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Biology major Hannah Salim receives Goldwater Fellowship and authors a review article

Biology major Hannah Salim ’09 has been awarded a Barry M. Goldwater Scholarship, which covers the cost of tuition, fees, books, room and board up to a maximum of $7,500 per year. She and Prof. André Cavalcanti have also published a review of the factors that affect why organisms use some codons more frequently than other synoymous codons.

• Salim, H.M.W., and A.R.O. Cavalcanti. 2008. Factors influencing codon usage bias in genomes. J. Braz. Chem. Soc. 19: 257-261. [pdf]

The secret code of ciliates

In the April issue of Protist Hannah Salim, Biology ’09; Karen Ring, Molecular Biology ’07; and Prof. André Cavalcanti report a strong bias toward low GC codons in two ciliated protozaons that have reassigned ‘stop’ codons to glutamine. They find, however, that this bias is smaller in highly expressed genes.

• Salim, H.M.W., K.L. Ring, and A.R.O. Cavalcanti. 2008. Patterns of codon usage in two ciliates that reassign the genetic code: Tetrahymena thermophila and Paramecium tetraurelia. Protist 159: 283-298. [abstract]

Women on ice!

An article in the Spring 2008 issue of AWIS magazine by Prof. Laura Hoopes features women scientists who are conducting climate change research in the Arctic, including our own Prof. Nina Karnovsky.

• Hoopes, L.L.M. 2008. Women on ice: Detecting global warming in the Arctic. AWIS Magazine 37(1): 16-19.

Prof. Johnson receives grant

Prof. Karl Johnson has been awarded a $10,000 grant from the SOMAS (Support Of Mentors And their Students) program. The program, which is sponsored by the National Science Foundation and Davidson College, supports the research of new neuroscience faculty and their students at predominantly undergraduate institutions.

Currents of climate change

At the 2008 Ocean Sciences meeting of the American Society of Limnology and Oceanography March 2-7 in Orlando, FL, Prof. Nina Karnovsky presented a paper showing how studies in the Greenland Sea can help to model future effects of climate change on upper trophic predators in subpolar seas. Pomona students Allison Bailey ’07 and Laurel McFadden ’06 were co-authors on the paper.

• Karnovsky, N.M., A. Harding, D. Gremillet, W. Walkusz, J. Welcker, J. Wiktor, H. Routti, S. Kwasniewski, A. Bailey, and L. McFadden. 2008. Contrasting conditions in the Greenland Sea: Implications for energy transfer to higher trophic levels. 2008 Ocean Sciences Meeting. [abstract]

Seabirds take a dive!

Prof. André Cavalcanti, Prof. Nina Karnovsky, Zach Brown ’07, and co-authors J. Welcker, and A. Harding, presented the paper “A Multi-Colony Comparison of the Diving Behavior of Little Auks (Alle alle)” at the 35^th annual meeting of the Pacific Seabird Group, February 29, in Blaine, Washington.

How to help women stay in science

In the January issue of The Scientist Prof. Laura Hoopes lists 10 things men can do to help women scientists. The article has generated quite a bit of discussion, which you can read here.

• Hoopes, L.M. 2008. Help women stay in science. The Scientist 22: 69.

Need help with your blots?

Be sure to consult Prof. Laura Hoopes’ article on nucleic acid blotting in Current Protocols: Essential Laboratory Techniques (Toronto: Wiley Sons, 2008), 8.2.1-8.2.24.

• Hoopes, L.M. 2008. Nucleic Acid Blotting: Southern and Northern, 8.2.1-8.2.24 in Current Protocols: Essential Laboratory Techniques Wiley & Sons, Toronto.

The old really are different from the young (yeast, that is!)

In the January issue of the Journal of Gerontology student Gloria Yiu ’08, Alejandra McCord ’07, Laty Cahoon, Alison Wise ’05, Rishi Jindal ’04, Jennifer Hardee ’05, Allen Kuo ’03, Michelle Yuen Shimogawa ’03, Prof. Laura Hoopes, and colleagues report that microarray analysis shows that old yeast alter expression of a number of pathways — they shift toward aerobic metabolism, decrease ribosomal gene expression, produce a partial stress response, increase certain DNA repair pathways, and alter regulatory proteins, among other changes.

• Yiu, G., A. McCord, A. Wise, R. Jindal, J. Hardee, A. Kuo, M.Y. Shimogawa, L. Cahoon, M. Wu, J. Kloke, J. Hardin and L.L.M. Hoopes. 2008. Pathways change in expression during replicative aging in yeast. J. Gerontol. Ser. A: Biol. Sci. Med. Sci. 63: 21-34. [abstract]

When ‘STOP’ doesn’t really mean stop!

In the ciliate protozoans Tetrahymena thermophila and Paramecium tetraurelia the ‘stop’ codons TAA and TAG don’t mean stop, they mean glutamine. In the January issue of Molecular Biology and Evolution Karen Ring, Molecular Biology ’07, and Prof. André Cavalcanti explore the evolutionary consquences of this altered coding and show that it greatly affects the amino acid substitution pattern for both closely related and highly diverged proteins.

• Ring, K.L., and A.R.O. Cavalcanti. 2008. Consequences of stop codon reassignment on protein evolution in ciliates with alternative genetic codes. Mol. Biol. Evol. 25: 179-186. [abstract]

Prof. Hoopes profiles biology educators

Prof. Laura Hoopes has begun a new feature in CBE Life Sciences Education that profiles an innovative life sciences educator in each issue. Check out the first two articles:

• Hoopes, L.L.M. 2008. Morris Maduro. CBE Life Sci. Educ. 7(1): 3-4. [html | pdf]
• Hoopes, L.L.M. 2008. H. Craig Heller. CBE Life Sci. Educ. 6(4): 275-276. [html | pdf]

Biology student Abril Iñiguez featured in Courier

The special section on “Women of Distinction,” in the January 26^th issue of the Claremont Courier featured Biology student Abril Iñiguez ’08 and her research on Hydra with Prof. Daniel Martínez.

Climate change and the arctic

Prof. Nina Karnovsky presented the results from last summer’s field season at the MariClim (Marine Ecosystem consequences of climate-induced changes in water masses off West-Spitsbergen) meeting in Tromso, Norway, on January 17-18.

• Karnovsky, N. 2008. Little Auk Research 2007 Hornsund Fjord, Spitsbergen Kap Höegh, Greenland. MariClim – Marine Ecosystem consequence of chimate changes in water masses off West-Spitsbergen. [PowerPoint presentation]

Can stable isotopes track trophic changes in seabirds?

In the Prof. Nina Karnovsky and colleagues from Alaska, Canada, Norway, and Poland have found that using stable isotope analysis to analyze trophic levels in Little Auks is more complex than previously thought. Their study, which appears in Polar Biology was published online in January.

• Harding, A.M.A., K.A. Hobson, W. Walkusz, K. Dmoch, N.J. Karnovsky, T.I. Van Pelt, and J.T. Lifjeld. Can stable isotope (δ¹³C and δ¹⁵N) measurements of Little Auk (Alle alle) adults and chicks be used to track changes in high-Arctic marine foodwebs? Polar Biology in press. [abstract]

Drosophila mutation affects synaptic transmission

Prof. Karen Parfitt, Sarah Jenkins ’08, Joyce Kim ’09, Laura Johnson ’08, and Kelly Sinnott, Scripps ’08, presented a poster, “Synaptic Transmission Is Altered in Palmitoyl Protein Thioesterase-1 (PPT-1)-Mutant Drosophila melanogaster,” at the Nature Neuroscience symposium on Biological Complexity: Genes, Circuits, and Behavior, held at the Salk Institute in January.

Getting the signal out

When a nerve signals a muscle to contract, the nerve impulse causes neurotransmitters to be released from vesicles into the synapse between the nerve terminal and the muscle to carry the signal on to the muscle. Proper transmission of the signal depends on having the neurotransmitter vesicles all lined up and ready for action in a specialized area — the ‘active zone’. How this zone is formed has been a mystery, but new findings have revealed key roles for certain proteins in assembling the active zone. These recent findings are reviewed by Pomona Biology student Emily Stryker ’07 and Prof. Karl Johnson in the November issue of the Journal of Cell Science.

• Stryker, E., and K.G. Johnson. 2007. LAR, liprin α and the regulation of active zone morphogenesis. J. Cell Sci. 120: 3723-3728. [abstract | html | pdf]

A profile in courage

In June 2007 Prof. Frank Douglas resigned from senior positions at MIT because of complex, insidious discrimination against minorities within that institution. Prof. Laura Hoopes discusses his decision in the Fall 2007 issue of AWIS magazine. You can read Douglas’s letter and more reaction here.

• Hoopes, L.L.M. 2007. Courageous decision of Frank Douglas. AWIS Magazine 36(4): 20-22.

Moore Foundation Grant supports Biology instrumentation

A new $730,000 equipment upgrade grant from the Gordon and Betty Moore Foundation will provide professors and their students in chemistry, biology, physics, and astronomy with state-of-the-art instrumentation for research and teaching.

• $730,000 in Grants Awarded to Pomona Science Departments - The Student Life article
• Grants Awarded - Gordon and Betty Moore Foundation

Sorting out sea anemones

Prof. Daniel Martínez, Pomona biology student Spencer McKinstry ’05, and colleagues from Universidad Nacional de Mar del Plata, Argentina, have found that the sea anemones called Aulactinia marplatensis and Aulactinia reynaudi are actually members of a single species, which will be called Aulactinia marplatensis. Their study, which used both morphological characters and sequence analysis of ribosomal RNA genes to establish the species’ identity, is published in the November issue of Hydrobiologia.

• Acuña, F.H., A.C. Excoffon, S.R. McKinstry, and D.E. Martínez. 2007. Characterization of Aulactinia (Actiniaria: Actiniidae) species from Mar del Plata (Argentina) using morphological and molecular data. Hydrobiologia 592: 249-256. [abstract | html | pdf]

Clearings in sea ice — important, but not all the same

A new book on polynyas — persistent open water areas in sea ice — includes a chapter by Prof. Nina Karnovsky and colleagues from J.T. Harvey and Associates, San Jose, CA, and Hollings Marine Laboratory, College of Charleston, SC. Focusing on three case studies — the Ross Sea Polynya in Antarctica, the North Water Polynya between Greenland and the Canadian mainland, and the Northeast Water Polynya off the east coast of Greenland — they report that production in all three polynyas is important for supporting top-trophic predators, such as sea birds, penguins, seals, and whales, but site-specific factors create considerable differences among the three.

• Karnovsky, N., D.G. Ainley, and P. Lee. 2007. The impact and importance of production in polynyas to the top-trophic predators: Three case histories. Chapter 12 in W.O. Smith, Jr. and D.B. Barber, eds. Polynyas: Windows to the World, Elsevier, Amsterdam. [Elsevier | Amazon (searchable)]

Meeting the goals of BIO2010

In the Summer issue of Cell Biology Education Prof. Laura Hoopes and colleagues in the Genome Consortium for Active Teaching (GCAT) report on how GCAT is meeting the goals of BIO 2010, a report by the Committee on Undergraduate Education convened by the National Research Council, on preparing research biologists for the 21^st century. GCAT’s program focuses on using DNA microarrays to bring modern genomics to undergraduate students in both student research and research-based laboratory courses. The GCAT program, which has already reached over 9,000 undergraduates, furthers the reports’s goals of a more interdisciplinary, research-based undergraduate laboratory experience and developing faculty expertise in modern disciplines such as genomics and bioinformatics.

• Campbell, A.M., M.L.S. Ledbetter, L.L.M. Hoopes, T.T. Eckdahl, L.J. Heyer, A. Rosenwald, E. Fowlks, S. Tonidandel, B. Bucholtz, and G. Gottfried. 2007. Genome Consortium for Active Teaching (GCAT): Meeting the Goals of BIO2010. Cell Biology Education 6: 109-118. [abstract | html | pdf]
• Committee on Undergraduate Biology Education to Prepare Research Scientists for the 21st Century. 2000. BIO 2010: Transforming Undergraduate Education for Future Research Biologists. The National Academies Press, Washington, DC. [National Academies Press Openbook]

Pomona biologists blog their Arctic expedition

Prof. Nina Karnovsky and Pomona biology students Nell Baldwin ’09, Derek Buchner ’09 and Zachary Brown ’07 are documenting their Arctic summer research project in a blog. They are studying how the foraging and reproductive behavior of Little Auks (Alle alle) is affected by perturbations in water temperature, as might occur with changes in climate. The Karnovsky group is studying Little Auks on the Norwegian island of Spitsbergen and will compare their results with those of a collaborating group studying Little Auks in Greenland.

• Arctic Auks - The Karnovsky Group blog
• Arctic adventure: Pomona researchers spend summer hard at work on windswept Norwegian fjord - Pomona College News Feature

Prof. Emeritus Carlquist honored at symposium

A symposium in honor of Prof. Emeritus Sherwin Carlquist was held at the 2007 Botany & Plant Biology Joint Congress held July 7-11 in Chicago. The introduction to the symposium notes Carlquist’s long and distinguished career, including contributions in “island biogeography, the systematic value of comparative wood anatomy, and the ecology of wood structural/functional relationships.”

• A Symposium in Honor of Sherwin Carlquist - Abstract for the Symposium introduction

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