degree of freedom and spectrophotometer

Degree of Freedom:

I think the easiest way to see them is as follows:

The degree of freedom is the number of values in a calculation that we can vary.

(http://www.statsdirect.com/help/basics/degrees_of_freedom.htm)
Another way of thinking about the restriction principle behind degrees of freedom is to imagine contingencies. For example, imagine you have four numbers (a, b, c and d) that must add up to a total of m; you are free to choose the first three numbers at random, but the fourth must be chosen so that it makes the total equal to m - thus your degree of freedom is three.

(http://www.tufts.edu/~gdallal/dof.htm)
A single sample: There are n observations. There's one parameter (the mean) that needs to be estimated. That leaves n-1 degrees of freedom for estimating variability.
Two samples: There are n₁+n₂ observations. There are two means to be estimated. That leaves n₁+n₂-2 degrees of freedom for estimating variability.

Spectrophotometer:

Spectrophotometer can be used to measure absorbance or transmittance of light source with respect to the sample.

http://www.chm.davidson.edu/vce/spectrophotometry/Spectrophotometry.html

First, the intensity of light (I₀) passing through a blank is measured. The intensity is the number of photons per second. The blank is a solution that is identical to the sample solution except that the blank does not contain the solute that absorbs light. 

Second, the intensity of light (I) passing through the sample solution is measured. (In practice, instruments measure the power rather than the intensity of the light. The power is the energy per second, which is the product of the intensity (photons per second) and the energy per photon.)

Third, the experimental data is used to calculate two quantities: the transmittance (T) and the absorbance (A).

The transmittance is simply the fraction of light in the original beam that passes through the sample and reaches the detector. The remainder of the light, 1 - T, is the fraction of the light absorbed by the sample.

In most applications, one wishes to relate the amount of light absorbed to the concentration of the absorbing molecule. It turns out that the absorbance rather than the transmittance is most useful for this purpose. If no light is absorbed, the absorbance is zero (100% transmittance). Each unit in absorbance corresponds with an order of magnitude in the fraction of light transmitted. For A = 1, 10% of the light is transmitted (T = 0.10) and 90% is absorbed by the sample. For A = 2, 1% of the light is transmitted and 99% is absorbed. For A = 3, 0.1% of the light is transmitted and 99.9% is absorbed.

When we did our practical on abs, with the coloured solution, the darker the solution, more light will be absorbed and thus there will be greater absorbance/less transmittance. 

Top 10 Questions from Term 1

1. Lignin as another extracellular component for plant

Firstly, when it comes to plant cells, they may have both primary and secondary cell walls. The primary cell wall is a more flexible, more permeable one that will allow the cell to continue to grow in size. Upon maturation i.e. cell stops expanding, another layer i.e. secondary cell wall may be formed between the primary cell wall and plasma membrane. Lignin is added to the secondary cell wall, making it more rigid and strong for mechanical support (main constituent for wood), and less permeable to water when compared to the primary cell wall. The composition of the 2 cell walls is different but cellulose is present in both. The hydrophobic nature of lignin allows it to transport water as an integral part of xylem. Also, wood consists mainly of secondary cell wall that hold it up against gravity.

(http://www.helium.com/items/1633330-the-structure-and-function-of-lignin-in-plant-cells) “Though useful to plants as they increase in size and girth, lignin does have its drawbacks. Beans, for example become enedible as they age due in part to lignin deposits and as paper is made, used and recycled, lignin tends to remain as it is hard and difficult to dissolve so each time you recycle paper, the content of lignin increases and this impairs the quality of the paper. Finding bio-friendly ways of removing it without resorting to chemicals like dioxin is a challenge for the future.”

2. Thylakoids

Indeed, thylakoids are the flatted sacs of a granum. ☺ Someone mentioned that the thylakoid membrane system is continuous with the inner membrane of the chloroplast – that is wrong. As I had highlighted in class, the thylakoid membrane system is independent. However, it is derived from the pinching of the inner membrane of the chloroplast envelope.

3. ECM versus interstitial tissue fluid (loved it!)

ECM is different from the interstitial tissue fluid. Do they interact? Yes they do but they are also different in composition and derivation (interstitial fluid comes from leakages of blood capillaries while ECM are from the secreted products of cells, released via exocytosis. Collagen as a macromolecules is released in soluble form but assembled readily extracellularly via H-bonding. When we consider the role of ECM with its collagen and proteoglycan mixture, we can think of the cellulose cell wall with its criss-crossing fibrils that is very much porous but offers support to the cell. In this case ECM keeps the cells of a tissue together and supporting them, helping to coordinate activity etc. Just as water can pass through the porous cell wall, interstitial fluid can pass through ECM.

https://docs.google.com/viewer?a=v&q=cache:MeINS3Mhm5IJ:microfluidics.epfl.ch/twiki/pub/PBCCourse/ReadingMaterial2012/Annu_Rev_Biomed_Eng_2007_Swartz.pdf+&hl=en&gl=sg&pid=bl&srcid=ADGEESjPtBIxgTsSeIIIjyYfMp9iXUu6-qdakvXt9ffhsWg0FZhHkLK__UyMzUFW0STu91KoTSCgMgbwwSFt5rPJTNFPpOccmXqigDOEjDjcYTlNMgQLeeYT2nRqCp2CPCcwFjpsO6wr&sig=AHIEtbQADXQBPg8rMRK2fN9Kp3od6PEynA

THE INTERSTITIAL SPACE

Cells reside in highly specialized extracellular matrices (ECMs) that provide mechan- ical support, determine mechanical properties, and importantly impart extracellular signals to the cell, both through the ECM molecules and the cytokines that they bind. The specific components of this ECM also vary greatly according to tissue type, but typically include the family of collagens, proteoglycans, laminins, and, in pathological cases, fibrin. The specific composition of the ECM largely determines the resistance to fluid flow, most notably fibrillar collagen and proteoglycans.

INTERSTITIAL FLUID FLOW

Interstitial Fluid It is estimated that up to 20% of the body’s mass is made up of interstitial fluid (24), and much of this fluid is in constant motion, albeit slowly….interstitial fluid pressure (IFP) results from numerous factors, including exercise, blood pressure, tissue metabolism, hydration, ECM composition, and cell density (31). For example, the integrity of the ECM is important in maintaining healthy IFP, with damage to connective components of the tissue such as collagen leading to a loss of ECM tension and subsequent change in IFP. Besides such passive structural changes, cells also play important active roles, maintaining tension in the ECM in a β1 integrin-dependent manner and therefore helping to regulate IFP (32).” 


4. Collagen (youth and old age)
http://www.smartskincare.com/skinbiology/skinbiology_collagen.html
http://www.science20.com/news_releases/shock_some_collagen_repair_skin_treatments_actually_work
http://www.prevention.com/beauty/beauty/collagen-drinks-do-they-actually-help-skin (on the not-so-effective collagen drink discussed in class)

With age, there is increased collagen degradation than with synthesis. The collagen fibers are also subjected to much damage with oxygen radicals and other agents that disturb the orderly structure of collagen, making it weaker than expected. As with any other cells, one may also expect fibroblasts which synthesise collagen to be less effective over time due to mutations. Nevertheless, one should note that the beauty of collagen is more than skin deep. Collagen is found in many other tissues as well and its degradation means more than just getting more wrinkles!

5. Endosymbiotic theory

As the story goes on the origin of eukaryotic cells:
http://highered.mcgraw-hill.com/sites/9834092339/student_view0/chapter4/animation_-_endosymbiosis.html
(animation; good)

http://www.biology.iupui.edu/biocourses/N100/2k2endosymb.html
(review of evidence as discussed in class)

6. Less cholesterol in plants than in animals

This is one reason the doctor may ask you to eat more veggies than meat – to reduce cholesterol intake. Anyway, while it is true that there is less cholesterol in plants, unlike animal cells where cholesterol is the sterol that dominates, plant cells produces an array of sterols like sitosterol, stigmasterol and 24-methylcholesterol which often predominate. Both sitosterol and 24-methylcholesterol helps to regulate membrane fluidity and permeability in a similar way cholesterol is to mammalian cell membranes.

7. If it is less energetically favourable, why do phospholipids bother to flip-flop?

Ahh. I had answered this question before some years back :P. A familiar feeling settled in when I located my source and saw my own note. While we talked about PL, we did not go further to discuss about the different types of PL present like phosphatidylcholine or phosphatidylserine etc. At the plasma membrane, enzymes known as flippases make use of ATP to flip the different types of PLs for an asymmetrical (PL) bilayer. The different PLs are known for the different roles they play in sending different signals within the cell or to other cells. For example, when apoptosis (programmed cell death) is engaged, phosphatidylserine, which tend to be located on the cytosolic side of the membrane will be flipped to the extracellular side where they serve as recognition markers for phagocytes to be engulfed.

8. Phagocytosis of encapsulated bacteria

mmm..I cannot remember the question very well but if I am correct, here is my response….. phagocytes (a type of white blood cells) have receptors on their plasma membranes that recognise and bind to specific protein markers (i.e. toll-like receptors) on the surface of the pathogens for phagocytosis to occur (cell-to-cell recognition). The associated question is on the capsule of bacteria which helps to protect the bacteria from phagocytosis by hiding the bacterial surface. The capsule is composed of polysaccharides and the type of sugar actually vary from one species of bacteria to another, making them good markers to differentiate amongst the bacteria as well. The capsule is important because it limits the ability of phagocytes to engulf it such that the bacterium can remain virulent/pathogenic. If a bacterium loses its capsule, it is no longer effective; nonpathogenic. For encapsulated bacteria, the antibodies produced in our body can assist in their destruction. Opsonization whereby (specific) antibodies bind to the specific sugar markers and help phagocytes to engulf the bacterium. As such, the polysaccharides are used as antigen/markers in vaccine to stimulate the production of antibodies in our body that can help the phagocytes. http://www.youtube.com/watch?v=TYXn2FhVVGM


9. Why flagellum of sperm is membrane bound
Just a note, the flagellum of sperm moves in a wave-like motion while that of bacteria is rotational. Also the flagellum of sperm is made of microtubules while bacteria’s is of protein flagellin. Consistent with the purpose of membrane in compartmentalization and regulating the interior environment, the beating of the flagellum is regulated by Ca2+ entry. Mammalian sperm are stored in a quiescent state in the epididymis and become capacitate/active/mature only after release into the female reproductive tract. In other words, chemical signals within the female reproductive tract helps to capacitate/activate the mammalian sperm including the facilitation of Ca2+ entry for the beating of flagellum. However, non-mammalian sperms do not require this capacitation stage; they are ever-ready although their movement is also dependent on ion exchange http://en.wikipedia.org/wiki/Capacitation The possible reason as to why bacteria do not have membrane bound flagellum is to be mobile while making sure a conducive and tightly controlled environment for the cell. For the sperm cell whose sole purpose is for fertilization, the entry of Ca2+ is more than to get the flagellum moving but for the whole maturation/capacitation process.

10. How does one get embryonic stem cell?

Typically from excess embryos from fertility treatment. Embryonic stem cells are taken from blastocyst, a ball of cells developed from the zygote after 4th -5th of fertilization. It consists of 3 parts: the inner cell mass, trophoblast and blastocyst cavity. The inner cell mass which is the source of ESC, will develop into fetus while the trophoblast will develop into placenta and other supporting tissues. As such, the inner cell mass cannot form an entire organism by itself – that is the argument for its use but highly debatable. Totipotent – able to differentiate into any cell types including the extraembryonic tissues such as placenta which nourishes the embryo – can form an entire organism. ESC of the inner cell mass is only pluripotent as it cannot differentiate into the extraembryonic tissues.
http://www.pbs.org/newshour/science/stem-cells/cellbasics.html .

thanks coach

Last night was the 60th bday celebration for my softball coach for his 21st years of service with Raffles. Tributes were made, generations of softballers came down, and it was an emotional affair for him. I was the only representative from my batch and it did feel a little lonely. I mingled with ex-students, ex-teammates, ex-teachers-in-charges. But at the end of the day, I realised that I had forgotten to get a gift for coach because my roles get a little confused over the years. with nothing but sincerity, I went up to my coach, representing my batch mates, thanking him for all that he had done during our formative years. I told him that I have always been the quiet one, and still is. So we shook hands in our expression of appreciation but he never let go as we talked about several other things. I guess we were both not men of many words. Thank you coach, we were the first batch of softballers whom you saw through for 6 years. Thank you for giving me the space to step up my game, never scolding me when I fell short of your expectations and giving me some of the highlights of my student life. I may be a fairly strong player in my time but I never had the fire for competition. Thank you for understanding. Through you, we learnt more than just the game but also the tenacity, resilience and comradeship. Your efforts and words have never been forgotten. Thank you from the bottom of our hearts.

Starting all over again? Really?

So to this site I return after 2 years, with all its memories still hanging around in bytes that reminds me of a time long past. Maybe it wasnt all that long ago in physical time but relativistically speaking, yes. I felt much older, more world-weary as I begun to shoulder the mundane responsibilities of a more rooted life. Or perhaps it was the uncontented and unsettled me struggling from a little dark corner, ruffling up the ebbs of life. I think I may be a little depressed. My ex-colleague said that when he went to work in UK for a couple of months in a research lab, he felt depressed for 6 months upon return. The stifling working climate, the rigidity etc. I was away for more than 2 years on my own, living a life of exploration and challenges. It wasn't easier when I first got back to school and while it is better now, there are times when I feel still in a limbo. So I told my friends not to contact me, leave me alone so that I may hibernate and get back my sense of being. Leaving behind a set of dreams and someone in another foreign land, I soldier on. I was encouraged to write a paper for my recent work because of its potential for future academic discussions and a topic close to my heart. Ground-breaking one professor said. I had wanted to do that this holiday but was beseiged by endless marking day after day. Before I knew it, it is Saturday and another set of paper still awaits but I will let it wait a little longer. Frankly, I don't remember the details of this holidays at all, except the late nights and the weariness. Yes, I am back into the game and is desperately trying to fit in again, and quickly. I was reliving those days of sleep deficiency and crazy marking, especially during the last week of school this term, when every day is about getting home at 6-7pm,have dinner, take a nap for an hour or so before working all the way until 2-3am. Such a crazy routine. A newbie life no less as I found myself working in a new system, new syllabus, new bunch of students. It was also amazing how when the heart aches at times, we can push it to one side and try to get the immediate work done.Is that why people turn to work as a coping mechanism for a sense of loss, for an imagined sense of achievement? sometimes, those who laugh the most, understand sadness the best. A new school and a new environment. I need to hit the restart button, get into the groove proper and reach out with the heart so that it does not stay caged. Weeks of observation (of the students, colleagues and system) have gone by, it is about time to move on and address it all with my core sense of being. To guide, to help and to have fun. I hope to laugh much again, as I had once done and dispel the moodiness readily on its visits. Life is more than just me. so we can smile and laugh with life. slowly but surely.