Author Archives: ubali1
Intro to Droplet Digital PCR
The utility of droplet digital PCR in gene quantification/copy number determination is becoming increasingly prevalent in industry. Its immediate benefits over traditional absolute quantitative PCR methods is hard to deny as it obviates the need to either generate rigorous standard curves or measure PCR efficiency of every gene pair to be measured. ddPCR delivers the same sensitivity as with conventional approaches with the added benefit of smaller errors. ddPCR relies on the Poisson algorithm and is essentially an end point measurement where the sample to be measured is randomly distributed into discrete partitions containing either none, one or more nucleic acid template copies. These individual partitions are then thermally cycled as in conventional PCR to their end point and then read to determine the fraction of partitions that are positive for the amplification. Continue reading
Gaddum modification of Operational Model of Efficacy
The effect of an antagonist on the efficacy of an agonist is based on the following equilibrium relationship wherein the empty receptor (R) competes with the antagonist (B) and the receptor can exist in an antagonist bound state (BR) as well:
When applying the law of mass action to these simultaneous equations, we can derive the following relationship: Continue reading
Del Castillo-Katz model of Efficacy
The standard model of measuring efficacy as a function of receptor occupancy was deemed to be insufficient to adequately explain the dose-response relationships often observed, that were steeper than those predicted by the law of mass action; or why sometimes a supra maximal drug concentration failed to elicit a maximal response within previously observed systems. This was predominantly manifested by a lack of a linear correlation, as predicted by the hyperbolic Langmuir isotherm, between the observed responses of a ligand on its tissues versus the fractions of occupied receptors. In 1956, R. P. Stephenson argued that the magnitude of response, in a tissue, to a given stimulus was the product of the intrinsic efficacy 
Gaddum -Reversible competitive antagonism
What happens to the log (concentration) vs response curve of a drug in the presence of a competitive antagonist? Assuming that the agonist and the antagonist are in equilibrium with the receptor-binding site, we will observe a parallel shift in the agonist concentration response curve. We can estimate the proportion of agonist and antagonist bound to the receptors by the concentration of the agonist and antagonist and by their affinities for the receptor as follows:
Under the laws of Mass Action, we can derive the following relationship: Continue reading
Derivation of Hill Langmuir Equation
A simple reaction scheme for the interaction of an agonist [A] with its receptor [R] can be described as:
Rate of forward reaction:
Rate of reverse reaction:
Black and Leff Operational model of Efficacy
This modified definition of receptor occupancy defined by the del Castillo-Katz model now allows us to re-define R. P. Stephenson’s original postulate in Eq. (1.0) as follows:
![Stimulus (SA) = e^*_A \delta_{occupied(A)} = S = e^*_A \frac {[A]}{K_{effective} + [A]}](http://s0.wp.com/latex.php?latex=Stimulus+%28SA%29+%3D+%C2%A0e%5E%2A_A%C2%A0+%5Cdelta_%7Boccupied%28A%29%7D+%3D+S+%3D+e%5E%2A_A+%C2%A0%5Cfrac+%7B%5BA%5D%7D%7BK_%7Beffective%7D+%2B+%5BA%5D%7D&bg=ffffff&fg=000&s=0 "Stimulus (SA) = e^*_A \delta_{occupied(A)} = S = e^*_A \frac {[A]}{K_{effective} + [A]}")
qPCR Data Analysis
At work, quantification of differential gene expression is undertaken using real time RT-PCR. The technology generates a quantitative end point threshold (Ct) value defined as the threshold cycle where the fluorescent signal of the reporter dye crosses an arbitrarily placed threshold. The threshold is usually placed in the exponential phase of the PCR amplification cycle and is inversely related to the quantity of the amplicon being amplified. The following guidelines review some basic concepts of qPCR data analysis using delta delta Ct with discussions on selecting housekeeping gene and replicate analysis and data reporting. The post is intended for those users who are already familiar with the technology and have a working knowledge of the basics of qPCR.
Some Thoughts on p-values and Reproducibility in Biological Testing
In biological testing, we often encounter statistical analysis that shows comparison between groups of data sets. A p-value is often used to show the strength of the evidence to support a difference in means between those two groups of data. These p-values are the bread and butter in both pair wise and multiple comparison hypothesis testing. Continue reading
Chiltern Challenge Ultra
Extreme energy hosted its first ever-single day ultra, the Chiltern Challenge Ultra on July 19th, 2014, geared towards enticing runners to the sport of ultra-running. Having previous completed the Pony Express in New Forest, Hampshire, with these fellas, I knew the Chiltern ultra would promise to be a good way to get back in the game. Continue reading
Pony Express New Forest Ultra – Race Report
This post is available for download as a PDF by clicking here!
THE WANDERING THOUGHTS OF A LONG DISTANCE RUNNER
Prelude to the race
It’s been 11 years, 7 months and 28 days since the last time…
The months on the calendar have, of late, whizzed past and there is, as of yet, no noticeable trace of evidence vindicating this particular undertaking in my mind. In fact, quite the opposite – events, of late, are actually working in defiance of my new goal, which lies in danger of being swallowed alive by the unpredictable whims of my procrastinating habit.
Time has crept up quite stealthily during the last few years while I was busy completing my ‘transmogrification’ into a professional and responsible near middle-aged adult. Of course, it hadn’t escaped my notice that my weekend warrior lifestyle was unable to curb the relentless growth of my waistline and my acquired smarts were not serving as a suitable substitute at the local watering holes, much to my chagrin. ‘It was high time to take a stand’ – I thought to myself.
Why Martial Arts???
Avid martial artists also get asked the same question as most ultra runners do. Why?? Why dedicate so much of one’s resources towards something so impractical, or likewise – where is the place in today’s society for something so inherently violent and dangerous. Certainly most long time practitioners have had to come up with their own answers to this, in order to justify their training. After all, the ancient martial artists were simply living their lives in a feudal society where the feudal warriors carried arms and defended their standard of living in a society where laws were scarce and human life underrated, quite often likened in the media to living in the ‘American Wild West’. This rationale is, in fact, not entirely that different from the modern day soldier who, ideally, acts in order to preserve and protect our customs and values against potential threats. In fact, the art of warfare and killing is best preserved and evolved in the modern armed forces and is the place to be if one wishes to be fluent in them. (Another source of information available, along similar line, at Japanese Sword Arts FAQ Version 2.7 tries to summarize the aim of Kendo and Iado training in contemporary society).
My ultrarunning two cents!
Running holds a special lure for individuals of a certain personality, which perhaps Tim Noakes puts it best in the introduction for his book: The Lore of Running. Most ultra runners, especially the ones attempting it for the first time are very misunderstood folks, often being dismissed as unreasonable or crazy and foolish. However, I believe that the reasons for most people wanting to attempt runs of this nature tend to be very deep-rooted and hardly worthy of a cursory glance. Human beings have evolved for endurance running and it’s not very hard to imagine what the mind and body can be convinced of achieving with proper training.
“The people dancing were judged insane by those who could not hear the music.” Continue reading
Monte Rosa – Italy
A few pictures from my trip to the Italian Alps in August, 2011 are attached below. This was my first Alpine adventure under the auspices of an ISM led guide and a fantastic confidence building experience.
Peaks summited:
Punta Giordani – 4064m
Vincente-Pyramide – 4215m
Castor – 4223m
Monte Rosa, Italy – Aug 2011
UK Challenge_Aviemore_2010
In June 2010, we put forward a team in the UK Challenge, a multi-sport adventure race that relied heavily on strategy, planning and team-work to achieve success. Attached is a link to a presentation outlining our experiences. Continue reading
Mulhacen – Spain
A few pictures from my first mountaineering experience climbing up to 3482m in the Spanish Sierra Nevadas in Feb, 2008. This trip was guided by Spanish Highs, an outfit, ideally suited to those looking for a lasting and memorable positive first experience in mountaineering.
