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.

Science Buzz Lunch, May 25, 2013

Science Buzz Lunch, May 25, 2013

Topics discussed included:

1)The novel technique  "CLARITY" for producing "transparent" intact brain and other organs for visualizing macromolecular structures, as described in:

"Structural and molecular interrogation of intact biological systems"

by K. Chung et al.

in Nature Vol 497 16 May, 2013

2) The recently elucidated molecular basis of the sensation of itch. The neural signal of itch is transmitted by the neuropeptide Nppb: natriuretic polypeptide b

as reported in

"The Cells and Circuitry for Itch Responses in Mice"

by S. K. Mishra et al.

Science, 2013; 340 (6135)

This finding about Nppb resolves a long-standing controversy about whether itch is simply one manifestation of low-level pain:  it isn't.

Science Buzz Lunch in Mixer Room, May 20 and 21, 2013

Science Buzz Lunch in Mixer Room, May 20 and 21, 2013

Topics discussed included:

1)  A report online in ScienceNews about a report by Lenore Pipes at the Biology of Genes conference at Cold Spring Harbor about how the selective mating of either the tamest or the most aggressive foxes since 1959 by Russian scientists has led to changes in not only the animals' behavior but also their brain chemistry.

2)  The genome contraction in smooth (Tetraodontid) pufferfish but not spiny (Diodontid) pufferfish in the last 50 - 70 million years, and how this genome contraction is similar in many ways (selective absence of retrotransposons, high genomic GC content, contraction after whole genome duplication, etc.) to that of the recently reported genome contaction of the carnivorous plant, U. gibba. Speculation about why the mechanisms might have been similar....

Science Buzz Lunch in Mixer Room, May 13 and 14, 2013

Science Buzz Lunch in Mixer Room, May 13 and 14, 2013

Topics discussed included:

1) the recent paper

Architecture and evolution of a minute plant genome

by Ibarra-Laclette et al.

Nature, May 12, 2013

about a "carnivorous plant that throws out "junk" DNA (non-coding DNA),
which calls into question whether such DNA is really needed in other species, including other plants, and also animals such as us humans.

2) the paper

Diffusion and scaling during early embryonic pattern formation

Proc Natl Acad Sci U S A >

v.102(51); Dec 20, 2005

by Gregor et al.

Science Buzz Lunch in Mixer Room, May 7, 2013

Science Buzz Lunch in Mixer Room, May 7, 2013

Topics discussed included:

1)  The role of P2Y receptor as a necrosis sensor and chemokine producer in mice

2)  Studies of Great Tit reproductive success in northern Europe as a measure of adaptation to climate change

3) Possible role of high dietary NaCl consumption in the recent increase of the incidence of autoimmune diseases 

Science Buzz Lunch, April 19, 2013

Science Buzz Lunch, April  19, 2013

Topics discussed included:

Two recent papers in Nature:

1) Circular RNAs are a large class of animal RNAs with regulatory potency
by Sebastian Memczak et al. in the March 21, 2013 issue of Nature

2) Natural RNA circles function as efficient microRNA sponges
by Thomas B. Hansen et al.  in the March 21, 2013 issue of Nature

Science Buzz Lunch, April 15, 2013

Science Buzz Lunch, April 15, 2013

Topics discussed included:

1) A recent paper by V. Salimpoor et al. in Science describing an  MRI neuroimaging study that revealed that activity in the nuclear accumbens could predict how much people were willing to pay for a new song that were listening to

2) A report in National Geographic magazine about a study showing that elementary school students learn math better when their teachers use gestures as well as speech to teach math compared to  when their teachers use speech alone

3) News reports about the reasons for the recently increased longevity in Nagano prefecture (including decreased dietary salt and increased exercise) and the decreased longevity in Okinawa prefecture (including increased meat consumption and obesity).  

Science Buzz Lunch, April 12, 2013

Science Buzz Lunch, April 12, 2013

Topics discussed included:

1)  The role of trichomes in anti-herbivore defence in Arabidopsis

2)  The ecological role of reproductive interference by various male insects and other animals 

Science Buzz Lunch, April 8, 2013

Science Buzz Lunch, April 8, 2013

Topics discussed included:

1) The history of HIV/AIDS: how HIV evolved from SIV, and theories of HIV origin and epidemic emergence, including especially the roles of unsterile injections, urbanization, and social changes

2)  The 1990 American movie Awakenings, based on Oliver Sacks' memoir with the same title, telling a story about the temporary benefits of the use of the drug L-Dopa to treat long-term catatonic victims of the 1917-1928 epidemic of encephalitis lethargica.

3) Experimental testing of functional brain scanning to determine the content of dreams

4) The development at Tohoku University of a Magnesium battery with several advantages over lithium batteries

Science Buzz Lunch in Mixer Room, Bldg 1, Room 214, April 1, 2013

Science Buzz Lunch in Mixer Room, Bldg 1, Room 214, April 1, 2013

Topics discussed included:

1) A recent report in National Geographic magazine about the seasonal migration of Galapgos Island adult (but not juvenile) Galapagos Tortoises
from low elevation to higher elevation (a distance of about 6 km at a speed of 300 m/day) during the dry season. This migration was known to local people, but not known to scientists until recently. We discussed how this migration might favor the survival of the juveniles due to decreased competition for food resources (grass) during the dry season.

2) A recent report about a series of fascinating links between toxoplasmosis and animal and human behavior in which the  obligate, intracellular, parasitic protozoan (Toxoplasma gondii) that causes toxoplasmosis affects host behavior in a way favorable to transmission of the parasite by inducing formation of GABA by dendrites that carry the parasite.

http://news.nationalgeographic.com/news/2013/01/220113-sneaky-cat-parasite-takes-over-human-brains-science/

3) Some prospects for rational design of effective immunogens for rapidly evolving, weakly immunogenic viral pathogens such as HIV, as described in the recent paper  

Rational HIV Immunogen Design to Target Specific Germline B Cell Receptors

by Joseph Jardine et al.

Science DOI: 10.1126/science.1234150

Science Buzz Lunch in Building 1, Mixer Room, March 8, 2013

Science Buzz Lunch in Building 1, Mixer Room, March 8, 2013

Topics discussed included:

1) A recent report in Cell Stem Cell showing that transplantation of human astrocytes into neonatal mouse brains results in mature mice that learn more rapidly:

Journal reference:  Han et al. Forebrain engraftment by human glial progenitor cells enhances synaptic plasticity and learning in adult mice. Cell Stem Cell, 2013; DOI:10.1016/j.stem.2012.12.015

2) The curriculum of Super Science High Schools in Japan

Science Buzz Lunch, Building 1, Mixer Room, March 4, 2013

Science Buzz Lunch, Building 1, Mixer Room, March 4, 2013

Topics discussed included:

1)  Ranking of Japanese prefectures according to longevity of males and females living there. Nagano Prefecture has the greatest longevity for females and males. Aomori Prefecture has the shortest. Contributing factors may include diet, alcohol consumption, and daily activities of the elderly.

2) Girls' Day Festival  (March 3rd) as celebrated at Shimogamo Jinja in Kyoto (with paper dolls floating away on the river to take away sickness from girls).

3) Plum tress are blossoming in Kyoto and Osaka.

Science Buzz Lunch in Mixer Room, Building 1, 2-25-2013

Science Buzz Lunch in Mixer Room, Building 1, 2-25-2013

Topics discussed included:

1)  The recent paper published in The American Naturalist  by Anthony R. Raffert et al. titled

Limited Oxygen Availability in Utero May Constrain the Evolution of Live Birth in Reptiles

2) A news article (titled "Two Minutes to Impress") published recently in Nature (Careers Section) about how researchers should compose a pithy "elevator speech" for very briefly (2 minutes) explaining their research to other scientists, potential employers, non-scientist acquaintences, visitors to their lab, etc. A different speech should be devised for these different types of listener, and just a few key points should be presented (and can be chosen and refined and memorized in advance).  

Science Buzz Lunch in Mixer Room, Building 1, February 4, 2013

Science Buzz Lunch in Mixer Room, Building 1, February 4, 2013

Topics discussed included:

1) The thesis topics of Division of Biological Sciences Master's degree candidates in lunch participants' labs, ranging from a survey of nematode parasites in skinks in the Japanese main islands, to the evolution of UPR (unfolded protein response) components from single-cell fungi through vertebrates, to the roles of Piwi proteins and piRNAs in planarian regeneration.
Master's degree candidates from the Department of Biophysics will give short presentations of their work (in Japanese) tomorrow.

2) The paper  "Dung Beetles Use the Milky Way for Orientation" by Marie Dacke et al. in the most recent Current Biology, Dung beetles are the first animals (other than humans) reported to use the Milky Way to guide their navigation.

3) The papers

Spatiotemporal Regulation of Epithelial-Mesenchymal Transition Is Essential for Squamous Cell Carcinoma Metastasis, by Jeff H. Tsai et al.

and
Metastatic Colonization Requires the Repression of the Epithelial-Mesenchymal Transition Inducer Prrx1  by Oscar H. Ocana et al.,

both published in the December 11, 2012 issue of Cancer Cell

These papers establish that plasticity of the cancer cells enabling an EMT followed by MET transition is required for the establishment of metastases by carcinomas

Science Buzz Lunch in Mixer Room, Bldg 1, Jan. 28, 2013

Science Buzz Lunch in Mixer Room, Bldg 1, Jan. 28, 2013

Topics discussed included:

1) A report in this week's Nature titled:  Japan's stimulus package showers science with cash

2)  A News & Views article in this week's Nature titled:  The to and fro of tumour spread. It features two papers in the most recent issue of Cancer Cell shedding light on the roles of cellular transitions between the epithelial and mesenchymal states during cancer metastasis, These papers reveal that cancer metastasis requires not only an initial EMT transition to escape the tumor site, but also a subsequent MET transition to establish new tumors at new sites. This provides insights into which cellular processes should be targeted in cancer treatment.

Science Buzz Lunch in Mixer Room, Bldg 1, Jan. 21, 2013

Science Buzz Lunch in Mixer Room, Bldg 1, Jan. 21, 2013

Topics discussed included:

1) Highlights of the International Biogeography meeting in Miami last week, including studies of the relationship between population differentiation and dispersal duration of murine species

    Sightings of one Green Anole on each coconut tree on the campus of          Miami International University

2) The paper in Nature this week by Jesse N. Weber, Brant K. Peterson and Hopi E. Hoekstra  about the use of genetic crossing and gene sequencing studies to identify the genes responsible for complex burrow evolution in Peromyscus mice

Science Buzz Lunch in Mixer Room, Bldg 1, Jan. 15, 2013

Science Buzz Lunch in Mixer Room, Bldg 1, Jan. 15, 2013

Topics discussed included:

1) The first deep-sea (about 800 meters depth) films made recently of giant squid (probably the kraken of ancient sea monster lore) near the Ogasawara Islands about 1000 kilometers south of Tokyo

2) Attendees' favorite scientific meetings, and how those good meetings differ from less rewarding meetings

Science Buzz Lunch in Mixer Room, Bldg 1, Jan. 8, 2013

Science Buzz Lunch in Mixer Room, Bldg 1, Jan. 7, 2013

Topics discussed included:

The probable inappropriateness of using brain volume or brain mass relative to body mass as a measure of a species' relative intelligence 

Science Buzz Lunch in Mixer Room, Bldg 1, Jan. 7, 2013

Science Buzz Lunch in Mixer Room, Bldg 1, Jan. 7, 2013

Topics discussed included:

1) A recent paper in Cell Stem Cell  12, 114 - 126  (Jan. 3, 2013)

by Toshinobu Nishimura et al. titled

Generation of Rejuvenated Antigen-Specific T Cells by Reprogramming to Pluripotency and Redifferentiation

We discussed potential applications of the iPS cell technology for adoptive immunotherapy.

2) A recent paper by Cullen et al. in PLoS ONE titled

Evolutionary Novelty versus Exaptation: Oral Kinematics in Feeding versus Climbing in the Waterfall-Climbing Hawaiian Goby Sicyopterus stimpsoni

which explains how the extreme waterfall-climbing behavior of this fish might have evolved by exaptation of an oral sucker used for feeding on algae