Science Buzz Lunch, September 27, 2013

Sea turtle monitoring // Pervasive genome transcription is initiated from distinct promoters

Topics discussed included:

1) How fishermen cooperate with scientists to enable location monitoring (tag and release) and genetic sampling of sea turtles (caught accidentally in fishing nets), yielding data about sea turtle movents in the oceans. Non-profit organisations are key to this cooperation. We speculated about what would motivate busy fishermen to bring these turtles to port for the scientific studies....

2) A recent paper illuminating some of the "dark matter" pervasively transcribed in the human genome:

Genomic organization of human transcription initiation complexes

by Bryan J. Venters and B. Franklin Pugh

published online last week in Nature

Using ChIP-exo followed by high-throughput DNA-seq, these authors identified about 160,000 transcription initiation complexes bound to specific site across the human genome. The vast majority of these complexes were bound to sites containing 4 core promoter elements: upstream TFIIB recognition element (BRE-u), TATA, downstream TFIIB recognition element (BREd), and initiator element (INR), in highly constrained positions. All but the INR also reside at Pol III promoters, where TATA-binding protein (TPB) makes similar contacts as at Pol II prmoters.

These and other data reported here seem to pretty persuasively indicate that the still-mysterious pervasive transcription of the human genome is generally promoter-specific rather than randomly initiated.  

Chestnut weevils in Kansai but not in Nebraska ?

At the Science Buzz Lunch held on September 9, 2013, topics discussed included:

1) Many green (immature) acorns attached to fallen oak twigs that we collected in Kyoto and Osaka in the past month or so had 1 pin-sized hole piercing through the cap of each acorn, and thus we thought that these acorns have been parasitized by chestnut weevils, with a weevil laying one egg inside each acorn. The weevils then seem to bite off a twig containing 2-3 acorns and a few leaves. One post-doc told us that in a month or so, the weevils will have eaten all the content of the acorn, and will emerge and burrow underground, where they will spend the winter and then emerge next summer to mate and repeat this whole cycle. (We're keeping a few parasitized acorns in a sealed box, and hoping to see the larvae emerge soon).
    However, during a visit to Lincoln, Nebraska last month, no immature acorns there were found to have such holes, so we guess they were not parasitized by weevils. Why not? These acorns were also still attached to the fallen twigs of oak trees, which I guess had been bitten off by squirrels for later collection on the ground.

2) One student described her travels in western Europe during summer vacation. Art and history museums, food, and communicating across language barriers were the major topics of discussion.