A recent addition to the list of discoveries that stay neglected for long before their full potential is realized – CRISPR – may revolutionize genetic engineering. Two and a half decades after its discovery in the bacterial systems, Clustered Regularly Interspaced Short Palindromic Repeats are now being seen as the tools to edit genomes with precision like never before. Continue Reading →
Synthetic biology tools have been used to develop switches, logic gates, timers, time-delay circuits, counters and oscillators to perform bio-computation in bacterial cells. Much of these are not as well characterized in multicellular populations of mammalian cells due to the prescence of cell-cell interactions which enable cell populations to communicate during development, adapt to the environment and to form or recognize patterns. Quorum sensing, a phenomenon of bacterial colonies wherein gene-expression is dependent on the population density, is a well-studied application of cell-cell communication in cell populations. Continue Reading →
Medicine is one of the largest industries globally. It is never hit by recession. On the contrary, when recession hits people feel more like seeing the doctor. But, this doesn’t mean that the field is immune to stagnancy. The pharmaceutical industry needs to frequently reinvent itself. The two major challenges that would upset the current pharmaceutical scenario are the end of the blockbuster era and the emergence of personalized medicine. Continue Reading →
A recent documentary by Dylan Mohan Gray, Fire in the Blood, reveals how western pharmaceutical giants manipulate patents to control global healthcare, often at the stake of the developing countries.
According to the documentary website, it is
“an intricate tale of ‘medicine, monopoly and malice’, FIRE IN THE BLOOD tells the story of how Western pharmaceutical companies and governments aggressively blocked access to low-cost AIDS drugs for the countries of Africa and the global south in the years after 1996 – causing ten million or more unnecessary deaths - and the improbable group of people who decided to fight back.
Shot on four continents and including contributions from global figures such as Bill Clinton, Desmond Tutu and Joseph Stiglitz, Continue Reading →
Biofuels have failed to live up to thier promise. Genetic variability, inability to implement in current automobile infrastructure and low conversion rate are the major challenges in using them extensively. Production of secondary metabolites and ligno-cellulose from plants is a skill-intensive and costly process. One of the major challenges in the field remains the exclusive quantification of a particular product without forming by-products. Tools of synthetic biology can be employed to engineer metabolic networks to optimize production of the desired product.
The following presentation (exhibited by me and friends in Plant Tissue Culture tutorial) explains a novel approach to develop an artificial positive feedback loop to increase the accumulation of cell wall polysaccharides, while reducing lignin deposition.
Let us say our universe is X years old, exact to the very day. What was then there X years and 1 day ago?
Physicists have long hypothesized that time is not linear as it seems to past. Such flexibility must allow the concept of multiple universes existing simultaneously. In one universe, you would find this boring and close the tab, but in other you would go on to read more about it. And in some another, you may die due to a blast in your laptop — Final Destination style.
In this TED video, cosmologist Sean Carroll explores time and universe and ponders why time exists at all. Continue Reading →
“We cannot tear out a single page of our life, but we can throw the whole book in the fire.”
- George Sand
Suicides are the tenth largest killers globally. More people kill themselves annually than are murdered. A lot many people attempt unsuccessfully. Depression is the most common cause and the only (subjective) indicator. The greatest risk is the fact that unlike other illnesses, people contemplating suicides do not tell anyone for obvious reasons. If we could predict suicidal intention clinically, it would be a major achievement. A communication published in Nature Molecular Psychiatry might be the first steps in the direction.
A group from Indianapolis claims to have identified blood biomarkers related to suicidality. The subjects picked suffered from bipolar disorder. Intra-subject and inter-subject comparisons were made to categorize individuals from low to high suicidal ideation (SI) states. Differential gene expression data of blood-based biomarkers was analyzed to identify biomarkers which varied significantly and in direct correlation to suicidal ideation. The major biomarkers identified include SAT1 (spermidine/spermine N1–acetyltransferase 1), phosphatase and tensin homolog (PTEN), myristoylated alanine-rich protein kinase C substrate (MARCKS), and mitogen-activated protein kinase kinase kinase 3 (MAP3K3). Continue Reading →
Biologists are usually afraid of mathematics. For a long time, the best they were at attempting a biological phenomenon mathematically were the second order differential equations regarding enzyme kinetics. Development, which is the most unclear of concepts in biology might benefit from mathematical characterization. I am currently studying a book, titled Modularity in development and evolution, on viewing genetic and development networks as modules which are repeatedly used across space and time.
Here are two beautiful excerpts from the beginning of one of the chapters in the book. The first describes how systems approach might go a long way in solving the puzzles of development.
“If one is seeking a biochemical understanding of development then the language of dynamical systems theory seems a natural one to use.
If we are serious about attempting to understand the hierarchy of developmental decisions in molecular terms then we do not just need to identify the molecular terms then we do not just need to identify the relevant genes and gene products but also to understand their dynamical behaviour. In the past this has proved to be necessary for understanding such things as the mechanism of nerve conduction or aggregation in slime moulds. In the future Continue Reading →
Evolution transcends down to every living organism on the face of the earth today from the last unicellular common ancestor (or LUCA). We have grown amazingly complex over the epochs. But, the essence of life or the one we know to say the least, remains the same. How organisms develop from a single cell to the myriad of cells in an adult shares a far greater mechanism across the taxa than the most ambitious of designers could have aimed for. But to say that looking at development is equivalent to looking at evolution, as Haeckel did in his famous hypothesis, ontogeny recapitulates phylogeny, would be an overstatement.
Evolutionary developmental biology or evo-devo is about looking at development processes of different species to deduce the ancestral relationship between them. Which factors, then, make the field more convincing than the recapitulation theory?
Modularity: Genetic networks are increasingly being looked at as modules. Different genes orchestrate together to achieve biochemical functions. To achieve the same function in different organisms, we would expect the concerned genetic module to remain intact across them. Modules are not restricted to the molecular level. Pentadactyly, for instance, is a phenotypic module.
Differential gene expression: A gene which may act as a switch in one organism may influence another gene in some other organism, leading to similar or different results. Surprisingly, the same gene may have different effects in the same organism at different times. The findings that large evolutionary changes occur due to differences in gene expression rather than evolution of new genes is proof that developmental changes precede evolutionary changes and not succeed them as originally expected.
Noise is generally defined as unnecessary elements that may arise during the course of generation or transmission of signals. Noise may be big or small, significant or insignificant, with or without any pattern, but one characteristic that remains constant is that it is unwanted. How do we define noise in biological systems, if there is any? How detrimental is it to our understanding of these systems? I will try to highlight these in this post, amidst a lot of noise in my head over the recent weeks.
Signal and noise – the inseparable duo
The very basic signal in biological systems is the state of the gene. It can be either switched on or off. But, the scenario seems more binary than it actually is. Two genetically identical cells with a particular gene switched on do not make equal amounts of proteins. Proteins are the secondary level of the signals in biological systems. Their concentrations have also been compared to binary units, high denoting 1 and low denoting 0. But again, the high’s of two genetically identical cells differ considerably. Genes, proteins and hence the noise associated are communication relayed not just across space (inter-cellular or inter-individual), but also across time by guiding evolution. Just as we come up with ways to minimize noise in our communication systems, we would expect nature to minimize noise in its systems too. Observers, in their obvious hate for biological noise, termed the deviations of the individual from the average as errors due to the limits of measurement.
Is noise really that bad?
Now with methods to analyze individual cells, we come to a counter-intuitive explanation. The noise is not a slight deviation from one of the two bi-stable states, but the decisive factor behind which of the two states exists under the given conditions and is shaped by evolution. The paper below explains the sources of noise in gene expression, its adaptive role and evolutionary importance.
Read more here
Viney, M., Reece, S. E., Adaptive noise, Proc Biol Sci. 2013 Jul 31