of nutritional and physiological factors affecting goat milk lipid synthesis and lipolysis
[4] Factors affecting milk composition
[5] The Highest Percentage of Fat in the Milk of an Animal
[6] Evidence for multiple alleles at the DGAT1 locus better explains a quantitative trait locus with major effect on milk fat content in cattle.
[7] Identification of novel single nucleotide polymorphisms in the DGAT1 gene of buffaloes by PCR-SSCP
[8] Scientists pinpoint gene linked to fat in cow’s milk
[9] Covariance among milking frequency, milk yield, and milk
composition from automatically milked cows
[10] MILK SECRETION: AN OVERVIEW
[11] Does a bigger breast give creamier milk?


What is this dark brown organism growing on a door frame? A few brown spots appeared on a door frame and within 1 week it has grown to this size (~15cm). I have no idea what it is. How do I remove it completely? I worry that if I just wipe it off, it will just regrow from within the door frame. I've attached 2 pictures to assist with the identification.
Edit: I poked it with a stick and tiny white insects (~2mm) came crawling out of the structure.
My location: South India

Termites.
Photograph the insects and we will try to identify further. If the insects keep running, freeze some. This could be a big problem, so get good information soon.
Online I see this article that might help.
" An identification guide to the wood destroying termites of south India"
Journal of the Indian Academy of Wood Science
ISSN 0972-172X Volume 8 Number 2
J Indian Acad Wood Sci (2011) 8:148-151
DOI 10.1007/s13196-012-0028-9


Can a relationship exist that is mutualistic/parasitic/etc. but not considered symbiotic? Wikipedia definition of symbiosis: "Symbiosis (from Greek σύν "together" and βίωσις "living")[2] is close and often long-term interaction between two or more different biological species."

Wikipedia definition of mutualism: "Mutualism is the way two organisms of different species exist in a relationship in which each individual benefits from the activity of the other."

In intro biology class, I (and many other people, I'm sure) was taught that mutualism is a type of symbiosis. However, now that I think more about it, it seems like some relationships that are mutualistic don't appear to fit the definition of symbiotic. Some relationships are clearly mutualistic and symbiotic (humans and gut flora, for example) but other relationships (like bees pollinating flowers) are mutualistic but don't appear to fit the definition of "close and often long-term interaction". The same of course goes for parasitic, ammensalistic, etc. relationships as well.

Thoughts, anyone?

TL;DR: mutualistic/parasitic relationships are members of symbiotic relationships class

So, first of all, there is a way to look it up.

Secondly, the very same article in wiki has subsection on parasitism. Reading it would be useful:

  This is also known as antagonistic or antipathetic symbiosis.

Also, brief search through Google Scholar will show how these words are used in context. papers include such as:

Fungal symbiosis from mutualism to parasitism: who controls the outcome, host or invader?
Mutualism and parasitism: the yin and yang of plant symbioses
Mutualism or parasitism? The variable outcome of cleaning symbioses
Enhanced growth as a manifestation of parasitism and shell deposition in parasitized mollusks. Aspects of the biology of symbiosis.


Does a reduction in stem cells mean possible earlier death? The basis of this question relies on my understanding of these 2 facts:

1) A person has a certain number of stem cells from birth
2) Stem cells are the basis of all cells and are used to repair and replenish

I read an article about stem cells being found in fat removed by lipsuction and that the trials that has been done on using these stem cells for repair elsewhere in the body.

My question is, if stem cells are used for repair in the body and you have a certain amount of them, if you "lose" some via liposuction, does this then mean you have less stem cells and therefore less chance of repair and could then theoretically die sooner?

It's more than likely my lack of knowledge on the subject but I would like to understand why.

Stem cells persist because they have the capacity to self-renew.  At birth you will have a finite number of each stem cell type (e.g. hematopoietic stem cells that make blood, gut epithelium stem cells that make gut lining etc).  The general picture is that as tissues require replenishment, a stem cell divides. One daughter cell starts to differentiate (and divide) into mature cells required by the tissue, whereas the other daughter cell retains stem cell function.

So a stem cell is typically defined as a cell with the capacity to: (i) self-renew and  (ii) to give rise to one or more cell types in a tissue. A hematopoietic stem cell can give rise to T-cells, B-cells, neutrophils, red blood cells, platelets etc.  The ability to self-renew means that, in general, stem cells don't 'run out' during a lifetime.

[ Its important to note that to define a cell as a stem cell, scientists use strange hybrid of: in vitro or animal assays + cell surface markers + location in the tissue + measures of 'having the capacity to make continued contribution to new cells'.  So lets just say that stem cells are only ever as well defined as our choice of assays combined with the interpretation of those results. ]

I mention the challenge of defining stem cells because, in recent years as assays and technologies improved, cells such a oocytes (eggs) or adult neurons, which were once thought to be finite, have been shown to have be replaced/renewed, presumably by some 'stem cell like' cell(s).

As noted above, stem cells are usually involved in the replenishment of a particular tissue type.  So liposuction, which will remove fat cells, should not affect the numbers of hematopoietic or neural stem cells and so on.

Any claim of clinical benefit of a 'stem cell treatment' using liposuction should be backed by clear data.

A longer answer would get into:
(i) the concept of 'plasticity' where the classical view - a fixed pathway between a stem cell giving rise to one daughter cell that  gives rise to mature cells and the other returns to a stem cell state - is open for debate, and
(ii) the idea that since stem cell definitions are only as good as our assays, there may be potential plasticity even among stem cells that we cannot 'detect' yet.


What does "Psychomodulatory" mean in the context of potentially psychoactive drugs? What does "Psychomodulatory" mean in the context of potentially psychoactive drugs? That is, in this journal article http://www.sciencedirect.com/science/article/pii/S0028390812001931 in the discussion (you will need special privileges to access the article via an institute or personal subscription or by paying for access) in the last sentence of the first paragraph it says

  However, euphol even when given in very high doses, (up to 100 mg/kg)
  it did not show any evidence of psychomodulatory effects in the CNS

To me, "psychomodulatory" would mean "eliciting a significant change (up or down) relative to baseline or compared to a control, placebo, or carrier," here specifically in CNS function.

This statement appears to refer to the results presented in section 3.8, Effect of euphol in the cannabinoid tetrad tests. Across a range of doses (3-100 mg/kg) and across four different assessments of CNS function: locomotor activity (rotarod), catalepsy (time to move off of a suspended ring), analgesia (tail flick in response to thermal stress), and body temperature (self explanatory). The results of these four are summarized in the figure below.

Basically the effects are not significantly different from each other between dosages or times. The lines sit more or less atop one another. Compare to this figure, where the differences are significant:


What's the role of bromelain in pineapple? Bromelain refers to one of two proteases found in pineapple and its relatives. Like other proteases, many believe it has therapeutic uses and it's the subject of a lot of research. But what role does it play in the pineapple itself? Why does pineapple (or papaya, for that matter) generate large quantities of protease when other plants do not?

Antifungal properties? as tested in below article.

López‐García, B., Hernández, M. and Segundo, B.S., 2012. Bromelain, a cysteine protease from pineapple (Ananas comosus) stem, is an inhibitor of fungal plant pathogens. Letters in applied microbiology, 55(1), pp.62-67. Available here


Troubleshooting bioconjugates migration in a SDS-PAGE gel? We do a lot of bioconjugation chemistry (click chemistry in particular but also NHS and Maleimide chemistries). Our method to valid the conjugation reactions have been to use SDS-PAGE gels followed with densitometry. However one particular challenge with such analyses is that proteins conjugated with non-proteins like DNA or PEG migrate with an inconsistent MW and also in a smear making it hard to isolate the relevant bands. I assume that this has to do with having a poly-disperse radius of gyration. Are there tricks that I can do to get tighter bands?

The first step in troubleshooting is to run controls - run lanes with your protein input alone, and the conjugate alone (you may need to play with the type/percentage of the gel if the conjugate molecule is much smaller than your target protein - attaching biotin to a 50 kDa protein, for example) to see if the smear shows up. Depending on the type of conjugation you're using, the number of acceptor sites on the substrate, and the time and conditions of the conjugation reaction, you may be adding a highly variable number of conjugate molecules to your substrate. For example, when I first started working with adding fluorophores like Alexa and DyLight dyes to antibodies, the fluor/protein ratio was highly variable from reaction to reaction and between antibodies in the same reaction.

This is most likely what is happening in your case - the number of conjugate molecules being added to each substrate molecule is highly variable. If you haven't already, I'd suggest getting in touch with your conjugation kit vendor's tech support, as they likely encounter this problem all the time. You may need to change the type of conjugation chemistry, get a higher-quality conjugate, or purify the substrate before and/or after the reaction. One of the solutions to my antibody labeling problem I mentioned above was to purify the reaction products through a size-exclusion column. This had the dual effect of separating out the un-reacted antibody and fluorophore, and allowing us to pick different fractions of the conjugated product and decide which were best for our needs.


What happened to the gypsy moth epidemics in the Northeast US? I remember that back in the 1980s, 1980-1984, gypsy moths were a veritable plague in the Northeast United States. They were literally everywhere. Sidewalks were covered with their squashed bodies (of the caterpillar). You would drive through areas and every single tree would have dozens of nests. Every summer would be gypsy-moth-a-geddon.

By the late 1980s this completely ended for some reason. I sometimes see a gypsy moth caterpillar here or there, but it is a rarity.

What happened? Did a predator proliferate? Was there a pathogen or disease that wiped them out?

It appears that the gypsy moths were controlled by pesticide spraying by the US Forestry Service.

The defoliation areas measured peaked at 12 million acres in 1981 and again at 7 million acres in 1990.

In response, there was significant spraying of various insecticides starting from 1982 through 1996, peaking in 1990. This spraying managed to keep gypsy moth defoliation areas under 2 million acres since 1993.


Is there an evolutionary reason for the 5 electron transport complexes in plants and animals? The electron transport chains of both the light reactions of photosynthesis (in plants) and oxidative phosphorylation (in animals) both contain 5 complexes including ATP synthase, as shown below.

Image Source

Image Source

Is this coincidence, or does this possibly suggest that both chloroplast and mitochondrion precursors derived their energy-obtaining mechanisms via an ancient evolutionarily-related metabolic pathway which diverged?

Your latter assumption is the best we have so far, to my understanding.
Here are a few excerpts from "Early Evolution of Photosynthesis" published in Plant Physiology, October 2010 (emphasis mine):

There is suggestive evidence that photosynthetic organisms were present approximately 3.2 to 3.5 billion years ago...
Overwhelming evidence indicates that eukaryotic photosynthesis originated from endosymbiosis of cyanobacterial-like organisms, which ultimately became chloroplasts (Margulis, 1992). So the evolutionary origin of photosynthesis is to be found in the bacterial domain.

And then there's the abstract from this paper: "Do photosynthetic and respiratory electron-transport chains share redox proteins?"

In purple nonsulfur bacteria and cyanobacteria, there is close interaction between the photosynthetic and respiratory electron-transport chains, which share identical redox proteins.

Purple bacteria and cyanobacteria are some of the oldest known lineages (>3BY, whereas Mitochondria parallel Eukaryotic origins at about 1.4BY - and the endosymbiosis which created Chloroplasts probably came after [plants have both Chloroplasts and Mitochondria, whereas most Eukaryotes just have Mitochondria]), and since the respiratory chain and photosynthetic chain share identical proteins in cyanobacteria and purple bacteria it's not a huge leap to assume that - yup - the 5-protein structure is probably the template used by both Chloroplasts and Mitochondria because of a common source.


What are the dimensions in angstrom of bacteria? I'm going to take a picture of a bacteria but I am unsure how large it is. What are the dimensions in angstrom of bacteria?

According to Wikipedia: 3 um long with a diameter of 0.5 um. That equates to a length of 30 000 A and a diameter of 5 000 A.

http://en.m.wikipedia.org/wiki/Helicobacter_pylori