Tag Archives: Genomics for General Public and High School Students

Genomics for future anthropologists & archeologists

An awesome use of genomics and proteomics in archeology and paleopathogenomics (yes I just invented the word!)

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Filed under Anthropology, Evolution, My Life My Thoughts

Origin of species: through gene regulation?

“How does evolution occur?” This has been a central question in biology. Does evolution occur because a new mutation results in a new protein or because the same gene is regulated differently? How do new morphological structures evolve? How does speciation occur? A recent paper in Science ties principles in evolutionary biology, development biology, and molecular biology to answer these exact questions.

Distalless protein (dll), which is highly conserved across many genera, seems to have EVOLVED A NOVEL FUNCTION in a particular species of insect (Rheumatobates rileyi) to generate male specific antennal appendages. Males possessing these appendages have increased chances of reproducing therefore, have higher fitness (see video below). There could be two reasons for the development of these antennal appendages: first, dll in this particular species is shorter than all other species and second, dll is differentially regulated in this species. Although dll in R. rileyi appears to be shortened,  I feel that its differential expression may be more important in creating this morphology. dll is an important protein in development and therefore, it is pleiotrophic (see figure on the right below). Thus, it is likely that any alteration of the original function by the shortened protein would result in death. One scenario could be that a cis-mediated regulatory change in dll expression causes it to be expressed at a novel developmental stage in a novel tissue where some other male-specific proteins are also expressed. Interactions between dll and such male-specific protein(s) results in the formation of antennal appandages.

So, what does this study tell us about how evolution occurs? Well, one way evolution by natural selection occurs is not through new mutations that alters the function of existing proteins but through mutations that result in modifications in regulation of existing proteins to acquire novel function. Existing proteins may acquire novel functions if they are ectopically expressed, i.e, in developmental stages or tissues where they are normally not expressed. Most of the times ectopic expression may either provide no benefit to the individuals or even be detrimental but sometimes, ectopic expression may allow these proteins to interact with other proteins expressed in that tissue at that developmental stage to perform new functions. This new function may confer some reproductive advantage to that individual, therefore enhancing what population geneticists/evolutionary biologists call ‘fitness’. Over time, these individuals will take over in the population. If this population remains isolated from the ancestral population for a long period of time, it may give rise to a novel species (not this study but can be imagined).

This is a cool example of how integrating many areas of biology (evolutionary, developmental, molecular, and entomology) can elucidate novel genetic mechanisms underlying phenotypic diversity.

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Filed under Evolution, My Life My Thoughts

Phylo: Crowdsourcing BIOINFORMATICS and GENOMICS

For many reasons multiple species DNA alignment is a hard problem. One reason it is hard is because as evolutionary relationship between organisms increase, the similarities in their DNA sequence decrease. Many times we encounter gaps and duplications that make accurate alignment very difficult.

Computer algorithms are getting better (compare CLUSTAL-W to  Clustal Omega), it is still pretty darn difficult to accurately align multiple species. A lot of time and effort is needed to manually inspect alignments performed even by the best multiple species aligner. A handful of scientists can only take it so far…so, crowdsourcing helps here.

One can use an algorithm to perform multiple species alignments of multiple genomes. These alignments can then be made publicly available to public such that they can, in their leisure, improve them by manually intervention. Recently, I came across PHYLO which is a GAME, yes a  GAME!!!! in which multiple species alignments of human genome that are potentially linked to various genetic disorders, such as breast cancer can be manually curated by the public. “Every alignment is received, analyzed, and stored in a database, where it will eventually be re-introduced back into the global alignment as an optimization.”

This is a wonderful opportunity for the public to learn a little about bioinformatics and to understand about evolution. So folks, substitute your AngryBirds with Phylo and help yourself increase your chances of living longer by helping the scientific community move closer towards finding ‘cures’ for these diseases.

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Filed under My Life My Thoughts

Visualizing biology: from conception to birth, cell division, and more

Visualization helps in learning anything. In biology visualization has traditionally been done using pictures or posters (right).
From conception to birth. But that is so 1970s. In the technocratic future, where lullabies are delivered via iPod and iPads are norm in kindergarten, figures or posters wond do any good. Kids would hate to learn from static images….they need videos! And if you are making videos, you might as well use real data…and Alexander Tsiaras does exactly that. Using advanced technology on real pregnant women he captures images of life from conception to birth. Mes merizing!

Okay, let’s take it to a molecular level now. Let us look at structure of DNA, cell division, and molecular machinery of cell division:

Cant have enough? Visit Drew Berry’s page.

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Filed under My Life My Thoughts

Mapping Human Brain:An awesome video at TED

This was an awesome presentation demonstrating appication of genomics to understand human biology. This would be wonderful to educate general public and high school students about the following:

  1. Biological systems are very complex: thousands of genes produce thousands of proteins at various times that mediate billions of neuronal interactions. Genomics tools (microarray: the things with green dots in this talk)
  2.  A lot of work and time is needed to learn fundamentals of biology: many scientists are needed to gather biological specimen, perform experiments, and to analyze data. In this video only 2 brains were used. Imagine using hundreds of tissues.
  3. Integration of computer programming in visualization: today, because of genomics massive amount of data can be generated in little time. However, in order to analyze and understand the data, computational tools are needed. Once the data is analyzed, computer graphics is needed to visualize the data (the brain with nice colors in this talk). Therefore, computational biologists and artists are becoming important components of the genomics community.
  4. Applications of such studies: Once we accumulate many such studies, they can be used to design drugs or to prevent a disease in general population. This takes even more time and resources.

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How Life Started 4 BILLION Years Ago:Experimental Demonstration

This was one of the most interesting TED talks in science in a while. Many of us are familiar with the Miller-Urey experiment (1952) that showed organic compounds can be formed from inorganic chemicals. Hanczyc takes it one step further by actually demonstrating tar-like chemicals can come together to form little pockets of life like creatures that are able to eat and replicate!

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Filed under Evolution