text:
Bacteria in our colons
During my education in Iran, until now, which I must say that I'm graduating high school this year and will go to college next year, our biology book has said that there's some bacteria in our colons and those little cells live there and use the celloluse of our food and because mostly they are anaerobic they produce methane or hydrogen and hydrogen sulfide and so on and sometimes they are the reason of the smell of our farts. Also they produce little amounts of B and K vitamins which is good for us and also, by using cellulose they make the rejection of feces better and easier. Anyway I wonder that where do these bacterias come from? I mean are they with us since birth? Then it means they come from our mother's body but, wait how our mothers have them? But maybe they are not there since birth and they come to colon from the food we eat during our life, but why don't they die in stomach. Even if we think that they go there by eating food, passing stomach easily, what if we don't eat the "food that can have those bacteria", then could it be possible to some humans don't have those bacteria? But they can't have a good release of feces.

Please read about your microbiota. The organisms both come from your mother and are acquired from the environment, including via food consumption.

It has been demonstrated that there are common patterns of microbiome composition evolution during life. In general, the diversity of microbiota composition of fecal samples is significantly higher in adults than in children, although interpersonal differences are higher in children than in adults. Much of the maturation of microbiota into an adult-like configuration happens during the three first years of life.
As the microbiome composition changes, so does the composition of bacterial proteins produced in the gut. In adult microbiomes, a high prevalence of enzymes involved in fermentation, methanogenesis and the metabolism of arginine, glutamate, aspartate and lysine have been found. In contrast, in infant microbiomes the dominant enzymes are involved in cysteine metabolism and fermentation pathways

evolution of the vertebrate gut microbiota :
Multi-cellular eukaryotes have existed for at least a quarter of Earth's history, or 1.2 billion years. Thus an already long history of interaction between multi-cellular lifeforms and microbial communities preceded, and likely shaped, the evolution of the vertebrates. The legacy of ancient associations between hosts and their epibiotic microbial communities is evident in the present day effects that the gut microbiota exerts on host biology, ranging from the structure and functions of the gut and the innate and adaptive immune systems, to host energy metabolism. Host responses to microbial colonization are evolutionary conserved among diverse vertebrates including zebra fish, mice and humans
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2664199/

"the human body is made up of about 10 times more microbial cells than human cells . Further, there may be millions more microbial genes than human genes in this human+microbiome system (which is often thought of as a human ‘superorganism’), and it is the ways in which these microbial genes interact with the human host that describe their ultimate role in our health. Scientists now believe that infants are sterile (meaning free of microbes) in the womb and receive their first inoculum of microbes from the mother during natural childbirth. This inoculum goes on to colonize the newborn and initiate a succession of events leading to the development of the child’s own microbiome. The newborn relies on this maternal vaginal microbial inoculum and the additional inoculum of microbes from mother’s breast milk for microbial colonization of all exposed surfaces in and on the infant’s body (e.g., oral, nasal/airways, gut, urogenital, skin).2 This is a dynamic process in which microbial abundances increase from effectively zero at birth to over six orders of magnitude (that’s more than a million times!) within just the first few weeks of life, with wide swings in the microbial membership of these communities until the microbiota largely stabilize in composition and numbers after approximately three years of life."
http://www.actionbioscience.org/genomics/the_human_microbiome.html

you can read about Gastrointestinal Tract Microflora here:
https://www.ncbi.nlm.nih.gov/books/NBK7670/
and normal flora :
https://www.ncbi.nlm.nih.gov/books/NBK7617/

It's true -  you are given a starter colony by your mother during a vaginal birth, covering your skin surface and intestinal tract.
The population of your gut is likely to change throughout life, depending on the environment you provide (food, exercise, antibiotics, etc).
It's also unlikely all bacteria are killed in your stomach when you eat, and only one cell is necessary to start a colony.
we've seen correlation of bacterial populations in the gut with certain disease states. I won't go beyond that since it's not my field.
try checking out an amazing paper my prof gave me - The Gut Brain Axis
have fun with your studies.

Which is a problem for caesarean births.

I wonder that where do these bacterias come from?

I'll answer this question since your post revolves around this question and the rest are follow-ups.
The infant gets its first bacteria (commensal or mutualist) from the mother's vagina as the amniotic membrane ruptures during parturition and gradually the diversity increases from its contact with other organisms and environment.

Nolte (1977) suggested that the body acquires its first microflora of the
  skin, nose, mouth and conjuctiva from the mother’s birth canal during normal
  vaginal delivery. The local environment is also important as a source from
  which neonates acquire bacteria (Mortimer et al., 1966; Nolte, 1977; Harvey,
  1979; Shinebaum, Cooke and Brayson, 1979). The colonisation of the skin
  surface starts at the umbilical stump (Mortimer et al., 1966)
The normal commensal flora of the oral cavity is more complex. The
  mouth is sterile at birth but is rapidly colonised by bacteria derived from
  attendants and the local environment. By the second day of life, aerobes and
  facultative species can be detected, but strict anaerobes do not appear until
  after the eruption of the deciduous teeth (Hurst, 1957; McCarthy, Snyder and
  Parker, 1965).

Reference: THE DEVELOPMENT OF THE BACTERIAL FLORA
IN NORMAL NEONATES
Also (updated)
A research published in 2013 has found that colostrum contain more than 700 species of bacteria! It being the only source of food for an infant also contributes to the infant's normal flora, though the composition of the bacteria colonising an infant's oral cavity is inconsistent with the composition of the colostrum.

The birth canal origin of the bacteria is not the whole story. It appear that most of the bacteria are acquired from the environment, which in naturally born infants does include the birth canal, but also included the mother's skin and dozens of other environmental contacts. The mature population of bacteria in the gut seems to be the same in both natural born and cesarean infants however the cesarean infants take significantly longer to develop this population indicating the birth canal is not the only factor.
It also appears that certain factors in breast milk encouraging the growth of the most desirable bacteria, and may have a stronger effect then form of birth.


text:
If a fully functional lab grown pancreas can exist, can it be used as a cure for type 2 diabetes?
Is it approximately equivalent to say that if a fully functional lab grown pancreas exists, then a way to cure Type 2 diabetes could soon exist?
Recently I've already checked out that only the remission exists with some gastric surgery.
reference: 1)http://care.diabetesjournals.org/content/34/Supplement_2/S361
2) http://www.medscape.com/viewarticle/733691(full access require membership)

Your question is not clear. I understand English is not your first language, but please try to rephrase your question to avoid being closed. I tried updating your title to capture what I think you are asking, but please address further...

@theforestecologist - is it looks good right now?

it is better, but still needs improvement. Please cite the source from which you "checked out" that remission exists. I'm also concerned that your question is too hypothetical (and therefore opinion based) and will likely be closed. Perhaps try to approach the question from a less hypothetical viewpoint.

You need to define what "remission" means. Millions of people live with well-controlled diabetes by monitoring their diet and using medications, obviously along with insulin supplementation. Also, please cite things that don't require "memberships" to read them.

Since the consensus is that the underlying initial problem in t2dm is the development of insulin insensitivity in the presence of a normally functioning pancreas, then replacing that pancreas at a more advanced stage of the disease will not cause normalisation of glucose levels.
http://journal.diabetes.org/clinicaldiabetes/v18n22000/pg80.htm

source: Stack Exchange

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

sort: votes


text:
Do lysosomes play any role in cell division?
My biology textbook includes a point that lysosomes stimulates cell division without further elaborating. But studying it, I felt eerie about this function of lysosome. Then, I checked on the internet; found nothing relating cell division to lysosomes.
Maybe, autophagy of lysosomes can play a role in this regard. Killing cells and thus 'stimulating' cell division. But this reasoning doesn't seem plausible as autophagy doesn't occur without extreme conditions.
Nothing else is coming into my mind.
So, is this point included in my book wrong or right?

You're incorrect about autophagy - it occurs all the time.

Really? I thought it occurred when there is a shortage of food or other extreme conditions.

Nope. Read Wikipedia for an intro, then go to PubMed for recent review articles.

It is actually not completely correct to include it as a fact in textbooks. The main cause of it is that there is not much research on this topic. See this article for reference. According to Allison and Mallucci (1964), during cell division, lysosomes either released an unspecified activator or some hydrolase that inactivated a repressor. Apart from this, Allison and Paton (1965) showed that treatment of human embryonic lung cells in tissue culture with photosensitizing agents allowed high frequency of chromosome breaks on irradiating the cells with light from a high intensity tungsten source. They claimed that these effects were observed only at lysosomal sites, from which they concluded that a cytoplasmic event was giving rise to structural alteration in chromosomes. This event was suggested to be release of deoxyribonuclease from the lysosomes. However, Chevremont et al, 1959 showed different results through their experiments. They grew mammalian cells in tissue culture in the presence of acid deoxyribonuclease. This treatment inhibited cell division, but allowed DNA synthesis to proceed and did not appear to alter the nuclear DNA. Hence, the contribution of lysosomes in cell division is not yet completely established and still comes under debate.
So, it should not be considered a total false, but is also not reliable enough to be printed in textbooks. Overall, we don't yet know whether lysosomes do play a role or not.
References:

TUATARA: VOLUME 18, ISSUE 1, JULY 1970
THE LYSOSOME
ALLISON AC, MALLUCCI L. LYSOSOMES IN DIVIDING CELLS, WITH SPECIAL REFERENCE TO LYMPHOCYTES. Lancet. 1964 Dec 26;2(7374):1371–1373.
Nature 227, 707 - 708 (15 August 1970); doi:10.1038/227707a0;
Chromosome Breakage by Deoxyribonuclease;
GILLIAN R. PATON & A. C. ALLISON
CHEVREMONT M, CHEVREMONT-COMHAIRE S, BAECKELAND E. [Action of neutral and acid desoxyribonucleases on living somatic cells cultivated in vitro. III. Histoautoradiographic study after incorporation of tritium-labelled thymidine]. Arch Biol (Liege) 1959 Oct-Dec;70:833–849.

Well, how can acidic deoxyribonuclease inhibits cell division without inhibiting dna synthesis?

I ain't sure, but nuclease would simply cut the DNA due to which cell would prioritize DNA repair instead of cell division. Thus it could inhibit cell division by creating breaks in DNA continuously.

Well. I can show how they could be seen to be linked.
Taking cell division to mean the full process of mitosis – producing identical copies of a particular cell.
The mitotic apparatus would be present to aid in the separation of chromosomes during metaphase. One protein associated with the mitotic apparatus is "Nuclear mitotic apparatus protein 1"
In order to carefully control and regulate the amount of this protein present, the lysosome is able to degrade the protein.
So the lysosome is responsible for regulating a key protein associated with and vital for mitosis. `

Jeffrey Van Ness, David E. Pettijohn, A. Klug, Specific attachment of nuclear-mitotic apparatus protein to metaphase chromosomes and mitotic spindle poles: Possible function in nuclear reassembly, Journal of Molecular Biology, Volume 171, Issue 2, 5 December 1983, Pages 175-205, ISSN 0022-2836, http://doi.org/10.1016/S0022-2836(83)80352-0.

`

Please add some references to your answer. Has this process ever been reported in vivo or in vitro?

Would you elaborate "In order to carefully control and regulate the
amount of this protein present, the lysosome is
able to degrade the protein."?

From what I have read and what is indicated however a mechanism is not provided.

Would you please elaborate the passage I pointed out?

@Mockingbird The article which I read merely mentioned this in passing. It said that the protein was degraded by  lysosomes. This as deep as it went into explaining the mechanism.

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


text:
Phoresis and mechanical vectors
According to wikipedia and Human Parasitology
By Burton Jerome Bogitsh, Clint Earl Carter, Thomas N. Oeltmann

Phoresis: In this type of symbiotic relationship, the phoront, usually the smaller organism, is mechanically carried by the other,usually larger organism the host.

So can the host acting as a carrier be called a mechanical vector?
On searching google.books I found some books mentioning:
Like Clinical parasitology

Hosts that transmit parasites to man are vectors. Those that are essential in the life cycle are biologic vectors; those that are not essential are phoretic or mechanical vectors.

Cheeky bump for my own paper: http://rstb.royalsocietypublishing.org/content/372/1719/20160085 :)

A mechanical vector just as biological vector transfers a parasite to its obligatory host but carrying it on the surface of its body while the host in phoresis is not necessarily carrying a phoront to an obligatory host (for parasitic interaction).
A parasite-mechanical vector relationship is possibly a kind of phoresis.


text:
Dorsal vs Posterior and Ventral vs Anterior
From prior reading, I thought that Dorsal is the same as Posterior and Ventral is the same as Anterior. However, when I checked in google images for these anatomical terms for a horse (just to strengthen my concept), i found that Dorsal is not the same as Posterior and Ventral is not the same as Anterior.
How is this possible? I have checked many websites but all state that Dorsal is the same as Posterior and Ventral is the same as Anterior. Am I going wrong somewhere?

Clearly you've been reading the wrong web sites. Look where the dorsal fin is on a fish.

Yes you were wrong before. This image is correct.

 Short Answer
This page on wikipedia gives a good synopsis of these concepts.
The confusion lies in the fact that many websites on anatomy discuss/describe/define these terms in relation to humans. However, in quadrupeds and fish (and birds), Anterior/Posterior lies orthogonal to Ventral/Dorsal and are instead synonymous with Cranial(Rostral)/Caudal. Examining the etymologies of the 4 terms in question will demonstrate why there seems to be an inconsistency in their usage:
Ventral -> "belly" side
Dorsal -> "back" side
Anterior -> "before" or "toward the front"
Posterior -> "after" or coming after (opposite to) the anterior

Based on the body orientation of the organism (often associated with forms of locomotion), these terms can sometimes overlap (as in bipedal humans) but often lie perpendicular to each other (as in quadrupeds, fish and most birds).

A note about quadrupedalism (as summarized on Wikipedia [my emphasis added]):

Although the words quadruped and tetrapod are both derived from terms meaning "four-footed", they have distinct meanings. A tetrapod is any member of the taxonomic unit Tetrapoda (which is defined by descent from a specific four-limbed ancestor) whereas a quadruped actually uses four limbs for locomotion.

 Long Answer
Think of ventral (Latin venter = "belly") as being associated with the belly side (with belly referring to "swelling" or "inflating") -- or typically the side of the organism containing the digestive and respiratory organs. Dorsal (from Latin dorsum meaning "back") refers to the body region/"side" opposite that of ventral (and typically called the "back").
Anterior (from Latin ante meaning "before" or "in front of") refers to the "front" of the organism (i.e., the part of the organism you'd encounter 1st or before other body regions). Posterior (from Latin, comparative of posterus ("following") from post- meaning "after") is the opposite and refers to the part of the organism encountered "after" (or opposite) the anterior side.
Depending on the orientation of the organism, these terms may be synonymous in some instances but be orthogonal in other instances).

Sometimes anterior/posterior would be synonymous with ventral/dorsal, as is the case in humans or other bipedal organisms.
In other instances (e.g., in quadrupeds, fish or birds), posterior/anterior lies relatively orthogonal to the dorsal/ventral orientation. In these cases, dorsal/ventral is instead synonymous with superior (from Latin superior, comparative of superus "that is above," from super "above") and inferior (from Latin inferus meaning "low" or "below").

Often in these cases, anterior/posterior are instead associated with caudal/cranial (common alternatives for cranial  include cephalic or rostral).  Caudal (from Latin cauda meaning "tail") refers to the tail side of the organism (i.e., the side associated with coccygeal vertebrae or sometimes simply the side of the organism where waste is excreted). Conversely, cranial (Greek kranion = "skull") or  cephalic (from Latin cephalicus, from Greek kephalikos, from kephalē meaning "head") refer to the side of the organism containing the head. Rostral (referring to rostrum from Latin meaning "beak") is another synonym for cranial and refers to being "situated or occurring near the front end of the body, especially in the region of the nose and mouth or (in an embryo) near the hypophyseal region."

Some notes:

This English.SE question addresses etymology of the suffix "-erior."

You can find a pretty good list of anatomical etymologies here, here, here, or by simply searching "[word of interest]  etymology" in Google.

Also, this Bio.SE post addresses anatomical terminology usage in plants and body organs.

More generally, a frontal plane always divides an organism into ventral/dorsal.

Although these terms differ between shapes/orientations of organisms, using such terms for more specific body parts (e.g., heads or feet) are not always as inconsistent.

For example, anatomical positional terminology for brains is consistent across organisms.

One final note:
This approach to anatomical positional terminology only works with bilaterally symmetrical organisms. See here for terminology usage for other organisms.

tl;dr refers to "Too long; didn't read" ... I provide a summary for those that don't want to read the whole text. This short summary at the beginning of my answer is demarcated using the common internet acronym tl'dr (often applied to instances in which an author introduces a short summation of a longer piece)


text:
DNA & mRNA During Transcription
Just a simple, quick question: how are the mRNA and the template strand of the DNA structured during transcription? I've seen models and videos of them when they're both flat/straight (is that just for simplicity?) and others where they're spiralling around each other. Could someone just briefly shed some light on my situation please?

Transcription occurs in a special structure known as transcription bubble. Inside the bubble are present the mRNA, template DNA being transcribed and the RNA Polymerase. Upstream of bubble is the DNA already transcribed and downstream is the DNA to be transcribed. There is not enough space in cell to have completely unfolded DNA for transcription, so transcribed DNA has to be re-annealed as soon as it is transcribed, giving a bubble-like appearance to the RNA polymerase-bound DNA. Hence it is called a transcription bubble. See this image for illustration:

Source
The mRNA formed quickly leaves the bubble and hangs behind like a thread coming from RNA polymerase.

Source

Cheers, is that RNA polymerase enzyme below? Why are there so many sections to it? All it does is separate the DNA strands and form an RNA strand, why would it need so many sections...

I did not explain it because it was not related to your question. RNA polymerase has many subunits which all come together to become the fully functional enzyme. It actually does much more than separating DNA strands from RNA strand. :)


text:
What is the mass or range of weights of individual microbial spores and or cysts?
Also looking for the overall physical dimensions of spores/cysts.  I am trying to estimate how much static charge a spore/cyst would require to overcome the pull of gravity.


text:
How to determine the fastest metabolism ?
Which is the fastest metabolism ? Fructose metabolism or Glucose metabolism

Can you please add some more details on what exactly do you mean by metabolism?

I meant Fructolysis and Glycolysis which is the fastest one ?

in vivo or in vitro? there are a lot of variables that affect metabolic flux in vivo - this is NOT a straightforward question.

@petersmith yah, but it was asked in our and semester paper.


text:
Allosteric regulation: why involve extra molecules
Why are molecules such as allolactose (for lac repressor) or 2,3-BPG (for haemoglobin) used for allosteric regulation rather than the actual molecules involved in biochemical pathways, such as lactose and 1,3-BPG? The formation of such "extra" regulators requires energy – what is the advantage of such organisation?

You might be interested in this.

@Metroplex Thank you! This is a great article. The argument makes sense for allolactose but I don't see how a similar one would work for 2,3-BPG or 2,6-biphosphofructose (regulating phosphofructokinase and fructose 2,6-biphosphatase).

It's an interesting question, and there are a lot of potential explanations.
I can at least hypothesize a little bit for the case of 2,3-BPG and 1,3-BPG. I think the key point is that it's not obvious to me why sensing the 1,3-BPG concentration would be useful. This concentration actually has to be maintained in a pretty tight range for glycolysis to function (note that the entire lower portion of glycolysis is very close to thermodynamic equilibrium). The reason that I think 2,3-DPG is a useful regulatory molecule is precisely because its levels can be regulated independently of the function of glycolysis. The activity of the enzymes in the 1,3-BPG -> 2,3-BPG -> 3PG shunt can controlled independently of the control of normal glycolysis and can be regulated by whatever physiological parameter you want 2,3-DPG concentration to represent.
One other thing to note is that typical red blood cell concentrations of 2,3-BPG are actually many orders of magnitude higher than 1,3-BPG. The very low concentrations of 1,3-BPG are a necessary consequence of the thermodynamics of glycolysis as mentnioned above -- if 1,3-BPG concentrations are too high, the GAPDH reaction will become unfavorable. Thus it may be that the typical concentration of 1,3-BPG is too low to be an effective regulator of anything (because it would have to bind very strongly). But I think this is a less important point than asking the question of "what does the concentration of my regulator represent".
There may be biochemical reasons at work in other cases -- for instance, some molecules may just bind better to the protein that you want to regulate, and that's why they're chosen by evolution. I think this is a case when it will be hard to come up with a blanket explanation -- it's better to look at each case, consider what signal biology is trying to measure, and look at the relevant constraints.
I don't know the answer for 1,6-FBP and 2,6-FBP, and note that in other species, 1,6-FBP does appear to be the major regulatory molecule. You could argue that by having 2,6-FBP be the regulator, there are more enzymes whose activity you can control and thus somehow you have more fine-tuned regulation </hand waving>.

Thank you! It's all much clearer to me now, and the argument about 2,3-BPG is very interesting.


text:
What is the perisomatic region of a neuron?
In the scholarpedia page on interneurons I encountered the following passage:

The perisomatic domain is responsible for the summation of postsynaptic potentials arriving from all dendritic branches [...]. Thus, the perisomatic region - and particularly the axon initial segment [...] plays a crucial role in the generation of output.

The page, however, does not define what the perisomatic region really is. What comprises the perisomatic region of an interneuron?

Sure mate. If these edits are not to your liking feel free to roll it back. It's just that in the linked Scholarpedia page the term is not explained anywhere. Quoting the relevant section shows that to other users nicely.

In cortical GABAergic cells with local axonal projections, the perisomatic region is defined as that part of the plasma membrane including the proximal dendrites, the cell body and the axon initial segment (Zabó et al., 2010).
Reference
- Zabó et al., Eur J Neurosci (2010); 31(12): 2234–46

Now that I read your answer, maybe I should have deduced it from the name.. However I didn't so... Thank you!

@user135172 - No worries and happy to help - I had to look it up too. Nice question and well researched +1

'Peri' = 'in the region of'
'soma' = 'cell body'
so the perisomatic region is the area in the region of the cell body - I thought the breakdown might be useful in future as 'peri' is used a lot.

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


text:
What is the difference between Reservoir and paratenic hosts?
Paratenic host
'In parasitology, the term paratenic describes a host that is not necessary for the development of a particular species of parasite, but nonetheless may happen to serve to maintain the life cycle of that parasite' until they are transferred to an obligatory host.
(from Wikipedia and Parasitology: A Conceptual Approach book)
Reservoir host

Reservoir hosts are such animals which accumulate in themselves the invasive larvae of the helminthes and contribute to their transfer to the definitive host, not being however an obligatory condition for the complition of parasite ontogenesis.

(from Proceedings of the First International Congress of Parasitology: Roma, 21-26 September 1964)
The source however says that Reservoir host is same as paratenic host which contradicts other sources
(like General Parasitology by Cheng) which says:

Reservoir host is an animal that becomes infected and serve as a source from which other animals can be infected. (the only difference I presume is that it may or may not be obligatory)

In many other books (book 1 & 2) a parallel definition is mentioned that a reservoir host is a host that harbors parasite until their transmission to human beings.
This inturn brings forth another question, is a reservoir host a biological vector then?
So the question : Are paratenic host and reservoir host same or different?
P.S. I don't know what the standard books on parasitology are which could have solved this issue. Reference to one such book will be really appreciated.

Reservoir host: The host of an infection in which the infectious agent multiplies and/or develops and on which the agent is dependent for survival in nature; essential host for maintenance of the infection when active transmission is not occurring.
Paratenic host: A host in which a parasite survives without undergoing any additional development (a transport host only)
Source: Diagnostic medical parasitology, pg 1161

and

Any animal that harbors an infection that can be transmitted to humans is called a reservoir host, even if the animal is a normal host of the parasite. Source: Pg no:4

So, we can conclude that paratenic host is different from reservoir host due to following differences:

Paratenic host don't harbour infective stages , if they harbour them, then they would be called as reservoir host but not paratenic host( see second definition)

No development takes place in paratenic hosts, whereas in reservoir host development and multiplication takes place( see 1st definition).

Is a reservoir host a biological vector then?

I too asked the same question, its answer is here.


text:
Retrograde/anterorade transport; kinesin/dynein; COP1/COP2; Endoplasmic reticulum/Golgi
I am getting slightly confused with all of the terms above and was wondering if someone could see if I have got this right:

I think transport from the ER to Golgi is almost always from the plus end of a microtutbule to the minus end, and therefore is carrier by a dynein. I think this is signalled by a COP1 protein, which can attach to the dynein for transport. I think that this is retrograde trnsport as it is from the plus end to the minus end, however this I am really not sure about.
Conversely, I think that transport from the Golgi to the ER, being from the minus end to the plus end, is carrier by kinesis and therefore the COP2 protein which attaches to the kinesis carries these vesicles. I think this is an example of anterograde transport.

My confusion lies in the fact that

I am not sure whether retrograde and anterograde transport refer to movement from plus and to minus end of a microtubule or vice versa (respectively) or whether they refer to general motion of cargo into and out of the cell (respectively). For example, if a vesicle was being transported from the plasma membrane to the Golgi and then to the ER, the first part of this journey would be along the plus end to the minus end of the microtubule, carrier by dyneins; the second part of the journey from Golgi to ER would be from minus and to plus and and therefore carried by kinesis. Would this transport therefore initially be retrograde and then anterograde, or do these terms simply refer to the general direction of motion of cargo into/out of a cell and therefore this whole motion would be described as retrograde?

Secondly, if I remember correctly my lecturer said that one of the COP proteins takes proteins from the Golgi to the ER and the other takes froteins from the ER to the Golgi to the plasma membrane. This is confusing me because it would mean that the same COP protein would take a vesicle from plus end to minus end of a microtubule from ER to Golgi, and then from minus end to plus end from Golgi to the plasma membrane, which surely can't be right as the same protein should not be recognised by the two different motor proteins, right? However if it were the other case, that say COP 1 takes vesicles from ER to Golgi and COP 2 takes them from Golgi to ER OR from the Golgi to the plasma membrane, what would distinguish whether the cargo was taken to the plasma membrane or back to the endoplasmic reticulum?

Thank you in advance!


text:
Hemoglobin oxygen affinity curve
I have a general understanding of the Bohr effect, and that Hemoglobin's affinity for oxygen will shift depending on the conditions of the lungs and tissues. However, I'm struggling with the following question; I feel as though I'm getting caught on the less-than-ideal answer choices, but I want to make sure I'm not missing a basic principle that could reason this answer more clearly.
Q) Which of the following best describes how a shift to the right in the dissociation curve results in more oxygen delivered to tissue?
A) The distance between the curves at 100 mmHg is less than the distance at 40 mmHg
B) The distance between the curves at 100 mmHg is more than the distance at 40 mmHg
C) On the right-shifted curve, Hb will pick up more O2 in the lungs
D) On the right-shifted curve, Hb will pick up less O2 in the lungs

My reasoning for choosing A is less-than-ideal: let me explain. First, I've been taught that a good rule-of-thumb for oxygen affinity is that Leftward shifts are related to the lungs, while Rightward shifts are related to the tissues. Therefore, because the answer choices C & D refer to right-shifted curves and the lungs, they can be eliminated. However, I'm not convinced this "rule" is so absolute - I can imagine that the curve can shift left & right within the tissues and the lungs. For the sake of argument though, I'll assume the rule works and eliminate answer choices C & D. Then, I can also eliminate answer choice B because it's not a true statement. As a result, I arrive at answer choice A. However, I don't feel as though it quite answers the question. Can anyone please provide some insights as to my reasoning, and/or perhaps what I'm missing? Thank you!

This is just a guess, but does the pH play a role in the answer? As the CO2 levels increase, the pH will drop, so it makes some sense that in tissues with high metabolism, they will release more CO2 and the pH will be lower. Because the hemoglobin can't hold as much O2 in these more acidic conditions, the bound O2 is released near the tissues that make the most CO2.

Comment: this question is a bit confusing, since none of the answers seems to directly explain how a shift to the right in the dissociation curve results in more oxygen delivered to tissue. Therefore, we'll try to choose the least wrong option...
This answer came out a bit long, so here's a TL;DR for you. I chose

 Option A

and here's why:
Although not stated explicitly, the pH in question is most probably the blood pH (this is a rather well-known graph from biochemistry undergrad studies). It shows that when blood pH drops or rises, the amount of %O2 saturation of hemoglobin deviates from the norm accordingly.
First of all, regarding your rule-of-thumb, it might be misleading in this context, since it may be true in both normal conditions and pathological conditions, depending on the site of measurement:

Under normal conditions, general blood pH is around 7.4 (7.35-7.45), blood pH in the tissues is around 7.2 (due to increased pCO2 resulting from cellular metabolism), and blood pH in the lungs is around 7.6 (due to the release of CO2 in the lungs for expiration, which results in lower pCO2 in the lungs) - see this reference and its references.
Under pathological conditions, general blood pH may rise above 7.45 (alkalosis) or fall under 7.35 (acidosis), regardless of the site of measurement [reference]. This means that a dissociation curve under abnormal blood pH value does not necessarily relate to normal conditions in a certain body site, but may also relate to a pathological condition in which blood pH is abnormal in general.

I believe the graph represents the latter situation, i.e. how hemoglobin behaves under the pathological states of acidosis (lower blood pH = right-shift) and alkalosis (higher blood pH = left-shift) compared to the normal state, since it depicts the change in %O2 saturation over the physiological range of pO2 and the curve is continuous (a depiction of blood pH only in the tissues or the lungs would not have resulted in a curve, since pO2 does not change significantly in each site, certainly not over the physiological range).
Now let us consider the possible answers:

Option A - The distance between the curves at 100 mmHg is less than the distance at 40 mmHg. This seems to be true in it's own right. However, other than describing the situation, it does not explain explicitly anything. It essentially says that the difference between oxygen release in the tissues is more pronounced than the difference in oxygen binding in the lungs, when comparing normal blood pH and acidosis. We can infer that if the right-shifted curve is below the normal and left-shifted curve, it means that less Oxygen is bound in the tissues (and also everywhere else, since this trend is consistent), i.e. Hemoglobin is less saturated, i.e. more Oxygen is released in the tissues in a state of acidosis than in any other state.
Option B - The distance between the curves at 100 mmHg is more than the distance at 40 mmHg. This is merely the opposite of A, and therefore is untrue by the same amount that A is true.
Option C - On the right-shifted curve, Hb will pick up more O2 in the lungs. This is a bit trickier. This option suggests that when pH is lower-than-normal (acidosis), more Oxygen will bond to Hemoglobin in the lungs. However, by observing the graph, we can see that the right-shifted curve is always below the other curves (both the normal and the alkalosis curves). This is also true in high values of pO2, which are present in the lungs. This renders this statement incorrect in itself, and it also does not explain why more oxygen is released in the tissues.
Option D - On the right-shifted curve, Hb will pick up less O2 in the lungs. Based on the analysis of option C, it should be rather evident that the opposite must be true. That is, if the right-shifted curve is always below the other curves, including in high pO2 values, then under this condition Hemoglobin is bound to pick up less oxygen in the lungs than in any of the other conditions. Therefore, this statement is correct, but it does not explain why more oxygen is released in the tissues.

According to the section titled The influence of pH on oxygen-hemoglobin binding in this excellent reference, "the presence of a low pH locks it [hemoglobin] in an unreceptive state, preventing it from binding oxygen molecules". This means that Hemoglobin's affinity to oxygen will be reduced, so that more oxygen will be released (in other words, less will be bound) in the tissues and less oxygen will be bound in the lungs. The two "less" in the previous sentence are in accordance with the curve of pH=7.2 being below the other two curves over the entire range of pO2. I highly recommend reading the above reference through and observing the figures.
To sum up, none of the possible options is satisfying enough, but option A seems to be the least wrong or unrelated to the situation described, so I would choose it.


text:
Books on machine learning applications in Biology
I have recently engaged with a collaboration, which requires me to construct, then train an unsupervised artificial neural network (ANN).
However, I have only a very coarse understanding of what machine-learning classifiers try to do, and how they work. For example, Chen et al.'s random forest (RF) classifier (ensemble of decision trees) for protein-protein interaction prediction. Additionally, I have very little idea about which types of machine-learning are useful to different classes of Biological problems.

So -if they exist- I would very much appreciate information on books that discuss applications of machine-learning classifiers in Biology/Bioinformatics. Preferable criteria are:

Intuitively introduces key concepts.
Illustrates a variety of Biological/Bioinformatics problems and their solutions by appropriate types of machine-learning (e.g. when is it appropriate to use ANNs versus RF classifiers?)
Relatively short (I'm planning to read from cover to cover).

Related

Stack Biology: Machine-learning for light microscopy problems to solve (I would consider this question a sub-class of the present question; personally, I am more interested in the sequence analysis / genetics domain of Bioinformatics problems)
Stack Biology: Historical connection between neuroscience and machine intelligence
Blogs about deep learning implementations in Biology
GitXiv: Collaborative on-going (and also published) computer science projects pertaining to machine-learning (search using relevant Biology-related queries to filter)

Tarca et al. 2007 could be a good reading.

At NIPS 2016 most ANN implementations I saw were related to biology were trained on imaging data, thus the kind of comprehensive book you are looking for probably doesn't exist yet.
However, if you utilize the search feature on Amazon.com you'll find:
Neural Networks for Applied Sciences and Engineering: From Fundamentals to Complex Pattern Recognition
Artificial Neural Networks (Methods in Molecular Biology)
and this, which seems to best meet your need:
Neural Networks and Genome Informatics, Volume 1 (Methods in Computational Biology and Biochemistry)

I own a book entitled Bioinformatics, The Machine Learning Approach, by Baldi and Brunak. I haven’t done more than glance at it, but it might be of interest. It’s more geared to bioinformatics than general computational biology.


text:
Do mucous membranes surround visceral organs?
Wikipedia claims that:

A mucous membrane or mucosa is a membrane that lines various cavities in the body and surrounds internal organs.

The first part of that sentence is clearly accurate, but I cannot find any reference from Google Scholar or books that states mucous membranes surround internal organs.
The mucous layer lines the lumens of the body: digestive, respiratory,urogenital tracts, as well as cavities leading to openings such as the ears and nose, and forms the conjunctiva of eyes. The surfaces of internal organs don't fit any of these categories.
I think wikipedia is wrong about the viseral organ part, am I right?

You are correct.
"Serous membrane" might be what the Wikipedia editor was thinking of, for example the pleura of the lungs; other examples include the pericardium and peritoneum.


text:
How can skeletal muscles in the human body be modeled as levers?
From what I understand, human arms can be thought of as third class levers, so that the distance from your elbow to the place where the muscle attaches is effectively the distance to the fulcrum, so that arms produce proportionally less strength on the end, and proportionally greater distance when lifting a load.  So this is somewhat of an anatomy question (although I suppose if it was to be used for an exoskeleton, it could be robotics) but can leg muscles and the muscles that attach to the ends of arms and legs be roughly modeled in such a way?  What muscles/muscle groups don't classify that way?

Interesting question. I feel like in many cases it would be hard to model the muscles attaching to the hand/foot because of the retinacula in those areas holding them in. I think similar considerations might apply to the muscles moving the fingers/toes. I assume many neck muscles, e.g. sternocleidomastoid might classify in this way, and maybe same for some abdominal muscles.

Well I can imagine the muscle that attaches from your back to your upper arm (pardon me for not using the anatomical name) as having the fulcrum at the attachment point, and maybe the same with the legs.

Your question is not that clear - the title asks how to model muscles as levers, while the body seems to focus more on if they can, and if so which ones can and can't. Going by the title, the question is too broad because you don't specify what sort of modeling you'll be doing. Going by the body, it's also too broad, because there are many different types of muscles with different modes of action and varying degrees of fitting into a "lever" model. Please [edit] your post to focus on a single, clear, answerable question.

AFAIK, you can't model muscles as levers, since they only contract.  The bones are the levers.  In (physical) model terms, you could think of the skeleton as a bunch of sticks bolted together, with ropes tide to the muscle attachment points.  Pull on the rope, and the stick/bone moves.


text:
Why would you plate cells at different densities in a colormetric assay?
The aim of my experiment is to see if a kinase inhibitor reduces cancer cell viability. I am using 2 different cell densities 50,000 cells/well and 100,000 cells/well and different doses of the kinase inhibitor.

What sort of research or thinking have you done? What could be some possible reasons for different plating densities?

I have been told to plate some of the wells at 50,000 cells/well and others at 100,000 cells/well, but haven't been told why. In all the papers about colormetric assays I have looked at only one plating density is used.

I have read that the lower the cell density per well, the more greater the effect of drug treatment.

Also at higher cell densities the metabolic state shifts from proliferative metabolism to quiescent metabolism.

The comments you have given are some reasons, although they also depend on the confluency of the cells. Your teacher/professor/advisor is also making sure that you can see an effect at low levels of drug, as well as making sure that changes in the signal are visible - for example, does a 50% reduction in viability due to drug activity give the same drop in signal as reducing the number of cells by 50%? You don't say what kind of assay you're running, but a fairly common and inexpensive one is the MTT assay, with some kits nowadays switching to XTT for greater sensitivity and a reduction in the number of steps in the assay (example kit from Cell Signaling compared to an MTT assay kit from ThermoFisher), as the final colorimetric product does not require solubilization before reading. Finally, depending on the lab you're in, the conditions for the assay may not have been optimized yet, so your instructor wants you to test a couple of different densities to see what works best.

Firstly thank you for answer, I really appreaciate it. I am still a little confused though, are you saying that if there is a 50% decrease in viabilitiy in 50,000 cells/well experiments at a given drug dose, then there should also be a 50% decrease in viability in 100,000 cells/well experiment at the same drug dose? In both my experiments (50,000 cells/well and 100,000 cells/well) I haven't reached a 50% reduction in cell viability.

@Bio124 no, what I meant was if there was a 50% reduction in viability of the 100k wells, the signal should be the same (or very similar) as the control 50k wells. It was just an example, don't worry if you're not treating with a high enough concentration of drug to hit 50%. If you click on the Cell Signaling link and look at the first data figure, you'll see how the viability curves vary at different plating densities, although in this case they're looking at signal over a period of time (as the cells grow and multiply) instead of varying the drug concentration.


text:
What are the possible reasons to get extra unrecognized band in agarose gel electrophoresis?
I ran 0.7% agarose gel electrophoresis of my plasmid DNA sample consisting of GFP vector, using NheI and HindIII restriction enzyme.
I used two types of plasmids, i.e., isolated by miniprep-alkali method, and another isolated by midi prep system (pure) of the same source E. coli.
The 4 and 5 lines show cut and uncut plasmid, respectively, isolated by midi prep system.
The 1, 2, and 3 lines show the 500 bp marker, cut, and uncut of miniprep isolated plasmid signal, respectively. In the attached image, we found an extra band in the plasmids isolated by alkali method (line 2 and 3), but in the pure samples (line 4 and 5) no such extra bands were found.
What are the possible reasons behind the result? How may I interpret this result? If anyone has experienced similar results, please share.

Not sure what it is, but I noticed this today as well on a gel. It was only present in plasmids (digested) that were grown in DH5alpha (and absent in the XL1 blue). Could be coincidence though.

Looks like genomic DNA contamination to me.
More importantly, does it really matter? I certainly appreciate the curiosity but, if your objective is cloning, I would just keep going and then do some diagnostic cuts of your plasmid after transformation. You can clearly see your vector or insert in the gel.

@SanjuktaGhosh Than answering as comment, maybe it is better to write directly the answer? As well as it doesn't look like a short hint but a really small answer because it seems there is not much things left to elaborate or cite.

If it was gDNA contamination I would expect to see many more bands...

@JoeHealey I would too but, to me, it's the most plausible explanation for such a large fragment.

Especially given that it is absent in the so-called "pure" fractions, which are presumably cleaner.

Could be several things...just off the top of my head. Without your vector map and expected sizes it will be almost impossible to say for sure.
You'll probably also have to give us more information about your incubation conditions etc.

Your original culture you prepped from might not be as homogenous as you think:

You've ended up with a mutant (perhaps in your restriction site in that particular clone)
Your original culture is contaminated, perhaps with a second E coli bearing a different plasmid.

This is probably unlikely, assuming your molecular/microbiology technique is decent, but does happen from time to time.

Incomplete digestion. Something in the eluate of your first extraction method has possibly inhibited your enzymes, that isn't happening in the other extraction mechanism, or you didn't leave the digest for long enough.
You missed something out of the reaction mix for one of the samples (I usually blame myself first when things go wrong so I usually just repeat it to be sure!)

How an incomplete digestion give rise to a molecular size far bigger than entire plasmid (track 4 and 5)?

Uncut plasmid can run at all sorts of lengths. If it's supercoiled, it will run further than it 'should' for its size. If it's circular but not supercoiled, it will run slower than it 'should' vs if it was a single linear fragment as it doesn't move easily through the gel.


text:
Is it ok if I define Genes this way in Biology?
Genes are found in chromosomes and their job is to show us the traits of someone (height/hair color)
I do know that alleles specify the height of the person (Tall/Short) and their hair color(blue/green), etc. So is it correct to define Genes this way in my exam?

Not all genes have a corresponding phenotype.

Obviously, otherwise we would all look the same..xD

@OkamaKsakas Not sure what you mean by that. There could be multiple alleles for any given gene.

The term gene has been defined (by Wilhelm Johannsen) much before we even knew about the structure of DNA (by Watson and Crick). As such, a gene is typically a vaguely defined functional unit in the genome that codes for a gene product (typically a protein). Have a look at the wikipedia entry for more info.
For a given gene, you might have different variants. Such variant is called an allele. Let's consider a given phenotype such as eye color for example. There would be a gene that we could call "EyeColor" and there could have different alleles at this gene that we could call "BlueEyes", "BrownEyes", "GreenEyes", ...
Of course, in reality it is rarely that easy. A given phenotype is often the result of the interaction of alleles at several genes. Also, the environment (type of food, temperature and many other things) affect a lot the phenotype of an individual.
From your comments, it is made clear that you do not understand the interplay of the different factors that affect variance for a phenotype in a population, you have to understand the concept of heritability. You might want to read Why is a heritability coefficient not an index of how “genetic” something is?.

Genes are found in chromosomes

This sounds like a chromosome is a box containing genes which is misleading. In this regard, I like the folded shirt analogy by @terdon below in the comments.

and their job

In science, always avoid the concept of purpose, of goal, of intention. Things just happen.

is to show us

As if genes wanted to please humans. Sounds very wrong.

the traits of someone (height/hair color)

Genetic variance in population does affect phenotypic variance in the population indeed.
Answer to comment

just want a clarification on why genes are found in chromosomes isn't clear?

No, it was not clear and it still is a bit unclear (but I'll give some info below that will hopefully help). The easier for you is probably to have a look at an intro course to molecular genetics such as this one by Khan Academy for example

DNA is found in chromosomes, and large strings of DNA are genes so why?

DNA is a big molecule which contain the genetic information. It looks like that

To be more accurate the genetic information is held in the sequence of base pairs (base pairs shown on the figure). In eukaryotes (animals, plants, fungi and others but not bacteria, archea or viruses) there are several big molecules of DNA and each one is organized into a chromosome. Here is a drawing to help you visualize that

If you screen through a human genome, you will realize that the vast majority of the sequences of base pairs are not within genes. There are many other sequences such as regulatory sequences, repetitive sequences and other things. Note, also that within a gene (but again the term gene is typically poorly defined) not everything will end up coding for a protein. Only about 1.5% of the human genome directly code for a protein.
Giving you a complete answer would require writing way too much. It is much simpler to seek for further information on such introductory questions in a introductory course to molecular genetics (as the khan academy course I recommended earlier).

I just want a clarification on why genes are found in chromosomes isn't clear? DNA is found in chromosomes, and large strings of DNA are genes so why? http://prntscr.com/dsilt0

@OkamaKsakas Please see edit.

@OkamaKsakas DNA isn't found in chromosomes, it is organized into chromosomes. The chromosomes don't "contain" DNA just like a folded shirt doesn't "contain" a shirt. It is a shirt.

Do you mean that chromosomes are the DNA and if so why do we call them chromosomes? and isn't the gene the sequence of DNA? so how come..

@OkamaKsakas You should really just follow an intro course, it would save you much time.

No.  A gene is a sequence of DNA that codes for a gene product, like a protein.  An organism's phenotype is determined by all its gene products, and interactions with the environment.


text:
What is the purpose of the brown louver-like structure on the underside of a mushroom?
On the underside of the cap of a mushroom is a structure with many brown leaves closely spaced together like slats or a louver.
What is the purpose of this structure?

These thin, closely-spaced structures are commonly called gills (in more formal contexts a gill is called a lamella).  Our most familiar mushrooms have gills, but there are other species that do not have structures of this form.
Photo by Jason Hollinger via WikiMedia.org
The gills exist for reproduction. Mushrooms spread by producing tiny spores that disperse on air currents.  (In fact the entire mushroom structure exists for this purpose; the main part of the organism, a fungus, is a diffuse web under the ground or other substrate.)
Mushroom spores develop on surface tissues so that they can be released into the air.  The gills evolved to provide more surface area so that more spores can be produced and released (up to twenty times the area of the supporting surface).  The gill spacing is important because the spores are shot out of the surface, are slowed by air resistance, and then fall downwards from between the gills. (Source: Why mushrooms form gills: efficiency of the lamellate morphology)

The structures you're referring to are called "lamellae" or "gills". They are coated in the spores that the fungus to reproduce. Specifically you find them on Basidiomycete and Agaricomycete fungi.
By being 'vented' and hanging beneath the cap of the mushroom, it allows the wind to blow past and dislodge the spores, to fall and then be carried off and plant themselves somewhere new - in much the same way seeds would fall from plants.
https://en.wikipedia.org/wiki/Lamella_(mycology)


text:
Aging and Hormone Levels
Hormone levels in humans decrease with age. The effects are especially detrimental for women after menopause.
Biologists state that turtles do not exhibit most of the phenomena related to aging. For example telemore shortening does not happen in certain turtle species.
Here is my question:
Do turtle hormone levels decrease with age as in humans?

Your first sentence does not make sense, as men do not undergo menopause.


text:
Classifying Polypeptides (and/or Proteins)
Since polypeptides are a linear chain of twenty amino acids, each having a single letter abbreviation (e.g. Alanine = A). So can a polypeptide be represented as just the sequence (say: ADN for an Alanine, Aspartic acid, Asparagine polypeptide)?
This method of classifying polypeptides would lead to a possible 8000 (20**3) variations just for 3-amino-acid-polypetides (3200000 for 5-amino-acid-polypeptides, etc.) and that there would be many variations; and for longer polypeptides - that is, proteins - there would be even more variations.
Or are only the important polypeptides and proteins named, since not every variation of polypeptides and proteins are found in the body? I would've thought that many proteins (and enzymes, etc.) are incredibly specific and so they could be classified in some methodological way, as opposed to just 'lipase' or 'carbohydrase' which provides no structural information (though it would have a long methodological name).

You can certainly refer to short peptides by their sequence. I don't know of any exact boundaries, but I've seen tripeptides referred to by either their three letter codes (Ala-Asp-Asn) or even the chemical name (alanylaspartylasparagine) although obviously that gets ridiculous pretty quickly.

As the largest known protein, titin also has the longest IUPAC name of
  a protein. The full chemical name of the human canonical form of
  titin, which starts methionyl... and ends ...isoleucine, contains
  189,819 letters and is sometimes stated to be the longest word in the
  English language, or any language. However, lexicographers regard generic names of chemical compounds as verbal formulae rather than English words

For more than around 5 amino acids, just the sequence makes more sense. It would be interesting to analyse scientific paper abstracts to see how many have the sequence as the 'name', but anyway.
When we get to proteins, it would be unhelpful to refer to them by their sequence. They usually have names - enzymes are often named by what they act on (like 'alcohol') and how they act on them (like 'dehydrogenase'). In addition, there are structured names called E.C. numbers - sarcosine dehydrogenase is 1.5.8.2, for example.
As you point out, there are a very large number of sequences that do not correspond to proteins found in an organism. To name one of these is tricky, and if someone synthesises one then they would have to come up with some naming scheme to refer to it.

Not to mention that referring to a full protein by sequence alone starts to become redundant because the primary structure becomes slightly less interesting when compared with 2/3/4-ary structure. While a peptide is still short (say less than 10 AA) it probably doesn't have much structure, so its sequence becomes responsible for its chemical activity primarily, and referring to it like that still makes sense.

Thank you, that all makes sense, but if single letters for the abbreviations of amino acids are only used not name polypeptides of length <5 amino acids, then what's the point in abbreviation it. Surely a 'ALRDNNA' polypeptide would have similar chemical properties (and/or functions) to a 'ALRDNL' polypeptide. If that's not what would categorise families of polypeptides, then how else?

I think you may need to clarify what you mean by polypeptide 'family'. The only polypeptides that are generally assigned names beyond just their sequence are ones which demonstrate particular functions or where someone has contracted the name for convenience. For example, I did some work on poly-glutamine and polyproline. They were stretches of 10,20,30,40,50 amino acids, but we're all proline or glutamine. It wouldn't make sense to refer to them as PPPPPPPPPPPPPPPPPPP when polyP(20) is easier.


text:
Are Na+/K+ active pumps and K+/Na+ "Leak" channels same as given in the figure?
Na+/K+ channels maintain the resting potential with other sodium and potassium channels. Then what are these "Leak" channels? are they the same Na+/K+ pump in a special condition? If so, what is it?
Source of Image: Guyton and Hall- Textbook of Medical Physiology

Pumps are active transporters,  channels are passive. They're different proteins altogether.

@Christiaan my doubt is that the image shows same/similar proteins. What are they? Same or similar?

I agree with @Christiaan because there is a huge difference between a pump and a channel. If you want to check the difference you can simply google it or check what the wiki says about that difference.

Below is the structure of a Na+/K+ ATPase, i.e., the sodium/potassium pump shown on the left in your figure:

(image from here)
Compare to the structure of a potassium leak channel (the type of channel depicted on the right in your question):

(see this publication; image from here)
It's clear they are quite different beasts, without much similarity at all besides both being membrane proteins with several transmembrane domains, which is a characteristic they share with countless other proteins with an incredibly wide range of functions.
The only similarity the pictures from your textbook are meant to convey is that they are both membrane-bound proteins and that they accommodate Na+ and K+; besides that, they are completely different. The figure clearly shows a different mechanism of transport, and the remaining similarity is just from the very abstract way that they are represented.


text:
What is the relationship between the e value reported by HMMER and BLAST? (Are they equivalent?)
Both HMMER and BLAST report an e value for alignments.  Is it calculated in the same way and - assuming that default settings are used - can they be compared directly (are the equivalent)?  If not equivalent, what settings can be changed to make them equivalent?

can  you add some background information so that others less familiar with the question can at least partially follow what is being asked?

They use very different algorithms so they should not have the same E-value. BLAST uses a position-independent substitution matrix (e.g. BLOSUM) while HMMER uses a position-dependent substitution matrix that is different for every profile. Check out the "Background and Brief History" section in the HMMER's user guide. It explains the conceptual differences at a very broad level.
Therefore, I don't think there's any way to make them equivalent.

E-value, in short, is a statistical measure of how likely it is that your sequence of interest could have arisen by pure chance. This definition is 'discipline-wide', so should be adhered to by any bioinformatics software that elects to provide it.
Thus, the longer and more complex your sequence is, the better (lower) E-value it will have when conducting sequence alignments.
As far as I am aware, they should be directly comparable. I don't see why they also wouldn't be calculated in exactly the same way.
HMMERs website does state that it utilises 2 different kinds of E-Value however:

The are then two E-values for the domain:
Conditional E-value - This is the E-value that the inclusion and
reporting significant thresholds that are measured against (if defined
as E-values). The conditional E-value is an attempt to measure the
statistical significance of each domain, given that it has already
been decided that the target sequence is a true homolog. It is the
expected number of additional domains or hits that would be found with
a domain/hit score this big in the set of sequences reported in the
top hits list, if those sequences consisted only of random
nonhomologous sequence outside the region that sufficed to define them
as homologs.
Independent E-value - This is the significance of the
sequence in the whole database search, if this were the only
domain/hit that had been identified. If this E-value is not good, but
the full sequence E-value is good, this is a potential red flag. Weak
hits, none of which are good enough on their own, are summing up to
lift the sequence up to a high score.

The calculation for E-Value via BLAST can be found here:
https://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html


text:
How can co-dominant alleles work in flower petals?
I am studying gene inheritance, and I understand complete dominance/co-dominance and incomplete dominant penetrance in flowers. I know how to recognize each case.
However, how does co-dominance work? If I understand correctly: when a gene is transcribed, both alleles are transcribed. Hence, for flower petals, if I have a "red" allele and "white" allele, and there is incomplete dominant penetrance, I get rose petals. However, if both alleles are co-dominant, why are petals either red or white? Aren't both alleles transcribed? Or perhaps, in the case of co-dominance, heterochromatin is responsible for shutting down one allele in lineage cells?
I hope that I am expressing myself correctly. Thank you very much for your time!

We tend to use "incomplete dominance" to describes situation of haplo-insufficiency.  The white flower petal has two broken alleles for making pigment, and one working copy doesn't yield enough pigment to make the flower look as red as it would if it had two working red pigment alleles.
"Co-dominance" is for two functioning alleles when the effect is that you can see them each, and the result is not an intermediate blend.  Like having a working A antigen and a working B antigen. A blood will not clot when mixed with A blood.  AB blood doesn't halfway clot, it also won't clot at all, just like A blood.


text:
Insect identification (SP/Brazil)
Found this insect in São Paulo/Brazil. Its length is ~2cm
Any help to identify this insect would be appreciated.

Also see my video

Well, it's a type of firefly, belongs to the order of 'Coleoptera' (beetles), suborder of 'Polyphaga', family of 'Lampyridae' (firefly beetles). It's quite similar to the 'Photinus obscurellus' species (and probably the same species too), however it doesn't always have a black head like yours, however, articles have suggested that  firefly species in Brazil (Sao Paulo State) have 'adapted to mesophyl tropical forests, secondary growths, marshy areas, and open fields' (source = https://www.researchgate.net/publication/233574632_Fireflies_Coleoptera_Lampyridae_from_Southeastern_Brazil_Habitats_Life_History_and_Bioluminescence).
This adaption may have led to species having black heads as oppose the more colourful head of the Photinus obscurellus. However the bodies and the dimensions match yours very closely.
This image is from Google Images (more specifically : http://bugguide.net/node/view/194980/bgimage)

Why don't you add a picture of Photinus obscurellus as reference? It will be easier for OP and other readers to comprehend your answer.

Alrighty then, done

The insect in the picture doesn't have a colourful head(prothorax)? Also mention the source if the picture isn't taken by you.

Yeah, I just found this photo know on google images, most are slightly different bum ur it is the same species, that's why I edited my answer to 'usually colourful'

Note that the systematics of fireflies is in a bit of a flux. Also, @LucasDyson-Diaz, please cite the source of the "articles" you've read (especially the one that you quote) and provide proper reference to the image if possible. It's always good to see where you got your info since the internet is so full of deviously wrong info


text:
Question about enveloped RNA virus viral genome
I am a newbie studying campbell biology. just a quick question about virus.
When viral genome(RNA) expose itself in the host cell, why does the host cell not eliminate the genome since it apparently not belong to the cell ? Is there any mechanism that the host cell can detect and eliminate the viral genome as in the step 2,3 in the figure below ?
Thanks in advance !

What research have you done before asking it here?

Your image illustrates the replication cycle of a negative-sense single-stranded RNA virus, where the viral genome needs to be "inverted" by an RNA polymerase into mRNA before being translated by the host. There are many examples of (-)ssRNA viruses, including filoviruses (Ebola, Marburg), paramyxoviruses (measles, mumps), orthomyxoviruses (influenza), rhabdoviruses (rabies), deltaviruses (Hepatitis D), and others.
These (and all) viruses evolved alongside their hosts, and consequently the hosts evolved various protection mechanisms. One primitive component of the so-called innate immune system in humans and other organisms (going back at least to plants) are proteins known as pattern recognition receptors (PRRs) which bind to conserved motifs found in microbes, including possible pathogens. The types of molecules recognized by these PRRs include certain types of carbohydrate moieties like LPS, peptidoglycans and other components of bacterial cell walls, fungal glucans, bacterial peptides, some types of microbial nucleic acids (such as single- and double-stranded RNA, more on this in a bit), chitin, and others.
One class of PRRs are the Toll-like receptors (TLRs), named after the Drosophila Toll protein. They recognize a wide variety of microbial patterns and activate downstream signaling to stimulate an immune response, including production of pro-inflammatory cytokines and anti-viral interferons. In our case, two of them are particularly important - TLR3 and TLR7. TLR3 recognizes double-stranded RNA, which occurs transiently during (-)ssRNA virus infection when the negative-sense genome is being copied to positive-sense mRNA. However, dsRNA is much more common in retroviral infections. TLR7 recognizes single-stranded RNA in endosomes, which would occur after macrophages, dendritic cells, or B cells consume dead virally-infected cells.
Unfortunately for the host cell, once it has been infected there isn't much that can be done to save it. Viruses evolved to hijack the cell's machinery and make more copies of themselves. This hijacking is generally one way, so the only way to fight the infection is to kill the cells producing the viruses. This is, for example, why you often get a sore throat during an influenza or rhinovirus (one of the most common causative agents of the common cold) infection - epithelial cells lining the throat get infected, and are killed by the immune system to prevent the spread of the infection. This leaves a "raw" area that must heal over time.

Hi, thanks a lot for replying and providing really clear explanations about the protection mechanisms for cells. This is my first time asking in the forum, and I am still newbie struggling in campbell biology. So..from your answer, protection or defense only comes from outside the infected cell, and put it bluntly, the infected cell can only wait to be kill since its interior can not do anyting to the viral genome or can not know whether to stop producing for the virusese ? (i.e infect cell has just no way to get back the cell machinery by itself ?)

@YaoHsiao yes, you are generally correct. These viruses have evolved alongside humans, and are extremely good at hijacking the host cell's machinery. Once the (-)ssRNA genome has been transcribed into mRNA, there really isn't a good method available to the cell to determine that those mRNAs are bad, while other self-produced ones are good. Yes, there are some sequence motifs that can be identified, but it's not enough for the infected host cell to clear the infection on its own. Instead, it tries to signal to the immune system that it is infected, allowing it to be killed for the good of all.

A common class of enveloped single-stranded RNA viruses are the Alphaviruses. They are typically spread through insect bites, usually mosquitoes. These viruses carry a single strand of "positive" RNA, which is 5' capped and has a 3' Poly Adenosine tail, making it appear like a normal mammalian messenger RNA, only much larger.
Because this RNA is positive, ribosomes in your cells can directly use this RNA to produce the enzymes needed to duplicate the RNA. These replicases use the positive strand to create many negative strands. Each negative strand can then be used to create additional copies of the positive strand as well many more copies of the subgenomic RNA, which is used to create the capsid and envelope proteins. Those proteins plus the positive strand RNAs are assembled into new viruses and bud off the cell.
The viral RNA protects itself by acting like a messenger RNA. This recruits host proteins that prevent degradation and promote translation to make the viral proteins. Most alphaviruses also shut down host-cell transcription and inhibit the interferon response. This prevents the cell from mounting a defense against infection, but also eventually kills the cell.
EDIT: I just noticed that your question is tagged "Retrovirus", but your image does not represent the retrovirus life-cycle. It looks more like an alphavirus life-cycle.

The image shown is of a virus with a a negative RNA genome - it must be copied to generate mRNA.

@MattDMo The image itself is labeled slightly wrong then. The caption says "Enveloped RNA virus", but the positive stranded RNA viruses are also enveloped. Too many types of viruses.

that is true, the image could be labeled more clearly. But, I think Step 3 indicates that the unnamed virus in question is negative stranded.

Depending on the nature of the viral genome there are multiple pathways (elaborated upon in previous answers and comments) that sense viral nucleic acids and trigger an interferon response. This can induce apoptosis and kill infected cells, or alternatively, it can set of a cascade of genes that induce replication arrest (which in the case of some viruses can be enough to thwart an infection because of viral dependence on host replication factors).
One byproduct of the induction of an interferon response is the induction of the APOBEC family of cytodine deaminases, which can hypermutate viral genomes (APOBEC1 hits RNA, multiple APOBEC3 proteins hit DNA/ssDNA that may potentially result from various phases of the replication cycle), and other related restriction factors.
However viruses have evolved to evade these responses, either by altering restriction factors themselves, or by evolving sequences that won't be detected by viral sensing molecules.
http://www.nature.com/nrmicro/journal/v14/n6/abs/nrmicro.2016.45.html
http://www.cell.com/trends/immunology/references/S1471-4906(16)30170-3
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3331687/

If you are trying to ask if the RNA can be destroyed, it is not likely unless you don't utilize siRNA.
SiRNA, a mechanism involved in the regulation of phenotype expression, plays a key role in avoiding lytic and lysogenic cycles that could potentially help the virus produce virions, helping the virus reproduce. This RNA, also known as small (short) interfering RNA, an RNA duplex, is able to target certain mRNA molecules, causing them to degrade.  This can eventually lead to gene knockdown.
Additionally, the lysogenic cycle, causing cells to lay dormant for some time before eventually releasing virions, contains a g0 phase.  The g0 phase is a period of the cell cycle in which the cell produces minimal proteins or undergoes little or no DNA replication.  Keeping the cell in this phase may help avoid virion synthesis.
Furthermore, being able to trigger immediate cell apoptosis would also help reduce the amount of viral replication.  However, this can be dangerous as the cell may be prone to undergoing the lytic cycle.
So yes, it may be possible without the use of siRNA, but it will be very unlikely.  Immune response can also help fight off the virions in the long run.

No, not all RNA viruses integrate into the host genome. Also, there are specific intracellular surveillance molecules looking for viral components like dsRNA, so that part of your answer is incorrect as well.

@MattDMo How does it look now?  I appreciate the feedback as I am new to this site.

There are still issues, mainly that you're talking about retroviruses, when the image in the original post clearly is not of a retrovirus at all. Second, lytic and lysogenic cycles are generally associated with bacteriophages, not viruses that infect eukaryotic cells like these, and the Wikipedia articles you reference are mainly about bacteriophages as well. Eukaryotic viral lifecycles have some similarities to bacteriophages, but there are many differences as well. Finally, you don't talk at all about the role of the immune system in surveillance and killing of infected cells.

@MattDMo Ok, I understand what you are talking about.  However, I still don't understand what's wrong about the siRNA part of the answer.

First time reading "it is not likely unless you don't utilize siRNA." Rather
RNase are infamous for existing everywhere and spoiling experiments. Is it really true that normally the protein-made enzymes from the host can not degrade intruder RNA?


text:
Why Milky serum in diet rich with Triglycerides?
When we eat the meal rich with triglyceride our muscle or blood after seperation of the serum the color of the serum will be milky. What is causing to happen in our serum ? Milky serum (lipemic serum)

Can you quote from your source?

I read this information in the some medical cases and also an A&Q website link . I know these are not suitable sources but i didn't understand so i wanted to ask .

(short hint) "These chylomicrons then pass into the lacteals, forming a milky substance known as chyle." .... Wikipedia. Seemingly it is due to Tyndall effect from coloidal nature of Chylomicrons

Tyndall effect makes a sense but still not clear. Cause according to these informations that milky color occurs in lacteals that is a part of lymphatic system and we dont get the serum from lymphatic vessels actually we obtain the serum from the blood.


text:
What is meant by bionomics of a vector?
What is supposed to fall under the title Bionomics (The study of an organism and its relation to its environment; ecology.)?
Suppose we are dealing with a vector, Anopheles sp. are the following going to be included in its bionomics:

Life cycle
Interaction with parasite (Plasmodium sp.)
Mode of transmission of parasite by this vector
Control
Diseases caused ?

Bionomics is indeed the 'thorough' study of living organisms and their relationship with the environment/ niche they thrive in.
Aim of Bionomics is mainly to decipher the driving factors for an organism to prefer a given niche. Given this key goal, it is apparent that one needs to focus on all aspects of an organism's life cycle and community dynamics.
So the answer to your question would be: Yes, one will need to focus on all the five points pertaining to Anopheles sp. (the 5th point i.e diseases caused) will more be an information resulting out of the study of its interactions with other living/ non-living forms), than a specific focal point for Bionomics.
References:
A good article on Bionomics
An amazing and detailed report on Bionomics of Entomophagous Coleoptera
Other references:
The dominant Anopheles vectors of human malaria in Africa, Europe and the Middle East: occurrence data, distribution maps and bionomic précis. Sinka et al., 2010
Description and Bionomics of Anopheles (Cellia) ovengensis (Diptera: Culicidae), a New Malaria Vector Species of the Anopheles nili Group from South Cameroon. Awono-ambene et al., 2004


text:
Is this how female and male gametes look like in plants?
In the red box, the pink one is female sex cell I presume and the blue one is a male sex cell.
http://prntscr.com/dsii2x Am I right? or are these chromosomes.. I'm confused.
This is law of segregation.

Gametes don't look like that. It is a simplified colourful diagram to explain Meiosis. Cells and cell components are not coloured in nature unless they have pigments in them (e.g. Nostoc sp. doesn't need staining it appears green under microscopel).

Then what is that though? And how do gametes look like?

The blue and red colours are to distinguish between the maternal and paternal chromosomes as you have thought. I don't find any other possible reason for colouring them differently.

I just have one more question though.. If these these two are diploid cells, and both of them separate then how is gametes related to this at all? is it because gametes are needed for this to occur in the first place (the occurring diploid cells?)

It's not very clear what you are asking.

@OkamaKsakas Please note that with the icon that looks like a landscape, you can insert an image directly in the post and not just a link to an image stored somewhere on a different site. It makes the post much more pleasant to read.

The comments are very unclear and your interpretation of the figure seems very wrong (no offense). You should have a look at an intro course (such as this one by Khan Academy) as asking such intro questions here will require for one to rewrite an entire course.
The pink and blue thingies on the image are chromosomes, not gametes. A gamete is a haploid cell (we can see 4 of them at the bottom of the figure). One chromosome (say the pink one) has been inherited by the mother of the individual and the other chromosome (say the blue one) has been inherited by the father of the individual.
Let's assume that the segregation we see on the figure happens in a female individual. So, on the figure we see female diploid cells and female haploid cells. The female haploid cells are called ovules (there is a bit of oversimplification here). You can imagine the same process of segregation could occur in a male individual. The male haploid cells are called spermatozoid (there is a bit of oversimplification here). The male and female gametes might fuse to become a zygote which will develop in a new fully grown individual. The colors of the chromosomes in this scenario indicate whether the chromosome originally come from the grandmother or the grandmother of the zygote.

Is there a way I can contact you in PM?

@OkamaKsakas You can find my contact information via my website which you'll find via my profile. Just click on my name and select the tab profile.

I'm not sure how to send you a message via twitter, unfortunately. I sent you a tweet though

Just send an email then. All the info is on my website.


text:
how long after death can a body exhibit an immune response
I suppose this is part of a larger question - at what point do the body's coordinated systems (Endocrine, Autonomic nervous system etc) begin to fail? Within hours? Days? Minutes?
Of course this must vary widely with the means of death but let's assume for the moment a sudden brain embolism or some such that would leave the organs intact.

You might be interested in this.


text:
What is the space between -10 promoter sites and start sites (+1)
Between the transcriptional start site of a gene and the -10 promoter region there is always a space of around 10 nucleotides, what is this space function and purpose?
Do you see the space between operator and promoter.. that is what I am referring to, even without an operator it is usually still there
Also, if I want to insert a specific promoter into a vector backbone, how much space should be between the promoter -10 and +1 transcription start site? Is it always 10 bp?

Please [edit] your question and clarify what you mean. Are you referring to the transcription start site  or the translation start site? I guess you mean the former, but it isn't very clear from your question.

I would say that you are referring to the kozak sequence
https://en.wikipedia.org/wiki/Kozak_consensus_sequence

Transcription start site

By "start site", do you refer to the "start codon"?
I think the spacing you are referring to is the 5' UTR.

The 5′ untranslated region (5′ UTR) (also known as a Leader Sequence or Leader RNA) is the region of an mRNA that is directly upstream from the initiation codon. This region is important for the regulation of translation of a transcript by differing mechanisms in viruses, prokaryotes and eukaryotes

Have a look at the wikipedia article for more information about its roles.
The 5' UTR is typically 3 to 10 nucleotides long in prokaryotes but can be much longer (up to several thousands of nucleotides) in eukaryotes. On which species did you notice this spacing of about 10 nucleotides?

I think the OP is referring to the transcription start site, not the ATG. Otherwise, their mention of a promoter doesn't make much sense.

No, the 5' UTR would include the -10, -35, Shine-Dalgarno and other operator motifs. The OP is specifically asking what the ~10 base pairs between the -10 box and the actual start codon are for.
As far as I'm aware, as a molecular biologist, the site merely serves as a spacer to allow the relevant enzymes to dock with the nucleic acids correctly. You have to bear in mind that just because the ribosomes binding site is only 6-8 bases, the actual amount of DNA that it's occluding will be considerably more potentially.

Yes that is exactly what I was referring to, the base pairs between the transcriptional start site which usually includes the 5' UTR and the upstream (-10) part of the promoter. There doesn't seem to be much information around what exactly this section function and purpose is. Even with an operator in a prokaryotic sequence, the space is still there...

@condo1234 OK, but please edit your question and clarify.

The major reason I am asking is say if I want to insert a specific promoter into a vector backbone, how much space should be between the promoter -10 and +1 transcription start site? Does it always have to be -10?

The question itself is unclear. However I guess that the answer, as it is written right now, looks as if it is requesting clarification. It appears more like a comment.


text:
Is there difference in stomatal density in young and mature leaf?
If stomatal density varies in young and mature leaves then what may be the reason for this.which surface of the leaf has more stomata?how to distinguish abaxial and adaxial surface in monocot.


text:
Are there birds that don't vocalize?
I am wondering whether there are birds that do not vocalize at all.
I know about the distinctions between songs and calls in passeriformes.
I know that there are species that vocalize very little, like the Ruff (Philomachus pugnax).
I was curious to know whether there is a species in which vocalizations, acoustic communication, do not play any role at all.

There are birds with non-vocal sound only. However, there might not be any bird without producing any sound. Thus, all birds appear to have some way of acoustic communication.
A better known example of a voiceless or near voiceless bird is stork per multiple credible sources.

Storks are voiceless or nearly so, for lack of a fully developed syrinx (vocal organ), but some of them clatter their bills loudly when excited.
https://www.britannica.com/animal/stork

Wikipedia claims that storks have a syrinx and rarely produce some sound with it and adds credible citations.

Although it is sometimes reported that storks lack syrinxes and are mute,[7] they do have syrinxes,[8] and are capable of making some sounds, although they do not do so often.[4][9] The syrinxes of storks are "variably degenerate" however,[8] and the syringeal membranes of some species are found between tracheal rings or cartilage, an unusual arrangement shared with the ovenbirds.[10]
https://en.wikipedia.org/wiki/Stork#Morphology

Even, just clattering is an acoustic communication between storks:

Identification of the sex of birds is important for captive breeding of endangered species. In the oriental white stork (Ciconia boyciana), an endangered species, both sexes produce an acoustic signal called "clatter" by rattling their mandibles together to generate sounds. https://pubmed.ncbi.nlm.nih.gov/15333993/

The only birds without syrinx might be New World vultures but they do produce sound also.

No New World vulture possesses a syrinx,[35] the vocal organ of birds. Therefore, the voice is limited to infrequent grunts and hisses.[36]
https://en.wikipedia.org/wiki/New_World_vulture#Description

Here is a relevant quote from ornitology.com about Non-vocal Sounds:

Kiwis stamp their feed when annoyed. Boat-billed Herons, Storks, and Albatrosses rattle or clap their bills. Woodpeckers drum. The Ruffed Grouse drums with its wings. The nighthawk and hummingbirds often make sounds with their wings or tails. A number of birds make whistling sounds as they fly through the air- may or may not serve a purpose.


text:
Measuring protein concentration, Bradford vs. Nanodrop?
I know that the bradford assay is a very standard way of measuring protein concentration after e.g. a purification. However, in the lab that I work in now they normally only use nano drop at the 280nm wavelength.
How trustworthy is this concentration? Say that I e.g. get 2.5 mg/mL, could I really trust this?

That depends strongly on your protein and how exact you need this concentration. Both tests (Bradford and the measurement at 280nm) only do an approximation.
The measurement at 280nm relies on the interaction of aromatic aminoacids with the UV light. If you have a protein with few or no aromatic amino acids, your measurement will be wrong.
The same is true for the Bradford assay. Here you form a complex between Coomassie Brilliant Blue and unpolar and cationic side chains of the amino acids. This test is more precise, since it includes more possible side chains, but is still dependend on the composition of the protein.
More precise is the BCA assay, since it utilizes the reduction of copper ions by the peptide bond of the protein.
What you could do is run a BCA assay (or at least a Bradford assay) from your sample and measure the same sample on the Nanodrop at 280nm and compare the results.
You can find an overview over the methods here and here.

I will aks the same as i did on Joe Boyle's answer, based on his common on extinction coefficient: when using the extinction coefficient for the protein in Nanodrop, how does it then compare to other methods? Does it then get more reliable

@CuriousTree knowing the exact epsilon value for a particular protein helps, but you're still stuck with the basic limitation of UV-based measurements - it entirely depends on the number of aromatic amino acids. The thing to keep in mind for any kind of quantitation assay is that you need to have a relevant standard. Not every protein is the same as, or even similar to BSA.

@CuriousTree When you know your protein very well, it might help, but in the moment you are analyzing protein mixtures (or something complex like cell lysates), this will not help.

The nanodrop should have an option that allows you to input an "extinction coefficient". This is a measurement of how much one mole of your protein will absorb at 280nm. The nanodrop will use this value to give you an accurate concentration reading.
To find the extinction coefficient for your protein, put its whole sequence into this server http://web.expasy.org/protparam/.
A few tips:

Use the exact buffer your protein is in as a blank.
Repeat your nanodrop reading a few times using a new pipette tip each time to ensure reproducibility
The purer your protein the more accurate your concentration reading will be! If there is a major contaminant in there, you will not get an accurate concentration reading.

thanks! Do you think this is comparable to Bradford then? because its specific for the protein?

Neither technique is perfect but they can both give good estimates. Bradford depends on your protein interacting with the Bradford reagent in a similar way to the known standard, unfortunately I don't have much experience using it.
If you need a precise concentration and have the time/resources then quantitative amino acid analysis would be my suggestion: link

@JoeBoyle if my peptide has no/few aromatic residues and I still want to use Nanodrop, will the use of  Expasy Protparam extinction coefficient input for Nanodrop become accurate enough?

@scamander If your protein has no aromatics you won't be able to use 280nm absorbance but if it has a low number you can still use the extinction coefficient. As usual, the quality of the reading will depend on how pure your protein is.

@JoeBoyle Thanks so much for your answer. Mine is a peptide (comes in powder).
How do you measure protein purity?

If you are dealing with a pure protein where there is nothing else present that will absorb at 280nm and if the E(1%, 280) of the pure protein is known or  may be calculated from the amino acid sequence, then A-280 measurement is a very accurate, fast, nondestructive method of determining protein concentration.
It is certainly much more reliable than any method that uses a standard curve, where the color produced may depend on the standard protein used.
It also has the additional advantage that the protein may be fully recovered after the measurement is made, often a consideration when dealing with precious samples.
It must be emphasized that the protein needs to be pure for this method to work.  When dealing with impure protein samples, the 'rule of thumb' is that a 1mg/ml solution will have an A-280 of 1, or E(0.1%, 280) = 1. But of course other substances such as DNA or toluene (in a yeast extract, maybe) may absorb at 280nm and play havoc with your readings.
A-280 measurements, being nondestructive, are usually considered adequate for monitoring eluates from chromatographic columns.
If the amino acid sequence is known and you wish to use the Perkins (1986) method to calculate the E(1%, 280) it is probably worth bearing in mind that this method takes no account of a bound prosthetic group (such as haem or tightly bound NAD), which could also significantly contribute E(1%, 280) value.
Some good refs
Perkins, S. J. (1986). Protein volumes and hydration effects. The calculation of partial specific volumes, neutron scattering matchpoints and 280-nm absorption coefficients for proteins and glycoproteins from amino acid sequences.  Eur. J. Biochem. 157, 169 - 180. [Pubmed]  [pdf]
Gill, S. C. & von Hippel, P. H. (1989). Calculation of protein extinction coefficients from amino acid sequence data.  Anal. Biochem. 182, 319 - 326.  [published erratum appears in Anal. Biochem. (1990) 189, 283].
Sober, E. K. & Sober, H. A. (1970). Molar extinction coefficients and E (1%, 280) values for proteins at selected wavelengths of the ultraviolet and visible region.  In Handbook of Biochemistry. Selected Data for Molecular Biology, 2nd edn.  Sober, H. A., Ed. pp C-71 - C-98. The Chemical Rubber Company, Cleveland, Ohio.
Edit
I can give an example of the Perkins method, if anyone is interested.

Best answer for purified proteins. With 280nm absorbance you can calculate a reasonably correct extinction coefficient from your sequence and then make a quick measurement on your nanodrop (using the UV module, not the protein module). This is more accurate than Bradford where you have a sequence-dependent error that you cannot correct for. Strictly speaking it is only valid for the unfolded state. You can measure in 6M Guanidinium chloride to be sure. In my experience, this is usually not necessary though and the value is pretty close for folded proteins, too.

The choice between colorimetric and direct quantification at A280 depends on both the protein to be quantified and the buffer being used. Generally A280 works well when you have a purified protein solution and the protein is well characterised. Entering the correct extinction coefficient will improve the accuracy of the concentration calculation. If using A280 it is also worth checking that your buffer does not absorb highly in the 280nm range. You can do this by blanking with water and running your buffer as a sample. If your buffer absorbs highly then you may be better off selecting another method.
For cell lysates and uncharacterised proteins you are better off with a colorimetric assay such as Bradford, BCA or Pierce 660. These can be run in microvolume but take care in the preparation, especially with assays such as Bradford that may have a lot of particulates.
Also, as you are measuring against a standard curve for colorimetric assays, the more similar your standards are to your sample, the better the results.
Andy