What is a genome? - a review from Aaron Goldman

Just published in the open access journal PLOS Genetics, with 3816 views in its first week on the site (open access truly does have a far reach!):

Goldman, Aaron David, Assistant Professor of Biology, and Laura F. Landweber. 2016. "What is a Genome?" PLOS Genetics 12 (7): e1006181.

Partial Abstract:
The genome is often described as the information repository of an organism... Several emerging areas of research demonstrate that this definition is an oversimplification. Here, we explore ways in which a deeper understanding of genomic diversity and cell physiology is challenging the concepts of physical permanence attached to the genome as well as its role as the sole information source for an organism.

Genotype-environment interactions in Arabidopsis thaliana - new publication from A. Roles

Roles, Angela J., Assistant Professor of Biology; Rutter, M.T., Dworkin, I., Fenster, C.B., and Conner, J.K. (2016). Field measurements of genotype by environment interaction for fitness caused by spontaneous mutations in Arabidopsis thaliana. Evolution 70, 1039-1050.

Journal banner @ Wiley Online

Partial abstract: As the ultimate source of genetic diversity, spontaneous mutation is critical to the evolutionary process. The fitness effects of spontaneous mutations are almost always studied under controlled laboratory conditions rather than under the evolutionarily relevant conditions of the field. We studied the fitness effects of 25 generations of accumulated spontaneous mutations in Arabidopsis thaliana in two geographically widely separated field environments, in Michigan and Virginia. We observed genotype-environment interactions in the fitness effects of new mutations, such that the effects of mutations in Michigan were a poor predictor of their effects in Virginia and vice versa. In particular, mutational variance for fitness was much larger in Virginia compared to Michigan. This strong genotype-environment interaction would increase the amount of genetic variation maintained by mutation-selection balance.
Full text online @OhioLINK Electronic Journal Center

Evolution - journal home page @Wiley Online Library

Learn more about the use of A. thaliana (a small flowering weed) as a model organism for genetic studies at The Ohio State University Arabidopsis Biological Resource Center.

Arabidopsis Protocols, 2nd ed., is online @Springer ebooks [access through OBIS]

Wildlife corridors - update from Sierra Club

If You Build It, They Will Come: Our highways and interstates present one of the greatest threats to wildlife—that's where critter corridors come in. --Sierra Club

Read more about wildlife management with these recent titles:

Handbook of road ecology / edited by Rodney van der Ree, Daniel J. Smith, and Clara Grilo [online at Wiley, access through OBIS]

The carnivore way : coexisting with and conserving North America's predators / by Cristina Eisenberg
[OBIS record] also online at Springer ebooks

The spine of the continent : the most ambitious wildlife conservation project ever undertaken / Mary Ellen Hannibal [OBIS record]

Publications from I. Rew (Class of 2017) and M. Moore (Biology)

Billups, K., C. Hudson, H. Kunz, and Isabelle Rew (class of 2017). 2016. "Exploring Globorotalia truncatulinoides Coiling Ratios as a Proxy for Subtropical Gyre Dynamics in the Northwestern Atlantic Ocean during Late Pleistocene Ice Ages." Paleoceanography 31 (5): 553-563.

From the abstract: Our results support that the coiling direction of this species is sensitive to variations in hydrography of the western boundary of the subtropical gyre. Because of the association between G. truncatulinoides (s) and precession maxima in both hemispheres, results support the importance of oceanic heat transport in half-precession climate variability in the North Atlantic.
[full-text online @ Wiley]

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Lewis, Emily M., Jeremie B. Fant, Michael J. Moore, Associate Professor of Biology, Amy P. Hastings, Erica L. Larson, Anurag A. Agrawal, and Krissa A. Skogen. 2016. "Microsatellites for Oenothera gayleana and O. hartwegii filifolia (Onagraceae), and their Utility in Section Calylophus." Applications in Plant Sciences 4 (2): 1500107.

Conclusions: The microsatellite loci characterized here are the first developed and tested in Oenothera sect. Calylophus. These markers will be used to assess whether pollinator foraging distance influences population genetic parameters in predictable ways.

[full-text online @ BioOne]

Citral shown to decrease cancer cell proliferation (new publication from R.J. Whelan)

New article from Rebecca Whelan, Associate Professor, Department of Chemistry and Biochemistry:

Modulation of oxidative stress and subsequent induction of apoptosis and endoplasmic reticulum stress allows citral to decrease cancer cell proliferation.

Kapur, Arvinder; Felder, Mildred; Fass, Lucas; Kaur, Justanjot; Czarnecki, Austin; Rathi, Kavya; Zeng, San; Osowski, Kathryn Kalady; Howell, Colin; Xiong, May P.; Whelan, Rebecca J.; Patankar, Manish S.

Scientific Reports, published online June 8 2016,  Article number 27530.  Open access at PubMedCentral.

Partial abstract:
"The monoterpenoid, citral, when delivered through PEG-b-PCL nanoparticles inhibits in vivo growth of 4T1 breast tumors. Here, we show that citral inhibits proliferation of multiple human cancer cell lines. ...This study indicates that citral in PEG-b-PCL nanoparticle formulation should be considered for treatment of breast and other tumors."

More about Scientific Reports, a NatureResearch Journal.

Indulging in nostalgia... the old Physics Reading Room and Kettering Science Library

Before the Science Center was constructed, the Physics Reading Room existed in the northeast corner of the second floor of Wright, and the Class of 1904 Science Library was crammed into the southeast corner of the first floor of Kettering (in the Chemistry wing of Kettering, razed after the north wing of the Science Center was completed).  Every summer, we were devoted to the tasks of preparing thousands of journal volumes for binding, transferring an equal number of older volumes to the old Carnegie Library for off-site storage, shifting the remaining collections and shelving the newly bound journal volumes on their return.  As the number of print subscriptions has dwindled from 365* to 65 (thereabouts), we are freed of the tyranny of shifting, always shifting, and the tedious labor of wheeling very full book trucks across the street, navigating doors, uneven sidewalks and thresholds, to maneuver in the elevator and the dark, musty stacks of Carnegie.  The Science Center is the perfect home for today's consolidated Science Library.  Come enjoy our lovely setting and peruse the new book area.  So many new books arrived in June!

*Why the decrease in print subscriptions?  They're all online, and oh so convenient.  We keep a core of titles in print that are really helpful for browsing - for learning awesome stuff about things you didn't know you didn't know.  It's a very different experience than simply finding that for which you're searching.  Pick up something new and you're sure to encounter a new idea, a fresh perspective, a spark for your imagination.  See you soon.

Too many to describe, come look!

The annual flood of new books arrived with the first week of June, as usual.  There are so many interesting titles!  Here are just a few, with links to OBIS for the full catalog record:

In our own image: savior or destroyer? The history and future of artificial intelligence.  OBIS

The new cosmos : answering astronomy's big questions.  OBIS

Hydrogen-bonded capsules : molecular behavior in small spaces.  OBIS

A world from dust : how the periodic table shaped life.  OBIS

Water as a social opportunity.  OBIS

Creating Africas : struggles over nature, conservation and land.  OBIS

Evolutionary medicine.  OBIS

The human advantage : a new understanding of how our brain became remarkable.  OBIS

Enjoy your summer reading!

Summer Reading - inside or out?

Whether you prefer the sunny tables on the Science Center piazza or the cool comfort of the science library, the time for summer reading has arrived.  Browse the new books at our front window, where views to the north and south are seen simultaneously.  So many to consider:

Take a road trip with a Roadside Geology... guide book;
Tackle history of science with books on Kepler, the Royal Society, and Aristotle;
Learn what inspired Audubon and F. W. Taylor;
Enjoy little know facts about Melon and Fats;
Consider possibilities for REDD to mitigate climate change.

See you soon!

45th Class reunion discussion groups gather in science library

What a delight to see so many alumni in the science library!  We are very happy to host the discussion groups here - welcome to all.  

Craters, spherules and ancient terrestrial impactors

New publication from Geology Professor Bruce Simonson:

Spherule layers, crater scaling laws, and the population of ancient terrestrial impactors

Johnson, Brandon C.; Collins, Gareth S.; Minton, David A.; Bowling,
Timothy J.; Simonson, Bruce M.; Zuber, Maria T.

ICARUS, 271 350-359; 10.1016/j.icarus.2016.02.023 JUN 1 2016

Partial abstract:
"Ancient layers of impact spherules provide a record of Earth's early bombardment history. Here, we compare different bombardment histories to the spherule layer record and show that …the flux of large impactors …was likely 20-40 times higher than today." (C) 2016 Elsevier Inc.
Subscriber access at sciencedirect.com

Extended Hours for Reading Period

photo: Maya Iverson '12

Holy cow, how is this the last week of classes already?  Sure, February 1 and the start of the semester seem like ages ago... still, the first week of May feels SO early for the last week of classes.  As Reading Period begins this weekend, we will be open until 10 pm on Saturday.  That's the only extension of science library hours for Reading Period through Exams.

We're always willing to help, let us know if you have questions about finding sources for final projects and papers!  Contact Alison Ricker [aricker at oberlin.edu], science librarian, or chat with ObieSci whenever the library is open.

Jason Belitsky and undergraduate research profiled by OhioLINK

OhioLINK frequently highlights researchers at OhioLINK institutions, illustrating the essential contribution of OhioLINK resources and the consortium's importance for successful research and teaching in the state.  Associate Professor of Chemistry Jason Belitsky is featured on the OhioLINK news page this month, with a focus on work in his lab on melanin and its potential role for water filtration - work that continues to involve student researchers.

"Through the research OhioLINK supports [with library resources], Belitsky and his students have found the same chemical in your hair that determines its color could soon be used to filter water."  Read more.

New publication by Wiscons, Zeller and Rowsell

pubs.acs.org/covergifs/cgdefu/title.gif

Wiscons, Ren A. ('15); Zeller, Matthias; Rowsell, Jesse L. C. ✝  2016. Anion Exchange in Cationic Frameworks: Structures of Channel-Forming Triarylpyrylium Tetrafluoroborate Salts.

CRYSTAL GROWTH & DESIGN, 16 (4):2201-2210; 10.1021/acs.cgd.6b00005 APR 2016
subscriber access at American Chemical Society Publications

Summer road trip? Take along a roadside geology guide.

Three new Roadside Geology books arrived in this week's new book shipment:

• Roadside geology of Colorado
• Roadside geology of Oregon
• Roadside geology of Utah

 joining the 30 or so books for other states in our collection.  These books are a great way to learn more about the physical environment you may be speeding through, and are a good excuse to stop and appreciate the locale - to enjoy the journey as much as the destination.

While you're considering landforms and formations, you could also identify birds, mammals, reptiles, snakes, invertebrates...  the library is brimming with helpful guides, both regional and world-wide in focus, to animals in various ecosystems.  Plants, too, for that matter!  Any currently enrolled student (as well as faculty and staff) who will be returning in the fall is welcome to borrow books over the summer.  Just ask!

Crayfish conquistadors, salamanders and ovarian cancer biomarkers: presentations by A. Roles, A. Blackman, and R. Whelan

New publications/presentations from Oberlin authors (noted in bold text), as indexed in Web of Science:

SICB.org

Freshwater conquistadors: The influence of hybridization and watershed structure in the invasion of the rusty crayfish into the native range of the congeneric Sanborn's crayfish in north-central Ohio.
Roles, Angela J.  (Assistant Professor of Biology)

Source:
INTEGRATIVE AND COMPARATIVE BIOLOGY, 56 E187-E187; 1 MAR 2016
Session abstract, Annual Meeting of the Society for Integrative and Comparative-Biology (SICB).  January 3-7, 2016; Portland, OR

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Do salamanders respond morphologically to introduced species?
Blackman, Augie R. (current junior); Novarro, A. J.

Source:
INTEGRATIVE AND COMPARATIVE BIOLOGY, 56 E261-E261; 1 MAR 2016
Poster Abstract, Annual Meeting of the Society for Integrative and Comparative-Biology (SICB).  January 3-7, 2016; Portland, OR

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Identification of nucleic acid aptamers for ovarian cancer biomarkers using multiple selection modes and high-throughput sequencing.

Whelan, Rebecca J. (Associate Professor of Chemistry); Kapur, Arvinder; Felder, Mildred; Shallcross, Jamie (OC '14); Patankar, Manish S.

Source:
CLINICAL CANCER RESEARCH, 22 2 JAN 15 2016
Abstract B42: AACR Special Conference: Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; October 17-20, 2015; Orlando, FL

Earth Day interview with Lab Girl author Hope Jahren

Catalog record in OBIS

NPR Morning Edition's Renee Montagne spoke this morning with geobiologist Hope Jahren about her book Lab Girl (now in new book processing, heading to the science library).  Jahren spoke eloquently about her experience of being the only female in her field (and lab) and the challenges that presented, as well as her commitment to guiding young women through similar challenges with more support and encouragement than she received.  As a scientist who studies plants, seeds and soil, she also expressed beautifully the role of trees in ecosystems, and implored listeners to plant a tree and "choose wisely."  A tree becomes a companion through life, doing so much for all forms of life in its environs.  To paraphrase, Jahren concluded by stressing, "I'm not saying, 'save the trees;' rather, that trees can save us."  Listen.

Jahren's words are a reminder to continue nurturing the tiny lilac tree I planted last year around Earth Day.  I'm happy to see it is sprouting new leaves this spring, sheltered on the south side of the house.

Read about trees in a changing environment (ebook with the same title) at SpringerLink.

Fascinating stuff on the new book shelf

What's on the new book shelf?

murder, skeletons, misinformation
spectroscopy, nerves, sexual selection
geophysics, genome, Jurassic plate rotation...

and so much more.

It never fails - a shipment of fantastic reading arrives just at the point in the semester when everyone is thoroughly engaged in required reading for courses and papers or stretched to the limit by rehearsals, performances, lectures and athletics.  April is so full of life, challenge and opportunity - come see your opportunities for yet more wonderful reading, just added to the new book shelf.

Laskowski contributes to "Insights" section of J Exp Bot

http://tinyurl.com/JExpBot

Scheres, Ben and Marta Laskowski, Professor of Biology. 2016. "Root Patterning: It Takes Two to Tangle." Journal of Experimental Botany 67 (5): 1201-1203. [review].  "The mechanisms that pattern lateral root primordia are essential for the elaboration of root system architecture, a trait of key importance for future crop breeding. But which are most important: periodic or local cues? In this issue of Journal of Experimental Botany (pages 1411-1420), Kircher and Schopfer manipulate growth direction to demonstrate the importance of both sources of patterning information."

Access at publisher's site or
OhioLINK Electronic Journal Center

Love Your Library During National Library Week

http://tinyurl.com/ALAbutton

Tell us what you love about the science library!  Spread a little cheer during National Library Week.  Look for the blue entry box at the circulation desk (under the hanging air plant). We'll read all of the entries on April 17 and post some of them here.   UPDATE: see the comment from Alison.

Top ten things we love about our library users:

9. Seeing you work together in group study rooms.
8. Knowing you're comfortable enough to nap at the window seats.
7. Cleaning up after yourself (gold stars for you!).
6. Remembering to take your print job with you.
5. Returning library materials on time ;-) -- so nice.
4. Leaving the cutting blade down when you're finished with the cutting board (that thing looks lethal).
3. Watching you help a friend figure out the scanning procedure.
2. Handing your ID to us with a friendly smile when borrowing items. 

And the absolute best thing:
1. Asking interesting questions about fascinating subjects.  That makes our day.

So ask away! Love your library all year long, and share the joy during National Library Week.

Suing the Federal Government and Fossil Fuel Industry on Behalf of Future Generations

From Our Children's Trust:

April 8, 2016:  Today, U.S. Magistrate Judge Thomas Coffin of the federal District Court in Eugene, OR, decided in favor of 21 young Plaintiffs, and Dr. James Hansen on behalf of future generations, in their landmark constitutional climate change case brought against the federal government and the fossil fuel industry. The Court’s ruling is a major victory for the 21 youth Plaintiffs, ages 8-19, from across the U.S. in what Bill McKibben and Naomi Klein call the “most important lawsuit on the planet right now.”

OBIS record

The decision by Judge Coffin coincided, incidentally, with the final day of Oberlin's first Global Issues Symposium: Climate Change Consequences, possibly as we were in the midst of discussion on "Connecting the Global and Local: Assessing the Future of Climate Resilient Action."

It is an interesting coincidence, given our focus on climate change consequences for indigenous peoples and Judge Coffin's words regarding those consequences on young people: ..."the intractability of the debates before Congress and state legislatures and the alleged valuing of short term economic interest despite the cost to human life, necessitates a need for the courts to evaluate the constitutional parameters of the action or inaction taken by the government. This is especially true when such harms have an alleged disparate impact on a discrete class of society." [page 8 of the ruling]

Do you avoid serious consideration of climate change and what it  means for your future?  Find out why: Don't even think about it : why our brains are wired to ignore climate change.