text:
What are the highest and lowest possible pH, paCO2 and HCO3 in the blood of living human?
What are the highest and lowest possible values of pH, $paCO_2$, and $HCO_3$ in the (arterial or venous) blood of a living human being?

You should look for the standard reference ranges for arterial blood gases, which will give you your answer

These give the normal values in normal people, not the possible in any living human body.

How would we know the numbers for any possible living body? The best you could rely on would be individual data points from someone whose blood happened to be checked for those quantities (i.e. highest and lowest recorded concentrations). Not a controlled experiment. And no way to tell if that's the highest possible.

Perhaps a more reasonable thing to find is the variance or standard deviation of the values of these quantities in normal patients.

Thank you @A.Kennard. I understand that. My question would be better rephrased as "what are the ever known highest and lowest values". This article mentions a range of pH between 6.8 and 7.8. A simple example why one may need an answer to this question is when a spreadsheet should reject the entry of "impossible" blood gas values in a living human.

Practically, in order for this to be answerable you'll need to comment on whether you consider a pulseless person during resuscitation efforts to be "alive." It's not uncommon to see a pH ~6.8 range drawn during CPR, but that's a different situation than normal "life."

Good point @Susan. I think it is sensible to include all   cases with successful resuscitation.

As discussed in the comments, there are theoretical and practical problems with arriving at such data. There have been controlled experiments using canines, but you have specifically stated your interest in humans. I offer a summary of a few observational studies that may be helpful.
In this study, 117 patients in intensive care units (who are likely to have the most abnormal blood gas parameters among the living) were monitored with continuous optode-based blood gas analysis system. Of the 1,341 measurements, the ranges were:1,2

pH: 7.14 to 7.64
PaCO2: 19 torr  - 98 torr
PaO2: 38 torr – 413 torr3

Another study included a total of 487 samples were obtained in ICU patients with severe respiratory failure and found the following ranges:

pH 7.23 – 7.55
PaCO2: 19 torr – 83 torr
PaO2 30 torr – 522 torr3

These are reasonable ranges for pseudo-stable ICU patients.
Contrast that with normal ranges (+/- 2 standard deviations):

pH: 7.35 – 7.45
PaCO2: 35 torr – 45 torr

On the other hand, you’re interested in the most extreme recorded values, which are likely going to occur during cardiac arrest. According to this case report and literature review, the lowest published arterial pH of an adult who survived cardiac arrest with neurologic recovery is 6.33. The caveat here is that this was a near-drowning victim, and the associated hypothermia provides neurologic protection. The authors go on to report several others including their own patient with pH in the range of 6.5 - 6.6 with neurologic recovery in the absence of hypothermia.

Notes

1. Bicarbonate measurements on whole blood are calculated rather than measured and so not included in such studies. The more accurate test for this measurement is serum chemistry. The bounds are usually defined by the assay. It’s possible for a living human to have HCO3 less than assay (5 mmol/L in most labs by serum chemistry) or greater than assay (~50 mmol/L by most labs).

2. All data provided are arterial. Venous blood gases are of little clinical utility except as a cop-out for obtaining an arterial blood gas.

3. These upper values are intubated patients breathing 100% FiO2. (The lower values are those about to be intubated breathing 100% FiO2....) The theoretical maximum PaO2 on room air is derived from the alveolar gas equation, ~100 torr.


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Circular mRNA to produce long proteins
Ribosomes can read mRNA and produce proteins, if we somehow make a circular mRNA for the ribosome to bind onto, it will make infinitely long "proteins", (since ribosomes can make very big proteins, I assume they can bind long enough before disassociating)
However after doing some search on this topic, it seems that I am able to find only about 2 related papers. One of them seems to be from 1998, while the other one is more recent.
These articles suggest that it's doable. If this works, we'll be able to produce biopolymers with the sequence exactly as we designed, there would be massive applications, but I'm curious why it's not getting much attention, or why aren't there more papers related to this area?

Non-covalent circularization is known to increase the protein steady state levels by increasing mRNA stability and translation efficiency. But certainly no long proteins are made by such a process. If there is no stop codon then the non-stop decay mechanism eliminates the mRNA. I am not sure how it works out in this case. I guess it may work out to some extent but is not very reliable.

If you read the two papers, in fact long proteins are made. They stated that they constructed a circular mRNA with infinite open reading frame. The 1998 papers makes poly-GFP 5~6 times long than the GFP (if i remember correctly). The 2013 paper makes very large proteins as can be seen on the southern blotting figures (i didn't find the numbers though).
I'm however curious about how the non-stop decay mechanism works. In the paper they used the PURE system, which is an artificially constructed reaction vessel that mimics the environment within the cell, but eliminates the decay mechanisms.

Yes I did see the paper; I found it interesting. But I am not sure if this can be reliably replicated and how the length of the product can be controlled. Perhaps those are the aspects that you are interested in when you plan to use the system to synthesize your biopolymer. (PS: it is the western blotting that is used for detecting the protein)

Yeah, western blotting, sorry for the mistake.

I'm familiar with those papers, and they were dissapointed in the yields. The issue seems to be that ribosome binding is the slow step, and the ribosomes don't stay on the mRNA forever. Made me wonder if you could tie the ribosome around the mRNA strand to lock it in place.

@user137 It looks like they were disappointed in the yields and then stopped doing further research!

non-stop decay in my understanding is probability of ribosome to unbind RNA (half-life time of RNA-ribosome complex is finite). The longer transcript, the higher is chance that ribosome will fall off and product will not be functional or will be degraded.

@user137 Some cysteines strategically placed in each subunit might do the trick.

In vitro translation is not as efficient as other chemical polymer reactions. For example, when proteins are synthesized using in vitro translation systems, many researchers have been using radio-labeling to see the products because the yield is too low to detect them by other methods, although few small proteins have been successfully produced at a microgram level. It should be noted that it is also difficult to produce exogenous long peptides at sizes more than 100kDa in E coli in vivo expression system.

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How can one accurately diagnose the cause of human hearing loss without surgery?
In a human, if you were to avoid a tympanotomy (surgical examination of the middle ear), how could you distinguish between a blocked Eustachian tube, a ruptured eardrum, or a perilymph fistula?
For instance, take the situation where a young man (suffering from a common cold) blew his nose violently, became dizzy for 1 minute, and then reported loss of hearing in one ear of about 40%.  What would your diagnosis be, possible treatments, and expected outcome?

I am not an ENT doctor, but I think the following diagnoses would suffice to determine each of the conditions:

Blocked Eustachian tube: Complaints would be of sudden onset and likely associated with a common cold, or ear infection. Providing the patient with standard decongestant should provide quick relief.
Ruptured eardrum: Patient should have subtle hearing loss apparent on audiogram and it would be relatively easily identified by routine otoscopic examination.
Perilymph fistula: This condition is hard to diagnose and I quote from Vestibular Disorders Association:

A physician can arrive at a presumptive diagnosis [of a perilymph fistula] through a thorough probing for events close in time to the onset of symptoms, along with a variety of tests. These tests can include hearing tests (audiogram, ECOG), balance tests (VNG, VEMP) and some form of a “fistula test.”

The periplymph fistula is by far the most severe condition and the one with the most prominent effects on the vestibular system (balance). Multiple tests and rigorous medical exam is necessary.
With regard to your presented case study: Again, I am not an ENT doctor but a ruptured ear drum can result in dizziness due to the fact that one inner ear is exposed to cold air due to a rupture and the other ear is not. Unilateral inner ear cooling can result in dizziness. However, blowing your nose is unlikely to cause a ruptured eardrum as it is generally caused by more serious barotrauma (diving accidents and in-air plane cabin pressure malfunctions) (Web MD).
Similarly, the fistula is most often caused by more serious traumatic injuries (Vestibular Disorders Association).
A blocked Eustachian tube sounds the most plausible, as it is associated with the common cold (Web MD). Violently blowing your nose can cause fluid to travel up the middle ear, and possibly cause subsequent infections.

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Quantitative Differences : DNA and Gene
After HGP, we are not having many databases which consist of several notepad files of ATCG....
Can we distinguish quantitatively a given A,T,C and G stretch as DNA or Gene?

What exactly do you mean with your first sentence? There are many databases containing nucleotide sequence data. One of the biggest is GenBank, which could be considered a collection of "notepad files of ATCG". Also, except for RNA viruses, all genes are encoded in DNA. So it does not make sense to say "DNA or Gene". It sounds like you are asking how gene prediction works?

I interpret your question as: Given a stretch of DNA sequence, can we determine if it encodes a gene? My summary of the answer would be: "Sometimes".
The problem you ask about is called "Gene prediction" and is described in some detail by Wikipedia:  http://en.wikipedia.org/wiki/Gene_prediction
The most basic indication that a gene may exist is the presence of an "Open Reading Frame" (ORF). An ORF is a stretch of DNA from which a single protein may be produced.  However, an ORF is not strictly required for a gene (as not all genes encode proteins), and not all ORFs are genes. There are many software tools for gene prediction available which use different rules to predict if a given region of DNA is functional (contains a gene or a regulatory element). They may be usable on any kind of DNA sequence, or on sequences from certain organisms only, depending on the program.
Two commmonly used gene prediction tool are GLIMMER (http://www.ncbi.nlm.nih.gov/genomes/MICROBES/glimmer_3.cgi, used for microbial genomes) and GeneMark (http://opal.biology.gatech.edu/gmhmm2_prok.cgi). See also http://en.wikipedia.org/wiki/Gene_prediction
As a quick check, you may also use NCBI BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi) to see if your sequence aligns to a known gene.

Thanks a lot for making me understood about the principle. I am anxious really how the genes are ordered as a finite length string of four bases? How random as a finite string of four bases when we consider it as a gene? My conviction is that genes are not randomly arranged as a finite string. There must be a beautiful organization. I would like to know in detail about the organization of them. And definitely that organization would be missing in any arbitrary DNA stretch.

Yes, the statistical properties of coding and non-coding sequences are different, and this is exploited by some gene-prediction programs. Note that some non-coding sequences might be the remains of a gene which is no longer expressed, and so may have similar statistical properties as an expressed coding sequence. Such sequences are called "pseudogenes".  The following links might be a place to start: NCBI Book on computational genomics (http://www.ncbi.nlm.nih.gov/books/NBK20261/) and a review on identifcation of protein-coding genes:  http://genomebiology.com/content/10/1/201

This is possible and is an important topic in bioinformatics. Lots of tools have been written and papers have been published, most important

A random sequence usually "encodes" only very short protein sequences before the "stop" codon (three nucleotide combination marking the end of the protein) is met just by chance. Coding sequence encodes a reasonably long protein.
Same amino acid can usually be encoded by multiple alternative sequences of three nucleotides (codons). In a real coding sequence they are not equally probable, some codons are preferred over others (which ones, is organism-specific).
It is possible to find characteristic nucleotide patterns inside or in some cases near the coding sequence. Dropping the coding sequence alone into genome would only result in a non-functional pseudogene.
Most often, encoded protein sequence is more or less similar to the sequence of some already known protein.

.. and so on. Try GenScan, for instance.

My conviction is that genes are not randomly arranged as a finite
  string. There must be a beautiful organization.

In bacteria, you will have a whole series of genes required for a pathway all next to each other, so that their expression can all be controlled from one point upstream of them.  We call that whole suite of genes and the upstream binding site an operon.
But in eukaryotes, there is no grand organization of genes with regard to their position on the chromosomes, in general.  Regardless of what you think they should look like, we don't observe a wonderful organization.  Evolution results in things looking pretty haphazard.  Go browse ensembl.org if you want to see for yourself.


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Giardia lamblia cases of infections
I am wondering if anyone has seen a data of Giardiasis (Giardia Lamblia) cases  in different countries on the world? I have found for different diseases and also for 'diarrhoea diseases' in general, but I need especially for Giardia Lamblia.
Any suggestion where I can try to look for this data will be useful.
Thank you very much!

If you have or can get access to it, you might try looking in the Incidence and Prevalence database: http://thomsonreuters.com/incidence-and-prevalence-database/
Another possibility is the GIDEON database: http://www.gideononline.com/. It is possible to sign up for a 15-day trial.
For Europe, statistics are available from the WHO CISID at http://data.euro.who.int/cisid/ (select "all infectious diseases", then "Giardiasis").
The WHO does not have any global statistics available on their website, so otherwise you might have to piece together data from individual publications. Some examples:
Thailand, 2005: http://www.ncbi.nlm.nih.gov/pubmed/16438174
Germany, 2006: http://www.ncbi.nlm.nih.gov/pubmed?term=19404678
United States, 2006-2008: http://www.cdc.gov/mmwr/preview/mmwrhtml/ss5906a2.htm
Portugal, 2002-2008: http://www.parasitesandvectors.com/content/5/1/22
Quatar, 2008: http://www.parasitesandvectors.com/content/4/1/211
Tajikistan, 2009: http://www.parasitesandvectors.com/content/4/1/195
Ivory Coast, 2009: http://www.parasitesandvectors.com/content/4/1/96
Tanzania, 2011: http://www.parasitesandvectors.com/content/6/1/3
Ghana, 2006-2009: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170632/?report=classic
Canada, 1999/2002: http://www.biomedcentral.com/1471-2334/5/72
Canada, 1990-1998: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC194172/
China, 2012-2013: http://www.biomedcentral.com/1471-2334/14/25
Ethiopia, 2009: http://www.biomedcentral.com/1471-2334/13/419
Kenya, 2010-2011: http://www.biomedcentral.com/1471-2334/13/243


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What are some of the known fungi with heat resistant spores
Are there any fungi whose spores can survive 100+ degrees for 15 minutes and grow in a sugar-deprived medium?

According to Sterflinger, some black yeasts may qualify: http://www.ncbi.nlm.nih.gov/pubmed/10081587

Rock inhabiting meristematic fungi are extremely tolerant against high
  temperatures, desiccation and osmotic stress. Their temperature
  tolerance increases with increasing dehydration of the fungal thallus.
  Air dried mycelia of black yeasts stand temperatures up to 120 degrees
  C for at least 0.5 hours

More recently, Suryanarayanan et al. (http://www.ncbi.nlm.nih.gov/pubmed/21872180) have published the discovery of several fungal environmental isolates able to survive dry heat sterilization for 2h at 100+ degrees C. Growth testing was done on Potatao Dextrose Agar (PDA).

Among 25 species of Ascomycota isolated from leaf litter, nine were
  able to grow after incubation in a drying oven for 2 h at 100 °C; the
  spores of two of these species survived 2 h incubation at 110 °C, and
  one survived exposure to 115 °C for 2 h." (...) Craphigera and Phoma sp.
  survived 2 h incubation at 110 °C; the conidia of Bartalinia sp. were
  the most resistant and survived exposure to 115 °C for 2 h

The isolates which survived at least 2h at 100 C were:

Bartalinia sp. (NFCCI 2307)
Chaetomella raphigera (NFCCI 2308)
Curvularia sp. isolate 2 (NFCCI 2311)
Drechslera halodes (NFCCI 2312)
Leptosphaerulina sp.
Pestalotiopsis sp. isolate 1 (NFCCI 2309)
Pestalotiopsis sp. isolate 2 (NFCCI 2313)
Phoma sp. (NFCCI 2310)
Pithomyces sp. (IMTECH 9398)


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Visualisation of phylogeography
I am working on phylogeography on one model species and I am a beginner. You can imagine one species that came on locality more than 5 mya (million years ago). It was a good environment, so the species expanded very quickly. After climatic changes this model species split in two refugiums (isolated locations for a once widespread species) and evolved into two species. This happened several times and now we have from that one ancestral species six valid species.
I have data from MrBayes and BEAST molecular clock. Can you recommend some phylogeographical program which can consider also expansion and contraction of model species?
My input data:
molecular identification (sequences)
coordinates (lat, lon) for each species
geographical data of a continent (altitude, precipitation etc.)
My goal:
Create a map where will be polygons (areas) of each species. These areas will expand and contract (step-by-step not like a do not want create video).
My problem:
I am able to make polygons by MCP, or kernel density, but unable to incorporate barriers into model. For example, polygons of species which lives in mountain region created by MCP include areas of lowland inside...

You might want to consider asking this question on http://biostars.org as well. Just to be clear, it is completely on topic and welcome to stay here, but you could also ask it on biostars.

@terdon thanks for recommendation..I try it :)

I think Spread will be best for this work.
SPREAD: Spatial Phylogenetic Reconstruction of Evolutionary Dynamics

(source: kuleuven.be)
Authors: Filip Bielejec, Andrew Rambaut, Marc A. Suchard & Philippe Lemey
Homepage: http://www.phylogeography.org
License: LGPL

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What are the purposes of granulocytes in acute inflammation?
I heard the phrase

Neutrophilic leucocytes are kings in the acute inflammation.

Neutrophils are granulocytes, while leucocytes are not granulocytes.
I think this statement refers to the fact that leucocytes have neutrophilic properties, instead of being neutrophils itself.
Acute inflammation players are, I think
Granulocytes, monocytes and leucocytes

while in chronic inflammation similar player but the main factor is macrophages so the phrase which I heard

Macrophages are the kings of chronic inflammation.

I think granulocytes are related to the Healing and Proliferation.
Eosinophils for instance in the allergic responses of acute inflammation.
I think granulocytes are phagocytosed by the macrophages and this way spread their functions through macrophages around.
Probably, neutrophiles are attached to the leucocytes such that they spread their function through leucocytes (so called neutrophilic leucocytes).
Let's cover first this, since we can after understanding it go to the chronic one.
What is the purposes of granulocytes in acute inflammation?

Have you read the WP article on neutrophilic granulocytes, the most abundant form? Essentially, they are the first infiltrating cells to arrive at the site of injury at the beginning of acute inflammation (bacterial infection, environmental exposure, etc.).

How are neutrophilic granulocytes related to neutrophilic leucocytes?

As far as I know they are the same thing. Neutrophilic granulocytes is another term (usually) for neutrophils. All granulocytes (white blood cells with granules in the cytoplasm) are leukocytes (or leucocytes), which literally means "white cells." Another term is polymorphonuclear leukocyte, which refers to neutrophils' unusual nucleus, generally having 2-5 lobes or sections.

MattDMo's answer

Essentially, [neutrophilic granulocytes] are the first infiltrating
  cells to arrive at the site of injury at the beginning of acute
  inflammation (bacterial infection, environmental exposure, etc.).

which I agree with.


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Can systemic intravascular thrombosis cause brain infarction?
I wonder if the thrombus can pass through the brain-blood barrier because I think small molecules like O2, CO2 and ethanol can pass it.
Probably, in some diseases where the permeability of the barrier changes.
Can systemic intravascular thrombosis cause brain infarction?

This question seems to stem from a misunderstanding of the nature of the Blood-Brain-Barrier, the circulatory system of the brain and of thrombi. The BBB is describes differences in the structure of the walls of the blood vessels of the brain, it is not a barrier to flow within the vessel, but a specialized barrier to flow out of the vessel. In many tissues the walls of capillaries (the smallest vessels) are not tightly adjoined, small molecules and even some proteins from the blood are able to pass through these minute gaps between the endothelial cells and into the tissue.
However, in the brain, these endothelial cells are tightly linked in a specialized fashion that prevents the non-specific travel of solutes between cells. Instead, molecules that cannot diffuse through the membranes of the cells must be actively transported across them (cannot leak across).
An intravascular thrombus is much larger than these minute gaps, it is often considerably larger than these small vessels and becomes lodged in larger arteries, blocking flow. There is no passage through the BBB, but there is no passage of the thrombus through the walls of other capillaries in the body either. The damage caused by the infarct is due to the blockage of flow in the larger vessels.
The circle of Willis is no magical stopping point either. Many important sites of infarct (such as the MCA middle cerebral artery), micro-infarcts in even smaller vessels can also cause difficulties.
In short, thrombi and the Blood-Barrier-Brain exist on different scales, the presence or absence of the BBB is irrelevant when discussing the capacity of a thrombus to occlude arteries.

No, a thrombus would be much too large to pass through the highly selective blood brain barrier.  However, there are some cases where intra-vascular thrombosis can cause stroke.
One example would be non anti-coagulated atrial fibrillation, where the inefficient beating of the heart causes blood to remain stagnant in the left atrium.  This can cause a thrombus to form within the atrium which can then throw off emboli, some of which may enter the cerebral circulation. These may then partially or fully occlude one of the arteries in the Circle of Willis (the brain's circulation system), however the blockage is proximal to the blood brain barrier.
See Management of atrial fibrillation (GY Lip,2007) or for those hitting a pay-wall the professional reference section on AF

It would be great if you can add references for the examples that you mention.

@WYSIWYG duly added a couple of examples of references, the phenomenon is very well known and understood so others viewing the question may find it easier to search for Atrial Fibrillation and Stroke

No, thrombi are far too bulky to cross the blood brain barrier. Now regarding the risk of stroke in case of systemic thrombi Yes, there are 2 situations where this can arise:

floating thrombus of the great circulation proximal to the aortic arch (i.e. Most of the time, chronic atrial fibrillation)
venous thrombus with an associated patent foramen ovale, allowing the thrombi to pass through the atrial septum and get to the great circulation.

It would be great if you can add references to your answer.

The question has a vague term cause which is confusing people here.
For me, it means that the event increases the risk of the outcome.
For some others, it means the event is a definite factor in resulting in the outcome.
So I avoid answering to the question Yes or No because of different interpretations of the term.
The systemic intravascular thombosis increases the risk of stroke, for example, through the two situations as described in Raoul's answer here but those are not sufficient for the accurate risk score of the stroke risk.
The factors of stroke risk interact with each other so we cannot leave this question just only about intravascular thombosis and stroke risk, but must consider stroke risk more generally.
CHA2VASc Score for General Stroke score
The Role of the Left Atrial Appendage in AF-Related Strokes, 2013.
Chads-Vasc score. CHA2 DS2-VASc.
                        SCORE
C    CHF or LVEF < 40\%  1
H    Hypertension        1
A    Age > 75            2
D    Diabetes            1
S    Stroke/TIA/ HF
    thromboembolism/     2
V    Vascular disease    1
A    Age 65-74           1
S    Sex Category female 1
                        Max points 9.

which specificity and sensitivity are not so high which has resulted in many variations of the initial CHAD VASc score, for example in this study:

We studied 94 patients, 66.0% male, mean age 64.4 years (standard
  deviation 14.2). A cardioembolic source was detected in 20 patients.
  ROC curve analysis identified as predictors of cardioembolic source
  CHADS2 score ≥4 (sensitivity of 75.0%, specificity of 66.0%, p=0.014)
  and CHA2DS2-VASc score ≥5 (sensitivity of 83.3%, specificity of 58.0%,
  p=0.009).

To improve this score is ongoing research:

CHADS2 as well as the CHA2DS2VASc risk score can exclude a large proportion of patients from having high risk of stroke or death, here
Negative predictive value for zero as cut off value for the endpoint Stroke between CHADS2 (solid dots) and CHA2DS2VASc (circles) in Figure 1

Figure 1: CHADS2 (solid dots) and CHA2DS2VASc (circles).

Sources of thrombosis

Atrial fibrillation and Left atrial appendix is the source where thrombus can spread into the great circulation
Patent Foramen Ovale and Stroke where risk factors anatomic variation (PFO size, ASA, eustachian valve anatomy), hemodynamic parameters, presence of venous thrombus identified through higher-sensitivity tests such as lower extremity/abdominal/pelvic MRI, and the presence of hypercoagulable genetic variables

BBB's permeability and Stroke risk
The interaction of the permeability of the brain-blood barrier with the stroke risk is much unknown.
The following factors interact with the BBB's permeability

Montelukast (increases)

Cerebral Blood Flow (CBF) and stroke and Stroke Risk
CBF interaction with the risk of stroke is unknown field

Alcohol effects on CBF in subjects with low and high responses to alcohol, here.
carbonated water increases CBF
aging decreases CBF (standard textbook MRI pictures)

Sources

Stoll, Guido. Molecular mechanisms of thrombus formation in ischemic stroke: novel insights and targets for treatment. 2009. Online available.
Homma, Shunichi, et al. Foramen Ovale and Stroke. 2005. Online available.
Citings in the body of this question.

@WYSIWYG Thank you for your comment! I was very young in this field when I first time thought about this issue. I extended my answer little by adding some relevant sources.

You should probably consider the internal carotid arteries and vertebral arteries too as potential sources of emboli

@RoryM Feel free to do so and add relevant references to your answer.


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Pathogenesis of chronic venous congestion in skin?
I think CVC cannot lead to heart failure primarily.
So let's think its pathogenesis in skin now only.
I think the pathogenesis is like this

dilation of veins and capillaries due to impaired venous drainage
reduced outflow of blood from a tissue
passive process
$\to$ local increase in blood volumes
$\to$ local increase in venous pressure
pathological
$\to$ shortage of oxygen and built-up metabolic waste
$\to$ structural changes in microvasculature
$\to$ increased venous permeability % hallmark of acute inflammation
$\to$ increased size of venous caliber
$\to$ emigration of leucocytes
$\to$ accumulation at site of injury
activation of acute inflammation
$\to$ protein into extravascular space
$\to$ increased viscosity of blood
$\to$ deoxygenated blood blood stasis
$\to$ congested tissue
$\to$ leucocytes move to endothelial wall (selectins)
$\to$ roll
$\to$ adhere (integrin to stop)
$\to$ migrate
$\to$ dysky reddish-bluish skin (cyanotic)
$\to$ healing via fibrosis
$\to$ scar
Causes: venous thrombosis; venous compression; heart failure;

I am not sure about the role of leucocytes exactly in this process.
I am not sure if they play a big role in the formation of cyanotic skin.
I think the outcome is mostly because of increased vascular permeability and its deoxygenated blood in extracellular space.
What is the right pathogenesis of chronic venous congestion in skin?

I extended this question to lungs to understand CVC enough well: http://biology.stackexchange.com/questions/15874/pathogenesis-of-chronic-venous-congestion-in-lungs/15875#15875

Probably so simple answer is enough

acrocyanosis (manifestation of heart failure) which lead to distant (acro - distant) cyanosis, bluish skin.


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What is the pathogenuc mechanism of brown pigment lipofuscin in muscle atrophy?
I think it is autophagy. Lysosomal degradation. Autophagocytosis.
Example of the brown pigment (lipofuscin) here:

I am not sure if autophagy is the right answer to the "pathogenic" mechanism of atrophy.
Is autophagy the pathogenic mechanism of atrophy?
Or what pathogenic mechanism is involved if you see lipofuscin in the histologic slide?

Simple answer: Atrophy through autophagy.

Downvoter! Please, comment or answer better.


text:
What insect is this? (India)
Can anyone tell me what kind of insect (if it is one) is this...!! Or is it the pupa of some insect?

Well I don't think that the whole big thing is the insect itself, it appears to be just a kind of protection or shelter which moves along with the tiny little thing that keeps on popping out and going it so as to move.
Location:  India

I think it is worth adding a few pieces of information, to aid identification: the case is grey, without grains on its surface and tufts of hairy projections present on each end of the case.

Might be useful : if the same Tineinae

Related: Identifying a creature that appears to be a worm wrapped in a cocoon, What is this black and white worm in a white case?,  Help in identifying an unknown arthropod, What insect is this? (India), Identify this smooth-cocoon worm from Southern India, Small worm living in some kind of cocoon......

Related:  What is this animal that hides in dustlike structure?, What in the world is this critter?, What is this hard shelled insect in my house?, What is this insect found commonly in coastal India?, Insect identification - pantry moth vs clothes moth

This is mostly a guess and loose suggestion, since the picture is not very clear (would need to see the larvae in more detail). However, Bagworm moths (Psychidae), Case moths (Coleophoridae) and Caddisfly larvae (Trichoptera, almost exclusively aquatic) all build similar cases. They construct their cases out if silk and often include debris, pebbles and other materials. I wouldn't be surprised if the larvae in your picture belongs to one of the first two taxa. Bagworm moths and Caddisflies generally include lots of external materials in their larval cases, which could point to Case moths for your specimen (which seems to have a weaker case mostly made of silk).
Here are two pictures of first a UK Case moth larvae (Coleophora deauratella) followed by a Bagworm moth (Dahlica triquetrella), just as comparisons. If you do google image searches of "group name + larvae" you will see many examples of what they can look like.

And just as a cool example - the larvae often use random material lying around to build their cases, which can give the following result, if caddisfly larvae are bred in a tank containing pieces if gold and pearls. For further information see this link.

I'll just comment that caddisfly larvae are aquatic and will typically only be found in clean streams, ponds, or lakes. The two moth families you mention are much more likely based on the terrestrial location of the OP's insect. I wouldn't remove your info about the caddisflies as it can be useful/interesting to others coming across this question, but the aquatic/terrestrial differences in these insects' ecologies definitively rules out caddisflies.

@theforestecologist I agree, which is also why I mention in the answer that Trichoptera are almost exclusively aquatic.

@fileunderwater Oops I missed that. Well just giving further acknowledgment to that fact then :).

It's a household casebearer, a kind of moth larva in the family Tineidae that builds this case around itself.
@fileunderwater is wrong

Can you substantiate your answer as why you thing so, ideally with citation and picture reference? Household casebearer as I'm aware of have dirt or grain covered case, when not covered in dirt, they are close to white and not grey. This species is not only grey but also has a smooth surface = no grains.

Could be, and, as I said in my answer, the ones I mention are loose suggestions, based on the rather poor picture. Could you maybe specify what makes you so sure that it is a Tineidae?


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Pathogenesis of Chronic Venous Congestion in Lungs?
I am thinking how CVC in lungs lead to the left-sided heart failure.

I think CVC lead to Pulmonary congestion and edema.
They produce heavy, wet lungs.
Pulmonary changes include

perivascular and interstitial edema, particularly in the interlobular septa;
progessive edematous widening of alveolar septa; and
accumulation of edema fluid in alveolar spaces which contain Hemosiderin and microhemorrhages

Now, the progression of the disease to heart should be discussed.
I am not sure if hemosiderin can go directly from lungs to heart or if it has to travel through circulation and then to left-side of lung.


text:
Real-time PCR result interpretation
I performed real-time PCR and I was looking for expression fold changes for 2 genes and I had two sample pools, one treated and the other not treated (for each gene). The problem is that my housekeeping gene (UBQ 30) got a fold change on the treatment. Therefore, what is the correct interpretation and data treatment?
I mean, is it correct to use each control and treatment I got for UBQ CT values to normalize the other two genes corresponding CT, as housekeeping genes are "by definition" expected not to change? (and that is why indeed they are used to normalize)
or should I rather make a mean of my whole UBQ CT-s and normalize all other genes CT values with that mean?

In principle the housekeeping genes should be constant. But: Changes, that happen to the whole cell, can happen. So it is advisible to have more than one housekeeping gene if possible.

You should try another housekeeping gene like GAPDH since the very definition of these genes is that they shouldn't change with your treatment

good advice - this is a list of even better ones...http://www.ncbi.nlm.nih.gov/pubmed/17394773

There is quite a list of genes that can be used - sometimes even GAPDH or Actin change. This needs to be verified for each experiment.

and how could i objetively discrimine if a given change for CT values is significable as to consider to change my housekeeping gene?

As Chris says you will have to verify that your housekeeping gene doesn't change between experiments.

As pointed out by others a reference gene should not change its expression between the control and test samples. Reference gene need not be a housekeeping gene; housekeeping genes are generally used because they are present in all cells are are not subject to any specific regulation. However, global changes in the cell, such as stress or development, can affect housekeeping genes.
When you are not sure about which gene to choose as a reference then you can use a spike in control.
The change in your experiment could be a result of human error. You should replicate the experiment to see if the trend remains the same. If your gene shows consistent trend in all replicates then the change is not likely because of human error.
In general you should choose the reference gene based on your prior knowledge about the condition that you are testing. For example if I am studying cell migration then I would not use Actin as a control. If you are studying processes that may affect metabolic rate then you should perhaps not use GAPDH as a control.
Another good reference gene(s) that is also constitutive would be that for a ribosomal protein.
Also have a look at this post for statistical analysis of RTPCR data.

I'm gonna throw a curve ball here. :) I think the "housekeeping" or "reference gene" concept is fundamentally flawed, because it rests on circular logic. In order to verify that a "housekeeping" gene X is constant across your samples, you must assume that the $C_t$ values themselves are actually a valid measure, so that you can assess the expression level of X directly. But if $C_t$ values are assumed valid, then you don't need a housekeeping gene in the first place! This procedure assumes what it intends to prove; therefore it is circular.
The normalization problem is just not solvable without additional assumptions. A spike-in control works if you are worried about technical variation, but it does not address biological variation. A reasonable assumption I think is that the total mRNA pool is constant; this underlies most normalization methods used in microarray or RNA-seq analysis. For RT-PCR, this assumption can be tested using cDNA dyes, as in this paper. (cDNA is advantagous rather than isolated RNA, because the reverse transcription step is notoriously noisy and should be controlled for.)
In my mind, housekeeping genes are only useful it you really know in advance that they must be constant, and do not need to check this assumption; then the logic is not circular. In this case, if you observe changing $C_t$ values for the housekeeping gene, then you must conclude that the experiment went wrong somehow, and the data should be discarded. But I think this is rarely the case in practise.
This is not the most common opinion on this often-debated matter, but I think it is the right one. :)

1. Regarding the vicious cycle of reference gene selection:  Ideally there should not be a change in Ct value if there is no change in expression. There may be no need to have a reference gene if situation was always ideal. Here, reference gene simply does the job of a loading control. The perfectly done experiment may not need one but getting that perfection is hard; but once you have established a right reference you can forget about perfection.

2. Regarding spike-in: In cases where there is biological variation of the gene pool, spike-in would be particularly useful. For example, during growth/development a lot of proteins accumulate, including housekeeping genes. They may even be subject to regulation. Spike in would let you know the absolute change in the RNA expression. In these cases the housekeeping gene can also be used to understand correlation and differentiate general regulation from specific regulation. In certain cases you can transfect the spike into the cells prior to RNA isolation.

I however concur that the choice of reference is dependent on prior knowledge about the condition. +1 for the alternate opinion :)

@WYSIWYG, regarding (1), my point is that in order for a  gene X to be a control for suspected variation in Ct, we must assume that gene X is constant, and we cannot verify this by measuring Ct; that becomes circular. For (2), yes spike-ins allows quantitation, but doesn't solve the normalization issue, you still need to relate the measurement to something --- tissue weight, cell number, total protein, or RNA (which I suggested).


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How can I re-format my DNA motifs' position weight matrices?
I am working with a set of DNA motifs that are predicted as potential regulatory motifs (e.g. transcription factor binding sites).
The motifs belong to several species, and I wanted to cluster these motifs via their Position Weight Matrices (PWMs) (also known as PSSMs) to collapse similar motifs together into groups.
There is a tool called MATLIGN (website here) that does what I need, but their required format for the PWMs are different to what I have, they claim:

"Matrices must be in the frequency matrix format (only integer numbers
  are acceptable)"

The problem is that my PWM matrices do not have integer numbers but decimals instead. e.g.:
     A        C        G        T
1    0.000000 1.000000 0.000000 0.000000
2    1.000000 0.000000 0.000000 0.000000
3    0.000000 0.000000 1.000000 0.000000
4    0.000000 0.421755 0.000000 0.578245
5    0.289407 0.000000 0.282556 0.428038

In other words, instead of the decimal values I have in my matrix I need to have integer counts. Could anybody suggest what I can do? Would I need to create artificial "pseudo-counts"?

Could it be so simple that they want counts of nucleotide occurances (the frequency) instead of proportions (e.g. your row 5 as (using n=60): 17 0 17 26)? Where do your numbers come from - I assume you have counts as raw data to calculate the proportions? Mind you, I have no experiance with these particular methods at all.

Thank you @fileunderwater for your comment. The problem is that the raw data is not available to me, what I have are the high level outputs the program had generated. I presume the whole integer counts are required by this software since proportions remain constant no matter how large the total.

ok, well then you have a problem, since there is no way of knowing the margin of error of the proportions. However, to get counts these proportions should just be multiplied by the number of binding sites included in the study. Don't you have that info (e.g. the number of sequnces that have been analysed)?

brilliant! I DO! you should make an answer of that! Thank you

Why not just multiply everything by 10? The PWM will still be correct since its values are relative to each other, you just make 1.00 into 10 and 0.28 into 28 etc.

Hi @terdon I was very tempted to do that before fileunderwater's answer came about. It turns out he was right, I eventually found in my dataset there was a "mysterious" variable called "nsites". After reading the small print of the docs, nsites is the number I should be multiplying by, since it is the number of DNA regions the motif was made under

Yes, his solution is cleaner but I doubt there will be any difference. Remember that PWMs are relative so multiplying by anything should be fine really.

@terdon As I wrote, I'm not familiar with this program/methods, but I assumed that the counts were used in the analysis to determine what confidence you can have in the proportions (i.e. more confidence in 33% from 40/120 than 3/9). But you might be correct that it doesn't make a difference in this case.

I'm not familiar with this program either but PWMs in general are always relative. What you get is a value indicating how often a particular residue is found a t a given position. Multiplying with an arbitrary value shouldn't affect the result in any way, as long as you multiple all values. Basically 1 means you always have that residue at that position. If you multiply by say 100, you can treat them as percentages. But yes, the implementations could vary depending on what you're feeding them to.

So what you need is basically your data expressed as counts instead of proportions. Even if you do not have the matrix of counts as raw data, these proportions only needs to be multiplied by the total number of binding sites used in the study (e.g. the number of sequences that have been analysed) to get the counts (since proportion = count/total number of binding sites). You should have that information somewhere.
@hello_there_andy: indeed there was this missing piece of information available to me, it came in the form of a variable called nsites which equates to the total number of DNA sites that the PWM was generated from.


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Can a fungus become resistant to a chemical such as Potassium Permanganate?
A friend used potassium permanganate solution to treat tinea on the hands/feet but after some initial success, the tinea seems to be making a comeback. Could the fungus develop resistance to potassium permanganate?

I hardly doubt it. The desinfective effect is based on the production of reactive oxygen species. The problem is that the solutions used for this purposes are not very stable. Did you always use fresh (or at least relatively fresh) solution or did you get it once and used it for the whole time?

@Chris, aha, you may be onto something there, the solution was mixed once and then used over a few days, so maybe it lost it's efficacy over time.

It is also possible that the fungus could have produced ROS scavengers to survive. What percentage of KMnO4 ??

@WYSIWYG, roughly 5 grams to 5 liters of water, ( so about 0.1% solution? ) . What would be effective strategies to overcome the ROS response.  Would (a) increasing the sol. strength and/or (b) increasing the duration of submersion and/or (c) increasing the frequency of submersion (number per day) help? Of the three, (b) and (c) would appear to minimize the skin corrosion/discoloration and hence be preferable to (a). Thanks for your input.

@WYSIWYG The cells definitely have some enzymes to overcome ROS. Thats why you have to use relatively fresh solutions, otherwise the cells can handle them.

No, it won't, but my experience that KMnO4 is not very effective against fungus. He should try something else, e.g. some pharmaceutical or essential oils like orange, cinnamon, clove, thyme, etc... As long as he is not diagnosed by a dermatologist it is not really sure that he has fungal infection, e.g. once I had warts misdiagnosed by a general practitioner as fungal infection.

I don't think a fungus would develop resistance to something so quickly.
As Chris suggested in the comments, it could be because "The disinfective effect is based on the production of reactive oxygen species. The problem is that the solutions used for this purposes are not very stable." So, if fresh solution haven't been used, it may be ineffective.
As commented by @inf3rno, fungal infections could be much deeper and hence, "treating" them superficially may not help much.

If it would be effective, it has no use, because it affects only the fungus which is on the surface of the foot. Fungal infections can be much deeper...

Fungi cannot develop resistance that quickly. Potassium permanganate is only used to clean wounds. Therefore, the reimmerging of the fungus may be because it wasn't killed in the first place. I suggest antifungal cream should be used generously to kill the roots of the fungus in his hands/feet.

The OP is not asking for medical advice. We discourage both asking for and giving medical advice.


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Why violets die in closed space?
I'm going to engage into making florariums (a garden in the bottle). I've heard, that violets die in closed space. Do anyone have an idea, what is the reason for that? Lack of oxygen or CO2 or moisture control issues?

We also have gardening and landscape SE. You can consider posting this there.

I believe it is because of the violets' propensity to collect mould. They seem to like warm, humid space, but in a closed-air type system, it is a breeding ground for mould.
There could be another reason as to why they die, but I would assume it would be an infection.

Hi!  Welcome to the site! It would improve your answer if you add some reference/source for your answer.

Thank you for your answer. As far as I know, violets perfectly exist in +20C, is it to warm to breed mould? If that's the point, I guess violets could grow in closed space, provided the mould is tackled (i. e. by chemicals).


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What is this plant?
I really like this plant--I'm just wondering what its name is (perhaps genus+species). I think this plant grows in the tropical rainforest in Malaysia.

Any suggestions?
Thanks!

To me it looks similar to a young Banana plant (Musa sp.). The genus is native to south east asia, and there are many wild species.

I agree, this looks a lot like the banana plant.

Reposted as answer. Hopefully a botanist can chime in later. @biogirl

@masoug the stem of the banana plant is peculiar. If you could upload the picture of your plant's stem, it would be helpful

If it is a banana plant; then its trunk(invisible in this photo) is not actually stem. The actual stem stays underground.  the trunk is actually the leaf-bases sheathing around. The stem comes-out in the form of "scape" (a sort of inflorescence stick) at a season. (quite-lin a manner of onion-scape); which contains the banana -inflorescence on its top.

any info. about its size?

I'm no botanist, but this looks very similar to a young banana plant (Musa sp.) to me. The genus is native to south east asia, and there are many wild species. There are also a couple of other similarly looking genera in the banana family (Musaceae).
Reasons why I'm thinking banana: the plant has tongue-shaped leafs with fairly short petioles, and the leaves have clear horizontal, unbranched veins and horizontal tears (common on banana plants). The leaves come from a single apical meristem and are scattered (not in e.g. distinct rows). Banana plants also have pseudostems, made out of packed leaf sheaths, but the stem cannot be seen in your picture. Here is a webpage on banana morphology, if you want to get some further information.
Some examples:

I'm not botanist either, but I think you are right--the  pattern of the leaves/stem matches the banana plant. Thanks!


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Sexual Differentiation in Monoecious plants with unisexual flowers
In monoecious plants having unisexual flowers (eg Zea Mays, Ricinus Communis etc), there must be some mechanism as to produce two sexually distinct flowers from the same genotype. Since both the type of flowers are placed on the same plant, the genetic constitution of the cells of both the type of flowers will be similar. What is the mechanism by which the development of two sexually distinct flowers is carried out in such plants?
Is the mechanism similar to the mechanism for differential gene expression in case of embryonic development (Homeobox genes)? And moreover, is the genetic constitution of the pollen produced by the male flower similar to that of the egg produced by the female flower, with respect to the composition of autosomes and allosomes (if any)?

This article might be helpful. It also provides a lot of other references.

There is a whole book on sex determination in plants - Sex Determination in Plants by CC Ainsworth. You can get it on google books. See chapter 12 for maize flower sex determination. It's pretty interesting.

why not try to make an answer out of it @biogirl?

I will be able to answer only a part of the question.
Sex determination in Zea Mays
Initially, all the flowers in the plant are perfect, ie they have both the male and the female
flowers. This is followed by abortion of stamen or pistil resulting in unisexual flowers.
Which part of the flower undergoes abortion is determined according to the location of the flower. The florets in the tassel undergo the suppression of the pistil primordia resulting in staminate flowers, while the florets in the ear undergo suppression of stamen primordia resulting in female flowers.

The hormone Gibberelic Acid seems to play a role in sex determination.
Source and other useful links :

Sex determination in Plants by CC Ainsworth.
Sex chromsomes in flowering plants
Sex determination in monoecious and dioecious plants
The sex determination process in maize

This review provides genetics of maize sex determination in (a surprisingly!) simple language.

Thank you for the answer. Just for the sake of aesthetic appeal, can you put all the links quoted in the comments at one place?

Dellaporta & Calderon-Urrea. 1994. The sex determination process in maize. Science 266(5190) is also relevant.

@SatwikPasani I haven't answered the second part of your question but I found some related information in Campbell - Interestingly, maize has a homolog of Hox genes calles KNOTTED-1, but unlike its counterpart in the animal world,KNOTTED1 does not affect the proper number or placement of plant organs. ....an unrelated class of transcription factors called MADS-box proteins play that role in plants.

@SatwikPasani I know that MADS-box plays the role of organ identity genes during flower development but I don't know whether they have a role in the process of sex determination.

@SatwikPasani Thought this is relevant -  Plants mostly follow position based mechanisms for cell fate determination (instead of lineage based as in animals) , so cell fate is usually determined late during development and largely depend on signals from other cells


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Association of shorter telomeres with heart disease
From this paper

Those with shorter telomeres in blood DNA had poorer survival,
  attributable in part to a 3.18-fold higher mortality rate from heart
  disease (95% CI 1(.)36-7.45, p=0.0079), and an 8.54-fold higher
  mortality rate from infectious disease (1.52-47.9, p=0.015).

What is the connection between shorter telomeres and heart disease ?

This seems a bit like a hen and egg problem. Telomere length is both associated with age and with heart diseases, but heart disease is also associated with age. The question here is, is one really causing the other here (short telomeres heart problems) or do they occur simultaneously? The other problem with heart disease is that it is a multi-risk disease, with many risks accumulating with age. The figure below sums this up, it is from the first paper:

Have a look on these articles:

Telomere biology in heart failure
Aging, telomeres and heart failure.
Telomeres and Cardiovascular Disease


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pI and pH relationship in context of ion exchange protein purification
I am confused about relationship between isoelectric point and pH in context of ion exchange protein purification. Why we cannot use this method for protein with pI below 7? Thank you very much for any tips.

Have a look at this table, it really depends on the buffers you use:

The table is from this website, which is definitely worth reading when you are interested (or work) with ion exchange chromatography.

The pI (iso-electric point) is the pH at which the protein (or other molecule), overall has a net zero charge.
As @Chris points out, the buffer you are using will change the pH the protein finds itself in.  This will change the charge of the protein.
In ion exchange chromatography, there are charged chemical groups on the resin and these can cause a protein to be retained on the resin if the protein is complementary (opposite charged)  to the resin.
So if you have a protein with a pI of 5 say, it would neutral with the presence of excess H+.  This implies that the protein has an overall negative charge.  A cationic resin would tend to retain this protein in a pH 7 buffer.
I hope that makes sense.
In most cases, ion exchange chromatography is used when most of the protein is separated out and there are a few proteins (maybe a couple of hundred) mixed together.  It can get tricky if you see that the protein is mixed in with something that is also negatively charged.  In that case you might change the pH of the buffer so that other negatively charged proteins are closer to their isoelectric point and come through the column faster than the one you desire to purify.


text:
Hidden Markov Model
I read about the hidden markov model in bioinformatics. I amn't able to understand what it is.
Can anyone explain me in brief and in very very simple words what it is ?
I have NO background in bioinformatics or programming and wikipedia article on it is too scary .

Markov models are used in almost every scientific field. In short, it is a kind of stochastic (random) model and a hidden markov model is a statistical model where your system is assumed to follow a Markov property for which parameters are unknown. Because it is not specific to biology, I would recommend you to ask your question on crossValidated.SE

This question appears to be off-topic because it is about a statistical/computational concept

<this is about to get closed. I think it could be on topic if you edit it to make it specifically about the applications of HMMs to biology. For example in gene prediction or in the building of sequence profiles (e.g. hmmer)

@terdon.. I guess this problem comes from the way bioinformatics is taught.. When you start introductory bioinfo and read about the different tools and databases you often see some vague statement like- The sequences are discovered using HMM and then a non redundant database is made. The term is heavily used but not explained. Nobody usually uses or are even aware of tools like HMMER at this stage. I have also remained confused about this term called HMM for a while. This is still a relevant question but is out of scope of this forum- that's why closing it.

@WYSIWYG this is exactly the reason why i asked the question. But i understand why this is out of scope.

A Markov model is a description of a system that follows a Markov process. In a Markov process the next state of the system is a function of its current state and does not depend on where from and how it started. For example Brownian motion can be called a Markov process. The transition from current state to next state is described by probabilities.
So to conclude, a Markov model is a probabilistic model of a system that is assumed to have no memory.
In a Hidden Markov Model (HMM) the state(s) of the system are not known (therefore hidden). However, there are some functions that depend on the state and their outputs can be used to approximate the state of the system. There goes the definition- it is not that easy to explain how it is applied to different concepts (not just bioinformatics).
Strictly speaking this is off-topic. HMM is not a biological concept. It is a statistical/computational concept (it is like asking what is Dynamic Programming- which is the underlying concept behind BLAST algorithm).

Thank you for answering my question though I now understand that it is not strictly on topic.

I read about this in relation to protein domains and motifs. What does that have to do with HMM ?

Motif finding algorithms use HMM to predict the correct motif..

You can check this paper out to know about how HMM is applied in motif discovery. It is by Sean Eddy who has developed many popular HMM based tools


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Why will world population keep growing if all women have only 2.1 children
Why is it that, even if we were going to immediately agree that every women will not have more than 2.1 children on average, the world population would continue to grow for another 60 years? I've learned that a TFR of 2.1 means the population is at 0 growth rate. I guessed the answer was the population-lag effect, but since we are assuming that ALL women immediately have only 2.1 children on average, wouldn't there be a 0 population growth immediately and not after 60 years? Thanks in advance!

Can you link some sources about the birth rates?

Sources for your fact about the 2.1 growth rate leading to 0 net population growth? What is the meaning of TFR?

As you mention, the population-lag effect is responsible for this. From The Wikipedia article on TFR: http://en.wikipedia.org/wiki/Total_fertility_rate#Population-lag_effect

A population that has recently dropped below replacement-level
  fertility will continue to grow, because the recent high fertility
  produced large numbers of young couples who would now be in their
  childbearing years.

Thus, even if the current TFR implies long-term stability, the recent history of TFR values will continue to affect birth rates, and thus population growth/decrease, in the future.
Imagine that you have a stable population, with static birth and death rates. Now imagine that the birth rate during a single year for some reason doubles before dropping back to normal the next year, thus transiently increasing TFR. Now, it is easy to see that when the newly born, larger-than-normal generation reaches reproductive age, the population will increase again because the birth rate will increase in proportion with the size of the generation, while the death rate is unaffected until the enlarged generation reaches old age and starts dying off. Later, the population will decrease to its long-term stable level, which will be larger than before the TFR spike.


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How can eating bacon not make me fat?
This page says it won't.
This page says it's the carb again http://www.mindbodygreen.com/0-10454/in-defense-of-bacon-why-eating-fat-can-help-you-get-thin.html
I don't see how eating fat will not make me gain weight while eating carbohydrates will, since fat is made of, well, fat.
It says eating carbs will make us fat. How can this be? Is this true?

I changed your title and text so that your question is a bit clearer, hope that's okay.

Fat in your body and the fat you eat are two different things. All the fat in your body is synthesized--made by the body. Dietary fat is not absorbed by the body. In fact, fat that you eat cannot even pass through the intestinal walls. It has to be broken down into carboxylic acid and monoglyceride. Carbs make you fat because the liver turns them into triglycerides, which is white fat. The liver also turns carbs into cholesterol hardening your arteries.

I think this question can also be said to be - how can the Atkins diet work?
Atkins and other low carbohydrate diets sound counterintuitive.  They vary in details, but the basic theme is: cut back on carbohydrates - e.g. bread, sugar, fruit, pasta, milk etc etc.  But eat as much fat and protein as you like - e.g. steak, ham, bacon, eggs, cheese etc etc.
These diets really do work.  Our metabolism allows us to draw food from two sources.  Glucose or fat. (there is also something called glycogen, but that is only used short term and not relevant for diets long term).
It was known in the late 50s that our metabolism will to switch over consuming fat, allowing weight loss, only based on the amount of carbohydrates we consume. low carb diets initiate this change from glucose to fat metabolism because our bodies make the switch based only on the amount of glucose available in the blood.  Our bodies think we are starving even if we are gorging ourselves on food which is has little or no glycemic index.
Low carb diets are not a hoax or snake oil - they really work.  They can be a shock to the system and so one should discuss with your doctor before engaging them.
The first link you have is also true though.  Eating fat will usually just make you gain weight.  The low carb response has to be induced by basically removing all carbohydrates from the diet.  If you break the low carb regime and eat a large amount of carbs, the body will switch practically instantly out of starvation mode and also take in all the fats you're eating.  Lots of people on low carb diets can gain a lot of weight rapidly if they break the diet.

It is still unclear, why bodies in the "starvation mode" do not absorb the dietary fat.

yes it doesn't entirely make sense either.  it may be that when drawing on the fat metabolism that its rare to be consuming fat... so storing fat and metabolizing it at the same time may conflict somehow.


text:
Do bacteria with capsular antigen always have a capsule?
Assume some bacteria have capsular antigen.
Do these bacteria always have a capsule?
I think not, I think the antigen only makes it possible.

This is a general question.

I personally see no problem with most of Masi's questions and I like this one.

Are you asking if the bacteria always will have a capsule or only if they will always be capable of producing a capsule?

@jarlemag Good questions! I mean the latter question. I think answer to your first question is no. I think the capsule is degraded in some phase eventually.

In short: It can depend on your definition of encapsulation.
According to the Oxford Dictionary of Biochemistry, a capsular antigen is defined as

any of the antigens, usually polysaccharide in nature, that are
  carried on the surface of bacterial capsules. The term K antigen is
  used for those that mask somatic (O) antigens.

In general, capsule polysaccharides have complex structures and are produced by a the action of several enzymes, with the genes necessary for production of the capsule typically making up a gene cluster in the genome (see for example Chen et al.: http://www.biomedcentral.com/1471-2180/10/274). On the face of it, it would seem somewhat unlikely that a bacterium would produce a known capsular polysaccharide antigen without retaining the ability to produce a capsule, as the selective advantage of the capsule then would be lost.
In actuality, the answer might depend on how you define "have capsular antigen" and "capsule". Historically, several methods have been used for demonstrating encapsulation. Methods based on staining microscopy or colony morphology observations tend to identify fewer strains as encapsulaed than does serotyping (reaction of serum with antigen). With this in mind, strains that can be shown to be encapsulated without serotyping are sometimes referred to as "highly encapsulated" to distinguish them from strains that test positive for encapsulation through serotyping only.
For discussions of capsule detection methods as applied to Staphylococcus aureus, see Sutra et al. (http://jcm.asm.org/content/28/3/447.full.pdf) and O'riordan and Lee (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC321462/).  O'riordan and Lee writes

Isolates belonging to the remaning serotypes produce nonmucoid
  colonies on solid medium, and their colony morphology is
  indistinguishable from that of strains lacking a capsule. Some
  investigators have referred to nonmucoid, encapsulated S. aureus
  isolates as microencapsulated to distinguish them from the atypical
  mucoid strains.

Thus, if both "have capsular antigen" and "have a capsule" is defined by a positive serotyping result for a capsular antigen, then all strains with a capsular antigen as detected by serotyping have a capsule per definition. If on the other hand you define encapsulation based on ink staining microscopy or colony morphology, there are definitely strains that produce K-antigens and don't qualify as "encapsulated".
Note that while bacterial capsules consist mostly of polysaccharides, capsule proteins make up a second class of capsule antigens. One example is the Caf1 capsule antigen protein produced by Yersinia pestis: http://en.wikipedia.org/wiki/Caf1_capsule_antigen

Thought I'd mention that there's also a K-antigen in E. coli, K30, which is present both in the bacterial capsule and as a low molecular weight-form lipopolysaccharide (LPS) on the cell surface, but as far as I can tell the second form is only present when there is also a capsule.


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What are the physiological roles of Hydrogen sulfide?
I am thinking why hydrogen sulfide has its effects in the body.
For instance, it is one Salmonella's virulence factor.
I am not sure if such a balance equations holds
H2O + H2S ←→ ...
Actually, I miss here some factors because I am not understanding the biochemistry enough to answer this.
I think H2S can exists in some sort of ionic form.
Hydrogen sulfide reminds me of ammonia.
I think it inhibits some systems.
By which mechanisms?
It is mentioned in many places the empirical effects: signaling functions similar to NO and CO.
But I am interested in how this happens.
What is the rate of adhesion of H2S to hemoglobin for instance?
H2S can change to sulfite and thiosulfate in mitochondria which are then excreted into urine.
I think most of the biological effects are done before these forms.
But in which forms?

According to my preliminary reading around this topic, although production of hydrogen sulphide is used as a convenient method for detecting the presence of pathogenic Salmonella, there is nothing to link this trait with virulence. Do you have a reference for this?

You are probably right. I read about this topic in Lange's Medical Microbiology mostly, and I cannot be find any mentioning that directly related to Virulence, but there are mentionings that H2S is related to signalling functions similar to NO and CO, which possibly have virulence roles.

I am not sure about this. I mean, yes it is used to detect sulfide production of Salmonella species (note that not every Salmonella produces H2S), but it is a gasotransmitter in the human body, which has a role for example in regulating immune responses. In small doses it has antiinflammatory effect, while in large doses it has proinflammatory effect. So I think it is possible that H2S is a virulence factor, but it is really hard to find a study about H2S as virulence factor, since it is a relatively new resource area.

$H_2S$ is the end product of sulfur related respirations (like sulfate respiration, sulfur respiration, etc...).
By aerob (oxygen) respiration the oxygen in $O_2$ has 0 oxidation number, by $CO_2$ the oxygen has -2 oxidation number, so it was reduced while the carbon was oxidized.
By the thiosulfate respiration of Salmonella enterica the following reaction happens by the reduction of thiosulfate: $S_2O_3^{2-} +2H^+ + 2e^- \to HS^- + HSO_3^{-}$. In this case the sulfur in $S_2O_3^{2-}$ has +2 oxidation number while the sulfur in $HS^-$ has -2 oxidation number, so the sulfur was reduced, it was an electron acceptor, just like oxygen by aerob respiration.
So in the case of Salmonella enterica $H_2S$ production is a byproduct of anaerob respiration. It makes growth faster.

Sulfate-reducing bacteria are those bacteria that can obtain energy by
  oxidizing organic compounds or molecular hydrogen (H2) while reducing
  sulfate (SO2- 4) to hydrogen sulfide (H2S).1 In a sense, these
  organisms "breathe" sulfate rather than oxygen in a form of anaerobic
  respiration.

wikipedia - Sulfate-reducing bacteria

Salmonella typhimurium produces H2S from thiosulfate or sulfite.

1987 - The phs gene and hydrogen sulfide production by Salmonella typhimurium.
2011 - Thiosulfate Reduction in Salmonella enterica Is Driven by the Proton Motive Force

S. enterica uses gut inflammation to enhance its sulfur related respiration to outgrow the resident microbes in the intestinal lumen (microbiota). The inflammation creates tetrathionate $S_4O_6^{2-}$ in which the sulfur has an average oxidation number of +2.5. This tetrathionate is reduced by the tetrathionate reductase into thiosulfate with sulfur having +2 oxidation number. So sulfur related respiration helps to make growth faster in order to colonize the gut.

Here we show that reactive oxygen species generated during
  inflammation react with endogenous, luminal sulphur compounds
  (thiosulphate) to form a new respiratory electron acceptor,
  tetrathionate. The genes conferring the ability to use tetrathionate
  as an electron acceptor produce a growth advantage for S. Typhimurium
  over the competing microbiota in the lumen of the inflamed gut. We
  conclude that S. Typhimurium virulence factors induce host-driven
  production of a new electron acceptor that allows the pathogen to use
  respiration to compete with fermenting gut microbes. Thus the ability
  to trigger intestinal inflammation is crucial for the biology of this
  diarrhoeal pathogen.

2010 - Gut inflammation provides a respiratory electron acceptor for Salmonella
2001 - The Alternative Electron Acceptor Tetrathionate Supports B12-Dependent Anaerobic Growth of Salmonella enterica Serovar Typhimurium on Ethanolamine or 1,2-Propanediol

Since $H_2S$ is a gasotransmitter in the human body, there can be other mechanisms which help S. enterica.

in small amounts $H_2S$ has anti-inflammatory and anti-apoptotic effects
in large amounts $H_2S$ has pro-inflammatory and pro-apoptotic effects

So S. enterica can probably cause inflammation due to killing cells with a fast release of $H_2S$ or prevent inflammation and keep infected cells alive with a slow release of $H_2S$. I found many evidence of the pro-inflammatory theory. By the anti-apoptotic theory I wasn't so lucky, I found only a single review about anti-apoptotic strategies of intracellular pathogens, but it did not mention $H_2S$ production as a possible mechanism. So it might not be true, further studies needed...

In the digestive system, H2S exerts potent anti-inflammatory actions,
  regulates blood flow and smooth muscle tone, modulates epithelial
  secretion and promotes healing of ulcers [4, 5].

2012 - Hydrogen Sulfide: A Rescue Molecule for Mucosal Defence and Repair

Hydrogen sulfide (H2S) is the most recent endogenous gasotransmitter
  that has been reported to serve many physiological and pathological
  functions in different tissues. Studies over the past decade have
  revealed that H2S can be synthesized through numerous pathways and its
  bioavailability regulated through its conversion into different
  biochemical forms. H2S exerts its biological effects in various
  manners including redox regulation of protein and small molecular
  weight thiols, polysulfides, thiosulfate/sulfite, iron-sulfur cluster
  proteins, and anti-oxidant properties that affect multiple cellular
  and molecular responses.
Understanding precise pathophysiological signaling mechanisms and the
  metabolism of H2S is a topic of active research. Unraveling H2S
  interactions within different tissues, with other biochemical
  molecules and various signaling mediators is becoming ever more
  complex.
These results demonstrate that H2S donors can down-regulate adhesion
  molecule and proinflammatory cytokine expression, therefore
  identifying H2S, its synthesis enzymes, and molecular targets (e.g.,
  KATP channels) as potential targets for novel anti-inflammatory
  therapies.
Thus, all of the above findings demonstrate that H2S induces
  cytoprotection by an anti-apoptotic pathway.

2013 - Hydrogen sulfide chemical biology: Pathophysiological roles and detection

A short course of H2S infusion was associated with reduction of lung
  and kidney injury. Prolonged infusion did not enhance protection.
  Systemically, infusion of H2S increased both the pro-inflammatory
  response during endotoxemia, as demonstrated by increased TNF-α
  levels, as well as the anti-inflammatory response, as demonstrated by
  increased IL-10 levels. In LPS-stimulated whole blood of healthy
  volunteers, co-incubation with H2S had solely anti-inflammatory
  effects, resulting in decreased TNF-α levels and increased IL-10
  levels. Co-incubation with a neutralizing IL-10 antibody partly
  abrogated the decrease in TNF-α levels. In conclusion, a short course
  of H2S infusion reduced organ injury during endotoxemia, at least in
  part via upregulation of IL-10.

2012 - A short course of infusion of a hydrogen sulfide-donor attenuates endotoxemia induced organ injury via stimulation of anti-inflammatory pathways, with no additional protection from prolonged infusion

H2S causes apoptosis in HPSCs by activating the mitochondrial pathway.
  It is suggested that H2S might be one of the factors modifying the
  pathogenesis of pulpitis by causing loss of viability of HPSCs through
  apoptosis.

2011 - Hydrogen Sulfide Causes Apoptosis in Human Pulp Stem Cells

The level ofendogenous H2S was increasing along with the infection
  occurrence and the gradient of infection aggravate. We can presume
  that endogenous H2S participated in inflammatory reaction of abdominal
  infection and could be one of the serology index which concerned with
  the gradient of infection.

2012 - P53 The level changes and clinical significance of endogenous hydrogen sulfide of patients with acute abdominal infection

The evidences showed that H2S has an obvious effect on colon smooth
  muscle contraction, and can increase the intestinal movements in slow
  transmit constipation. Our experiment states that H2S has
  anti-inflammation effect in prophase of acute peritoneal cavity
  infection.

2014 - P48 Regulation of hydrogen sulfide in digestive stystem
2010 - Hydrogen Sulfide Improves Neutrophil Migration and Survival in Sepsis via K+ATP Channel Activation
2012 - Hydrogen sulfide and resolution of acute inflammation: A comparative study utilizing a novel fluorescent probe
2008 - Staying alive: bacterial inhibition of apoptosis during infection

H2S is believed to have two contradicting roles in inflammation. It
  acts as both pro- and anti-inflammatory molecule(9). Li et al.
  reported that the physiological concentration of H2S has
  anti-inflammatory effects, while higher concentrations of H2S can
  produce pro-inflammatory effects(10). The H2S inflammatory role was
  also studied in different systems. In the gastrointestinal tract, the
  H2S regulating role functions by activating KATP channels in order to
  promote the inflammation response(57). The similar H2S function was
  observed in pancreas(7), but the actual mechanisms are largely
  unknown. In conclusion, H2S pathway is a possible route for targeting
  the inflammation treatment. However, much work needs to be done for
  understanding the mechanisms of the contradictory roles of H2S in
  inflammation.

2012 - The Crosstalk between H2S and NO Signaling Pathways
2013 - Gasotransmitters, poisons, and antimicrobials: it’s a gas, gas, gas!

Developing evidence suggests that dysbiosis (abnormal microbial
  composition or function) can contribute to if not cause chronic
  intestinal inflammation. 5,7 This inflammation can be caused either by
  an abnormal composition of entericbacteria with an elevated ratio of
  aggressive vs protective species, defective production of short-chain
  fatty acids and other protective microbial products, or enhanced
  production of hydrogen sulfide and nitrates that block butyrate
  metabolism and disrupt the mucosal barrier.

2010 - Inflammation and Nutrition in Chronic Disease
2013 - Potential Role of Hydrogen Sulfide in the Pathogenesis of Vascular Dysfunction in Septic Shock

These results showed that physiological concentrations of H2S can
  induce apoptosis of PDL cells and HGFs in periodontitis, suggesting
  that H2S may play an important role in periodontal tissue damage in
  periodontal diseases.

2009 - Hydrogen sulfide induces apoptosis in human periodontium cells
2010 - Bacteria-derived hydrogen sulfide promotes IL-8 production from epithelial cells

We have shown that inactivation of H2S producing enzymes
  (cystathionine beta-synthase, cystathionine gamma lyase, or
  3-mercaptopyruvate sulfurtransferase) and NO-synthase in several Gram
  (+) and Gram (−) bacteria render them highly sensitive to different
  classes of antibiotics (Gusarov et al., Science 325 (2009) 1380–1384;
  Shatalin et al. Science 334 (2011) 986–990). We also presented
  evidence that Bacillus anthracis-derived NO is critical at the early
  stage of infection (Shatalin et al. PNAS 105 (2008) 1009–1013). Here
  we show that: (1) cbs/cse and nos mutations change Bacilli global gene
  transcription profile; (2) apore formation process in cbs/cse and nos
  mutants of B. anthracis is affected; (3) virulence of cbs/cse and nos
  mutants of B. anthracis is diminished. These results demonstrate that
  bacterial H2S and NO are an important virulence factors, and that
  enzymes generated these gases may serve as an attractive target for
  antimicrobial therapy.

2014 - S7-6 Role of H2S and NO in Bacillus anthracis spore formation and virulence

Btw. there is non-hydrogen sulfide producing S. enterica too, which can probably (no study about this yet) cause salmonellosis. So using thiosulfate as electron acceptor and producing $H_2S$ might not be essential by the infection. (There are other non-sulfur electron acceptors e.g. nitrate, fumarate, etc... for the case of anaerob metabolism.)

2013 - Genetic Analysis of Non-Hydrogen Sulfide-Producing Salmonella enterica Serovar Typhimurium and S. enterica Serovar Infantis Isolates in Japan
2011 - Salmonella enterica Serovar Typhimurium Colonizing the Lumen of the Chicken Intestine Grows Slowly and Upregulates a Unique Set of Virulence and Metabolism Genes
2013 - Salmonella Uses Energy Taxis to Benefit from Intestinal Inflammation
2006 - Role of Gluconeogenesis and the Tricarboxylic Acid Cycle in the Virulence of Salmonella enterica Serovar Typhimurium in BALB/c Mice
1981 - Aerotaxis in Salmonella typhimurium: role of electron transport.
2010 - IDENTIFICATION OF NOVEL VIRULENCE GENES OF SALMONELLA ENTERICA
2014 - Increasing prevalence of hydrogen sulfide negative Salmonella in retail meats

Overall hydrogen-sulfide and other gasotransmitters are important virulence factors of many pathogens.

You are right. This is very new research area (since 2011 most focus put) such that it has not been bound to virulence in any articles. Much discussion about gasotransmitters: http://en.wikipedia.org/wiki/Gasotransmitter but not reached any major textbooks. Feel, free to update your answer when you hear more about this topic and updates.

@Masi "These results demonstrate that bacterial H2S and NO are an important virulence factors, and that enzymes generated these gases may serve as an attractive target for antimicrobial therapy." - But you are right studies about gasotransmitters and virulence are very rare. Nice question btw., I have not known that gasotransmitters exists until now... :-)

Neither me. I just noticed now that your answer make sense, just because you have this term gasotransmitter. There is no mentioning about them in Mercks' manual nor Harrison. Could not find in any Medical textbooks.

@Masi http://en.wikipedia.org/wiki/Gasotransmitter it is a pretty old word - since 1981. The discovery that H2S is a gasotransmitter is about a decade old story.

Yes, time is relative. Very little has been done in the research of this topic. No mentioning in any major medical textbooks. Thank you for doing some meta-analysis! It would be helpful to all if you could reorganise your answer and make introduction and summary at the end. Now, the main point can disappear.

@Masi It is maybe because H2S is under extensive research but still not in the medical practice. Maybe in 5-10 years... Afaik NO is used in the medical practice currently.

Alan Boyd's answer

Production of hydrogen sulphide is used as a convenient method for
  detecting the presence of pathogenic Salmonella, there is nothing to
  link this with virulence.

which I agree with.


text:
Pippin prep kits - expiration date
Do you use Pippin prep? We would like to buy it, but we need more info. What is the expiration date of kits for Pippin prep? Thanks!

Have you contacted the manufacturer to ask?

@Atl LED of course yes, but they dont answer yet. I need this info right now :)

You tried calling 800-284-8474 and they didn't know off hand?  Ask to speak to tech support if you don't get anywhere else.  Best not to make lab purchases when you have to make a decision in less than half a day...

According to this document (page 11) the shelf life for the cassettes is 1 year. The other ingredients (running buffer, DNA size markers, loading dye) appear to be standard reagents. Of those, the DNA size marker will probably have the shortest shelf life, but it stands to reason that the reagents should have a shelf life at least as long as the cassettes, seeing as only their shelf life is mentioned. It is possible to buy reagent replacement kits.


text:
PCR enzyme units or concentration?
When performing PCRs, usually in every protocol enzyme amount is specified as 1.25 U as optimal per 50 uL reaction. Then, when running 25 uL PCR reaction should i use 1/2 he amount the enzyme or should i respect the value on Units thus using the same volume as in 50 uL reaction?

I usually use 1 unit per reaction in 20ul reactions. Using less makes the reaction less reliable in my experience.

You have to scale amounts of all PCR components proportionally depending on the volume of the reaction. The polymerase is no exception in this respect, the only difference is that you measure it in terms of activity - units. So in your protocol you have 0.025 U/µl and you have to maintain this concentration when changing the volume.


text:
Why is Homo sapiens not categorized as an invasive species?
According to Invasive Species Advisory Committee (ISAC), the definition of the invasive species is “a species that is non-native to the ecosystem under consideration and whose introduction causes or is likely to cause economic or environmental harm or harm to human health.”
But considering the following facts, why is this species not categorized as an invasive species?
Homo sapiens:

is non-native to the most of the ecosystem which it is inhabiting, since it originated from a certain area of Africa and spread quite recently.
has often caused environmental problems by decreasing the local species after its introduction, as it is known that the number of species in the planet is drastically decreasing ever since the advent of Homo sapiens.
is likely to cause the same problem after introduced to new environment where homo sapiens hasn't inhabited yet.

http://www.invasivespeciesinfo.gov/docs/council/isacdef.pdf

Well I bet the answer is as easy as: "Because we just wanted to ignore that Homo sapiens is an invasive species!". Following a strict definition of invasive species (although current definitions are not that strict!) we should add Homo sapiens in the list. Adding Homo sapiens would not change anything to the way conservation actions are performed, we will always consider Homo sapiens very differently than the other species. Do you feel concerned about this issue? Do you think it would change anything adding Homo sapiens to this list?

Because we are not invasive ones, we expansive ones...

Thanks. I didn't know that the definition isn't so strict. Yes, there's actually no special reason for us to call human as an invasive species. Only thing in the real world which it matters with is probably my final grade for the third quarter. If human is an invasive species, I could get A instead of A-.

Haha.. because we are the ones who are setting up the organizations, making categories and writing books.

I'm voting to close this question as off-topic because it does not concern biological classification but classification by governmental or inter-governmental bodies for purposes of husbandry. The question is framed to appear "clever". It isn't.

I'm voting to close this question as off-topic because this list is concerned with biology, not policy decisions of civil authorities. This appears to be political posturing rather than a genuine request for information.

Ignoring for the moment the question of politics, let's consider the various definitions of the term "invasive species" that are in use. Colautti and MacIsaac write in their discussion of invasive species terminology (1):

The greatest confusion [among the discussed ecological terms]
  surrounds the common term ‘invasive’ and its various derivatives
  (Richardson et al., 2000a). Explicit or implicit definitions for
  ‘invasive’ include: (1) a synonym for ‘nonindigenous’ (e.g. Goodwin et
  al., 1999; Radford &Cousens, 2000); (2) an adjective for native or
  nonindigenous species (NIS) that have colonized natural areas (e.g.
  Burke & Grime, 1996); (3) discrimination of NIS established in
  cultivated habitats (as ‘noninvasive’) from those established in
  natural habitats (e.g. Reichard & Hamilton, 1997); (4) NIS that are
  widespread (e.g. van Clef & Stiles, 2001); or (5) widespread NIS that
  have adverse effects on the invaded habitat (e.g. Davis & Thompson,
  2000; Mack et al., 2000).

Note that except for #2, all the definitions require that the species is a nonindigenous (non-native) species in the area under consideration. Therefore, while humans may be considered to have been an invasive species for much of our species history, under most definitions of the term we no longer qualify because except in a few places (mainly the arctic, antarctic and marine environments, where human presence is minimal) we are now a native species.
See also http://www.smithsonianmag.com/science-nature/are-humans-an-invasive-species-42999965/?no-ist

This argument seems to hinge on the pretty arbitrary decision of the point at which an invasive species can be considered indigenous...

Well, yes. How can it be any other way?

That's not what the term native species means, don't confuse the legal term native with the biological term.

I don't think there is a good answer.

Many people and organisations do not even consider Homo sapiens when making such lists.  Why? Because we have been for millennia a narcissistic species (think about religious narrative). This is similar to non-scientifically talking about animals. Homo sapiens is usually implicitly excluded from considerations.
Although Homo sapiens is present on all continents apart from Antarctica, Homo as a genus has been present for millions of years in Eurasia. Homo erectus has been there particularly long. Homo sapiens has outcompeted these species.
Ecosystems do change. Whether or not Homo sapiens is sufficiently long to be a native species is not a well posed question. Any answer would depend on arbitrary cutoffs. For instance if the first migration of Homo sapiens to Americas happened 14k years ago and it took 20 years per generation, then Americas are populated only for 700 generations. Is it a lot or is it little?
However, there are places in the world (mostly islands) where Homo sapiens settled very recently. Mauritius was first settled in 1638. And it is clear that since then many bird species (not only the famous dodo) went extinct and most of the area was converted from forests to sugar cane fields and towns. So yes, in this case there is no doubt the migration was recent and that it drastically changed the ecosystem, therefore it fulfils the definition.
Pragmatism. Probably the most important of it. We define invasive species for a reason: to give them a negative connotation and possibly plan a future removal. Doing these actions against humans are completely different from the legal point.

To sum up: a external observer would classify humans as an invasive species in at least some regions (Mauritius) and not in other (Africa south of Sahara). But people don't classify themselves as such because of political, moral, legal and pragmatic reasons.


text:
What is happening in each iteration of PSI-BLAST?
I understand that the first BLAST yields almost the same results as blastp. The second time the iterated blast generates different results as it uses different matrix based on our first result.
But I don't understand how exactly the second matrix is generated.

Addition to previous answers:
PSI-BLAST is a sort of machine learning algorithm which uses the results of the first alignment (PSSM) to score the next iteration of alignment. I would recommend you to refer to the NCBI bookshelf page on PSI-BLAST.
PSI-BLAST adopts a scoring scheme (PSSM) that is built based on a given set of data (the aligned sequences), rather than using a generalized scoring matrix. This improvisation updates the prior knowledge of the homologs and helps to detect similar sequences that were otherwise undetectable. With iterations the PSSM keeps getting updated, thereby, making the BLAST more sensitive in finding homologs.
How PSSM is constructed:
If a position in the alignment is conserved (i.e same residue in many sequences), it receives a high score whereas a position with low conservation gets a low score.
Score is based on relative counts of a residue in a position. If you want to know the details see here.

Hi ! Thanks. Please see the comments to gergana's answer.

Check the link that I mention in the answer. It has some examples too.

I read that this method is much more sensitive for detecting distant relationships. What does this mean ? How using PSSM improve its senstivity ? (Sorry for bugging you so much but am really excited to learn this new(for me!) stuff !)

PSI-BLAST is Position-Specific Iterated BLAST.
I'm probably out of my depth here, but my understanding is that the results of the first, essentially standard, BLAST search are used to create a multiple sequence alignment. This alignment is then converted to a Position Specific Scoring Matrix (PSSM). (The linked Wikipedia entry shows this for DNA sequences, but the principle is exactly the same for protein sequences.) This matrix can then be used as the probe for the next round of BLAST, and the results of that alignment can be used judiciously to improve the matrix, and so on until the results converge.
Here is a link to some slides by Stephen Altschul which go into lots of detail.

From Russ Altman (Stanford University) lecture:
Blast takes as an input a sequence, it searches the database, and outputs a set of alignments (a top ranked alignment, followed by a second-top ranked, a third, and so on). Then you take the top scoring sequences (you might use the E-value as a cutoff) and you can create a position-specific scoring matrix (PSSM) based on the occurrences of amino acids in all the columns of these alignments. This is allowed, because there is a high chance that these sequences are homologous to the query sequence and thus looking at the amino acids would give you a good sense of the variability in position that is allowed in the initial query sequence. The next step is to re-search the database for more hits. So now instead of searching with a sequence, you are searching with a profile, and you get another set of hits. You can iterate a few times which would give you a much more sensitive search.

Hi! Thank you so much. So each time we iterate , a new PSSM is formed ?

I also do not understand the significane of using this type of blast instead of standard blast. What specific/new information can i get by doing this type of blasting ? When wud i use this type of blast ?

Yes, each time you iterate a new PSSM is formed. You might want to use it if you would want to identify homologs that are undetectable by simple BLAST.