Nut weevil larvae thrived, eating all acorn contents and leaving needle-like feces

Topics discussed included:

1) Nut (acorn) weevil larvae: Two weeks ago we sliced open the weevil egg-infected acorns we had collected from the Yoshida Jinja hiilside in August and found that healthy-looking nut weevil larvae had grown to fill much of the space inside the shells and had eaten all the acorn contents, leaving needle-like feces. One person in our group found a wonderful video link

http://www2.nhk.or.jp/school/movie/clipbox.cgi?das_id=D0005401434_00000&keepThis=true&TB_iframe=true&width=920&height=480


showing how the adult weevils lay eggs inside holes they have drilled in the acorns while they are still on the twigs of the trees and then crawl back along the twig and spend hours sawing away at it until they cut through it and it falls to the ground, carrying the egg-infected acorns with it. We wonder: Why do the weevils go to all the trouble to cut the twig off like that? 

Diversity of Ocean Research in Kyoto University

Diversity of Ocean Research in Kyoto University

November 25, 2013

Topics discussed included:

The special exhibit going on at the Kyoto University Museum until December 1, 2013:

Diversity of Ocean Research in Kyoto University 

Some of the most interesting topics explored in this exhibit include:

1)  The origin of water on earth, especially as it applies to the water in the oceans. It's not certain how water originated on the earth. Some theories that might explain it in part or entirely include:

--  an extraterrestrial source, such a comets or asteroids

--  release of water stored in hydrous minerals

2)  The formation and changes over time of ocean floors via tectonic plate movement and other forces. The exhibits focused especially on The Sea of Japan, which was long ago a landlocked sea when the landbridge of East Asia existed.

3)  Computer simulation and modelling of the formation of ocean currents worldwide.

4)  Green sea turtle life activities (feeding, napping, navigation, breathing, sleeping, and mating) in the shallow sea waters surrounding the Ryukyu Islands, as uniquely revealed by biologging using small video cameras reversibly attached to the shells of adult turtles.

Uri Alon TED talk // ID of virus causing SFTS

Science Buzz Lunch, September 30, 2013

Topics discussed included:

1) Uri Alon's recent TED talk, in which he describes getting lost in a "cloud" of confusion and depression repeatedly as a graduate student when his research got stuck and he lost all sense of which way to turn in order to start making progress again. He then goes on to explain some general principles he found helpful for himself, and later for his students, to get out of such unavoidable clouds. These principles included generally responding to suggestions with "Yes, and...." rather than arguing against them.

Alon is involved in improvisational theater as a hobby, and has used insights from this hobby to inspire his approach to guiding and motivating scientific research efforts.

2) How do researchers identify the causative agent of a newly emerging disease? One of our attendees descibed his reading about how the tick-borne virus causing SFTS (Severe Fever with Thrombocytopenia Syndrome) was recently identified.

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.
    

Science Buzz Lunch in Mixer Room, Bldg 1, June 17th and 21st

Science Buzz Lunch in Mixer Room, Bldg 1, June 17th and 21st

Topics discussed included:

1) the paper

LBR and Lamin A/C Sequentially Tether Peripheral Heterochromatin

and Inversely Regulate Differentiation

by Irina Solovei et al. in Cell 152, 584-598, Jan. 31, 2013

The authors start by pointing out that the chromatin organization is highly exceptional in the rod photoreceptor cells of nocturnal mammals: to reduce light loss via scattering in the retina of these animals, the euchromatin is localized to the nuclear envelope, and heterochromatin occupies the interior part of the nucleus.

They found that this phenomenon, and indeed the normal distribution of chromatin in other cells, can be explained by the status in these cells of the two mechanisms that can tether heterochromatin to the nuclear envelope: an LBR (lamin B receptor)-dependent mechanism and a lamin-A/C-dependent mechanism. The rods of nocturnal mammals lack both of these mechanisms.

2) the paper

A Bilirubin-Inducible Fluorescent Protein from Eel Muscle

by Akiko Kumagai et al. in Cell 153, 1602-1611, June 13, 2013

The authors describe the first fluorescent protein identified in a vertebrate. They isolated this protein from the Japanese freshwater eel Anguilla aponica, and named it UnaG (after unagi, the Japanese name for this eel). UnaG fluoresces when it binds bilirubin, a naturally occurring breakdown product of hemoglobin.

3) the paper

High-molecular-mass hyaluronan mediates the cancer resistance of the naked mole rat

by Xiao Tian et al. in Nature(

Published online

 

19 June 2013)

Naked  mole rats are naturally strongly protected from developing cancer by their production of high levels of the extracellular matrix component h

igh-molecular-mass hyaluronan, which signals their cells to control cell division via induction of p16.

Hyaluronan makes skin supple, and the authors speculate that naked mole rats evolved to have high levels of hyaluronan in their skin to accomodate their life in tight underground tunnels.

Interestingly, the same group of scientists showed a few years ago that a second mole rat species (the blind mole rat) uses a different mechanism (secretion of beta interferon, and resultant cancer cell death) to achieve its high cancer resistance.

4) a discussion in Nature News online this week titled: 

Dog genetics spur scientific spat:

Researchers disagree over canine domestication.

Three research groups have recently reached significantly different conclusions about where and when dogs evolved from their wolf ancestors. It should be interesting to follow this research for the next few years to see how the conflicting ideas get resolved.

Science Buzz Lunch in BP-3 (Bldg 1, Room 104), June 3 & 7, 2013

Science Buzz Lunch in BP-3 (Bldg 1, Room 104), June 3 & 7, 2013

Topics discussed included:

1)  The different benefits of communicating in English versus communicating in one's native language for non-native speakers of English. These benefits may not be the same for biologists (with much need for English communication) as for mathematicians (with not so much need for English communication because they use strictly defined terms and formulae in their work).

2) Recent news reports about the current status (not yet successful) of mathematicians' attempts to verify the proof of the "ABC conjecture" published last year by Kyoto University professor Shinichi Mochizuki.

3) The recent paper "Developmental Basis of Phallus Reduction during Bird Evolution" by Ana M. Herrera et al. in Current Biology. 06 June 2013

This paper reveals the molecular basis of the puzzling evolutionary loss of the phallus in most (including chicken), but not all, lineages of birds (ducks, for example, have a phallus). They show that distal expression of Bmp4 in the developing chick genital tubercle causes apoptosis and regression of the embryonic chick phallus. Basal birds and ducks lack this distal Bmp4 expression and develop elongated phalluses.  The authors say that Bmps have played major roles in reshaping (generally reducing) vertebrate teeth, limbs, digits, genitalia, etc. during bird evolution.