Thursday, January 03, 2019

New publications by FitzGerald and Howard


-->
 Stephen A. FitzGerald, Professor of Physics
publisher's site
       
Kapelewski, M. T., T. Runcevski, J. D. Tarver, H. Z. H. Jiang, K. E. Hurst, P. A. Parilla, A. Ayala, T. Gennett, S. A. FitzGerald, C. M. Brown, and J. R. Long. 2018. Record High Hydrogen Storage Capacity in the Metal-Organic Framework Ni-2(m-dobdc) at Near-Ambient Temperatures. Chemistry of Materials 30:8179-8189.
Access from OhioLINK Electronic Journal Center

Christopher D. Howard, Assistant Professor of Neuroscience
publisher's site
       
Schuweiler, D. R., C. D. Howard, E. S. Ramsson, and P. A. Garris. 2018. Improving in Situ Electrode Calibration with Principal Component Regression for Fast-Scan Cyclic Voltammetry. Analytical Chemistry 90:13434-13442.

Access from OhioLINK Electronic Journal Center

Thursday, December 20, 2018

Faculty publish in Astrophysical Journal and Physics of the Dark Universe

Recent publications co-authored by faculty in Physics and Astronomy:

Scudder, Jillian M.
Pan H, Lin L, Hsieh B, Xiao T, Gao Y, Ellison SL, Scudder JM, Barrera-Ballesteros J, Yuan F, Saintonge A, Wilsons CD, Hwang HS, De Looze I, Gao Y, Ho LC, Brinks E, Mok A, Brown T, Davis TA, Williams TG, Chung A, Parsons H, Bureau M, Sargent MT, Chung EJ, Kim E, Liu T, Michalowski MJ, Tosaki T.
The effect of galaxy interactions on molecular gas properties. Astrophysical Journal 2018 DEC 1;868(2):132.
Stalnaker, Jason E.
Afach S, Budker D, DeCamp G, Dumont V, Grujic ZD, Guo H, Kimball DFJ, Kornack TW, Lebedev V, Li W, Masia-Roig H, Nix S, Padniuk M, Palm CA, Pankow C, Penaflor A, Peng X, Pustelny S, Scholtes T, Smiga JA, Stalnaker JE, Weis A, Wickenbrock A, Wurm D.
Characterization of the global network of optical magnetometers to search for exotic physics (GNOME). Physics of the Dark Universe 2018 DEC;22:162-80.

Stinebring, Daniel R.
Brook PR, Karastergiou A, McLaughlin MA, Lam MT, Arzoumanian Z, Chatterjee S, Cordes JM, Crowter K, DeCesar M, Demorest PB, Dolch T, Ellis JA, Ferdman RD, Ferrara E, Fonseca E, Gentile PA, Jones G, Jones ML, Lazio TJW, Levin L, Lorimer DR, Lynch RS, Ng C, Nice DJ, Pennucci TT, Ransom SM, Ray PS, Spiewak R, Stairs IH, Stinebring DR, Stovall K, Swiggum JK, Zhu WW. 
The NANOGrav 11-year data set: Pulse profile variability. Astrophysical Journal  2018 DEC 1;868(2):122.




Friday, November 23, 2018

Thompson, Katz and Sheehan: Chemical comparison of Prunus africana bark and pygeum products marketed for prostate health.

New publication from Rob Thompson, Professor of Chemistry, with senior Daniel Katz and Brendan Sheehan (OC'18, biochemistry).

Chemical comparison of Prunus africana bark and pygeum products marketed for prostate health.
Journal of Pharmaceutical and Biomedical Analysis Vol. 163, 30 January 2019, pp. 162-169

Access this title at the OhioLINK Electronic Journal Center or at the publisher's site, Elsevier's ScienceDirect.

From the introduction and conclusions:
"Pygeum is the powdered bark of Prunus africana (also called Pygeum africanum), an evergreen tree that grows across the mountainous regions of Africa. Both the powder and a lipophilic extract are sold commercially under the same name... Ingestion of pygeum has been found to inactivate the androgen receptor and inhibit prostate cancer cell growth."
[Conclusions after chemical analysis of samples of both bark and pygeum powder:]
Harvesting Prunus africana bark. 
Credit: SouthWorld, May 1, 2016
"The amounts per gram of the BPH-active compounds atranorin, atraric acid, total ferulic acid, and total beta-sitosterol and the fractions of free beta-sitosterol were quite different in bark from Prunus africana and in the contents of commercial pygeum capsules, contents purported to be derivatives of the same bark. This was unexpected and suggested that the BPH-active components in commercial pygeum may not be fully sourced from natural materials as labeled. Also unexpected was that no N-butylbenzene sulfonamide was found in any sample. The variation in the composition of four bark samples, two of which were botanical reference materials, demonstrated the need for a phytochemical standard for pygeum, with reference values for the BPH-active compounds studied here."

Tuesday, September 18, 2018

What Neil deGrasse Tyson Thinks Higher Ed Gets Wrong


In this interview with The Chronicle of Higher Education, Tyson discusses "how to explain science to the masses and [rips] into what he sees as higher education’s misguided incentive system, valuing research over teaching and public service and not creating space for people like him to flourish. 'It’s a sad fact,' he says, 'for the future of science in America.' "

Astrophysics for People in a Hurry is one of Tyson's most recent books.  The science library's copy is checked out, but there are plenty of other copies to borrow through OhioLINK.

Wednesday, August 08, 2018

Jordan Price and students publish in Journal of Bacteriology

New publication by Jordan Price, Assistant Professor of Biology, with students Kallie Jiang and Abby Galantowicz, and collaborators at Univ Calif Berkeley:

Price, Jordan V.; Jiang, Kallie; Galantowicz, Abby; Freifeld, A., & Vance, R. E. (2018). Legionella pneumophila is directly sensitive to 2-deoxyglucose-phosphate via its UhpC transporter but is indifferent to shifts in host cell glycolytic metabolism. Journal of Bacteriology, 200(16), 176. doi:10.1128/JB.00176-18 ER
Importance of this research:  "We explored the relationship between macrophage glycolysis and replication of an intracellular bacterial pathogen, Legionella pneumophila. Previous studies demonstrated that a glycolysis inhibitor, 2-deoxyglucose (2DG), blocks replication of L. pneumophila during infection of macrophages, leading to speculation that L. pneumophila may exploit macrophage glycolysis. We isolated L. pneumophila mutants resistant to the inhibitory effect of 2DG in macrophages, identifying a L. pneumophila hexose-phosphate transporter, UhpC, that is required for bacterial sensitivity to 2DG during infection. Our results reveal how a bacterial transporter mediates the direct antimicrobial effect of a toxic metabolite. Moreover, our results indicate that neither induction nor impairment of host glycolysis inhibits intracellular replication of L. pneumophila, which is consistent with a view of L. pneumophila as a metabolic generalist."

Monday, August 06, 2018

New publications by Stinebring (Physics & Astronomy) and Moore (Biology)

Recent publications by Dan Stinebring, Francis D Federighi Professor of Physics; and Mike Moore, Professor of Biology:

Lam, M. T., Ellis, J. A., Grillo, G., Jones, M. L., Hazboun, … Daniel R. Stinebring, et al. (2018). A second chromatic timing event of interstellar origin toward PSR J1713+0747. Astrophysical Journal, 861(2), 132. 10.3847/1538-4357/aac770 ER

an Open Access journal
from Taylor & Francis
Zhu, Z., Wang, J., Cai, Y., Zhao, K., Michael J. Moore, & Wang, H. (2018). Complete plastome sequence of erythropalum scandens (erythropalaceae), an edible and medicinally important liana in china. Mitochondrial Dna Part B-Resources, 3(1), 139-140. 10.1080/23802359.2017.1413435 ER

Thursday, July 05, 2018

Angie Roles publishes in Ecology and Evolution

Blandy Experimental Farm, Boyce, Virginia
Recent research by Associate Professor of Biology Angie Roles and collaborators "assessed phenotypes associated with survival and reproductive success in over 30,000 plants representing 100 mutation accumulation lines of Arabidopsis thaliana across four temporal environments at a single field site." The authors conclude, "The combination of large environmental variance with a mean effect of mutation near zero suggests that mutations could contribute substantially to standing genetic variation."

Rutter, Matthew T., Roles, Angela J., & Fenster, Charles B. (2018). Quantifying natural seasonal variation in mutation parameters with mutation accumulation lines. Ecology and Evolution, 8(11), 5575-5585. 10.1002/ece3.4085  (Open Access)

Monday, June 18, 2018

Dan Stinebring contributes as part of the NANOGrav collaboration.

published by Institute of Physics IOPScience
Dan Stinebring, Professor of Physics and Astronomy, is one of 60+ authors, representing 41 organizations and institutions, who contributed to the research described in this recent publication:

Arzoumanian, Z., Baker, P. T., Brazier, A., Burke-Spolaor, S., Chamberlin, S. J., Chatterjee, S., . . . NANOGrav Collaboration. (2018). The NANOGrav 11 Year Data Set: Pulsar-timing Constraints on the Stochastic Gravitational-wave Background. Astrophysical Journal, 859(1), 47. 10.3847/1538-4357/aabd3b

Partial abstract:
"We search for an isotropic stochastic gravitational-wave background (GWB) in the newly released 11. year data set from the North American Nanohertz Observatory for Gravitational Waves (NANOGrav). While we find no evidence for a GWB, we place constraints on a population of inspiraling supermassive black hole (SMBH) binaries, a network of decaying cosmic strings, and a primordial GWB. For the first time, we find that the GWB constraints are sensitive to the solar system ephemeris (SSE) model used and that SSE errors can mimic a GWB signal."   Learn more about NANOGrav

Sunday, May 27, 2018

Michael Moore publishes two articles in American Journal of Botany: Tree of Life special issue

Associate Professor of Biology Michael Moore is among twenty-one collaborators on the first paper listed below, which also appears in Tree of Life virtual issue:

From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales.
Joseph F. Walker, … Michael J. Moore, Stephen A. Smith.
American Journal of Botany  105 (3): 446-462
First published: 08 May 2018 https://doi.org/10.1002/ajb2.1069  (open access)

Moore also co-authored this guide:
Using and navigating the plant tree of life.
Douglas E. Soltis, Michael J. Moore, Emily B. Sessa, Stephen A. Smith, Pamela S. Soltis.
American Journal of Botany, Special Issue
First Published: 27 April 2018
https://doi.org/10.1002/ajb2.1071 (open access)

Wednesday, May 23, 2018

Senior August Blackman publishes in Behavioral Ecology

Senior Augie Blackman is co-author of this paper resulting from research supported by the National Science Foundation Research Experience for Undergraduate program at Mountain Lake Biological Station, University of Virginia. 

Plethodon glutinosus, from Caudata.org
Salamander climbing behavior varies among species and is correlated with community composition.
Tori D Mezebish, August Blackman, Alexander J Novarro.
Behavioral Ecology, Volume 29, Issue 3, 9 May 2018, Pages 686–692,
https://doi.org/10.1093/beheco/ary022 (open access)

Partial abstract: Species coexistence is often facilitated by behavioral strategies that minimize competition for limited resources. Terrestrial, kingless salamanders (genus Plethodon) coexist in predictable assemblages of body size guilds, but little is known about the behavioral mechanisms that promote such coexistence. Here, we considered the hypothesis that Plethodon salamanders use climbing behavior to reduce competitive interactions, thereby promoting coexistence through spatial partitioning.  (As indexed in Web of Science)

Friday, May 11, 2018

Galaxy pairs and galaxy mergers featured in new publication from Jillian Scudder

https://bit.ly/2wzalwx
New publication by Jillian Scudder, Assistant Professor, Physics and Astronomy

Violino, Giulio; Ellison, Sara L.; Sargent, Mark; Coppin, Kristen E. K.;
Scudder, Jillian M.; Mender, Trevor J.; Saintonge, Amelie.  Galaxy pairs in the SDSS - XIII. The connection between enhanced star formation and molecular gas properties in galaxy mergers.


Monthly Notices of the Royal Astronomical Society, 476 (2):2591-2604; 10.1093/mnras/sty345 MAY 2018 

Published by Oxford University Press, Academic on behalf of the Royal Astronomical Society.

Thursday, May 03, 2018

Senior Jacob Rosenthal (Biology) co-authors paper in GBE

About GBE
Congratulations to Jacob Rosenthal, who co-authored this article in Genome Biology and Evolution, an open access journal published by Oxford University on behalf of the Society for Molecular Biology and Evolution:

"Patterns of Population Variation in Two Paleopolyploid Eudicot Lineages Suggest That Dosage-Based Selection on Homeologs Is Long-Lived."

AUTHORS:  Hao, Yue; Washburn, Jacob D.; Rosenthal, Jacob; Nielsen, Brandon; Lyons, Eric; Edger, Patrick P.; Pires, J. Chris; Conant, Gavin C.

GENOME BIOLOGY AND EVOLUTION  Volume: 10  Issue: 3  Pages: 999-1011
DOI: 10.1093/gbe/evy061  Published: MAR 2018
 
Partial abstract: Genes that are inherently subject to strong selective constraints tend to be overretained in duplicate after polyploidy. They also continue to experience similar, but somewhat relaxed, constraints after that polyploidy event. We sought to assess for how long the influence of polyploidy is felt on these genes' selective pressures. We analyzed two nested polyploidy events in Brassicaceae: the At-a genome duplication that is the most recent polyploidy in the model plant Arabidopsis thaliana and a more recent hexaploidy shared by the genus Brassica and its relatives... Our results paint a picture of the long-lived effects of polyploidy on plant genomes, suggesting that even yesterday's polyploids still have distinct evolutionary trajectories.

Co-authors include researchers from North Carolina State University, Cornell University, Clarion University of Pennsylvania, Michigan State University, and University of Missouri.  As indexed in Web of Science.

Monday, March 26, 2018

Brody WorkLounge Takes a Corner

Something new in the library - give it a try!  The Brody WorkLounge, by Steelcase, was delivered during Spring break.  It might become your new favorite.  Let us know what you think.  Leave a comment here or email the Science Library.  Enjoy.

Monday, March 19, 2018

New Books! So many, fantastic reading options. Take a look.

Catalog record on OBIS
So many new books have arrived in the past two months that we can't keep up with presenting them on our tumblr account.  Here are just two of the new book covers to entice you to view more, and look them up in OBIS.  Better yet, stop in the library and peruse the new book shelf!
Catalog record on OBIS


See many more book covers in a PowerPoint presentation.  Go ahead, judge a book by its cover.  Then come read it!

Recent publications: faculty, students and alumni in Biology, Chemistry and Physics

Listed below are publications from Oberlin College faculty, students and alumni, as indexed in The Web of Science during the past four weeks.  Oberlin affiliated authors are indicated in bold font: 

Fitzgerald, Stephen. A. (Professor of Physics), Shinbrough, Kai '17 ; Rigdon,  Katharine H. (current senior) ; Rowsell, Jesse L. C. (deceased, Assistant Professor of Chemistry); et al.  (2018). Temperature-programmed desorption for isotope separation in nanoporous materials. Journal of Physical Chemistry C, 122(4), 1995-2001. 10.1021/acs.jpcc.7b11048 (subscriber access)

Krasnoshchekov, S. V., Schutski, R. S., Craig, Norman C. (Emeritus Professor of Chemistry), Sibaev, M., & Crittenden, D. L. (2018). Comparing the accuracy of perturbative and variational calculations for predicting fundamental vibrational frequencies of dihalomethanes. Journal of Chemical Physics, 148(8), 084102. 10.1063/1.5020295 (open access)

Journal cover, from Science Direct (Elsevier)
Oberdick, S. D., ...  Hunt-Isaak, Ian '17 ; Pan, Hillary '17; Ijiri, Yumi (Professor of Physics); et al. (2018). Spin canting across core/shell Fe3O4/MnxFe3-xO4 nanoparticles. Scientific Reports, 8, 3425. 10.1038/s41598-018-21626-0 (open access)

Yan, M., Fritsch, P. W., Moore, Michael J. (Associate Professor of Biology), et al. (2018). Plastid phylogenomics resolves infrafamilial relationships of the Styracaceae and sheds light on the backbone relationships of the Ericales. Molecular Phylogenetics and Evolution, 121, 198-211. 10.1016/j.ympev.2018.01.004  (access at OhioLINK Electronic Journal Center)

Monday, December 11, 2017

Communicating science: two new books just received

Catalog record in OBIS
Hope Jahren, author of Lab Girl, is the guest editor of The Best American Science and Nature Writing, 2017.   Jahren is the recipient of three Fulbright Awards and is one of four scientists, and the only woman, to have been awarded both of the Young Investigator Medals given within the Earth Sciences.  Included among the essays is "Out Here, No One Can Hear You Scream," by Kathryn Joyce (Huffington Post).  It is an all too timely account of sexual harassment and hostility targeting women who work for various national and state agencies that protect America's natural heritage.

An essay by Elizabeth Kolbert, author of The Sixth Extinction and Field Notes from a Catastrophe, also appears in this volume.  "A Song of Ice" (from The New Yorker) recounts her visits to Greenland, where the effects of global warming are extraordinary and devastating.

 Catalog record in OBIS
All of the essays, as always in this series, are important reading.  Borrow the book over Winter Term - an essay a night will get you through the month of January with a lot to ponder.

Learn more about the science of science communication with this new handbook from Oxford University Press.  A key question considered in the handbook is: "What can we know empirically about the impact of the full range of scientists' linguistic choices and potential alternatives on public debate?"  Given the importance of scientific literacy (or at least realistic perceptions of scientists' work) for a healthy, just society, David Kirby's chapter on "The Changing Popular Images of Science" is very instructive.

Find these books on the new book shelf.

Monday, November 20, 2017

Elemental Haiku, by Mary Soon Lee

Haiku embedded within the Periodic Table, Aug 4. 2017.  Brilliant!  How did we miss this earlier?  Find more, and write your own on Twitter, #ChemHaiku

http://vis.sciencemag.org/chemhaiku/
If you need inspiration, check out The elements : a visual exploration of every known atom in the universe / Theodore Gray ; photographs by Theodore Gray and Nick Mann or
The secret life of the periodic table : unlocking the mysteries of all 118 elements / Dr. Ben Still.

Tuesday, November 14, 2017

Recent publications: Craig, Moore, Peters, Roles, Schmidt

Acryloyl fluoride, Chihuahuan desert gypsophiles, crayfish genome skimming, catchment sediments, autophagy pathway: key topics of recent publications. Oberlin faculty and student authors are identified in the first line of each paragraph below.

Krasnoshchekov, et al.
Norman C. Craig, Emeritus Professor of Chemistry. 

Krasnoshchekov, S. V., Craig, N. C., Koroleva, L. A., & Stepanov, N. F. (2018). Anharmonic vibrational analysis of s-trans and s-cis conformers of acryloyl fluoride using numerical-analytic van vleck operator perturbation theory. Spectrochimica Acta Part A-Molecular and Biomolecular Spectroscopy, 189, 66-79. 
Michael J. Moore, Associate Professor of Biology; Zoe Feder ’17; Helene Tiley, Junior. 

Muller, C. T., Moore, M. J., Feder, Z. Tiley, H. & Drenovsky, R. E. (2017). Phylogenetic patterns of foliar mineral nutrient accumulation among gypsophiles and their relatives in the Chihuahuan desert. American Journal of Botany, 104(10), 1442-1450. 
Maureen Peters, Associate Professor of Biology.

Hsieh, P. N., Zhou, G., Yuan, Y., Zhang, R., Prosdocimo, D. A., Sangwung, P., . . . Jain, M. K. (2017). A conserved KLF-autophagy pathway modulates nematode lifespan and mammalian age-associated vascular dysfunction. Nature Communications, 8, 914. 
Angela J. Roles, Assistant Professor of Biology.  

Grandjean, F., Tan, M. H., Gan, H. M., Lee, Y. P., Kawai, T., Distefano, R. J., . . . Austin, C. M. (2017). Rapid recovery of nuclear and mitochondrial genes by genome skimming from northern hemisphere freshwater crayfish. Zoologica Scripta, 46(6), 718-728. 
Amanda H. Schmidt, Assistant Professor of Geology.

Neilson, Schmidt, Bierman, et al.
Neilson, T. B., Schmidt, A. H., Bierman, P. R., Rood, D. H., & Gonzalez, V. S. (2017). Efficacy of in situ and meteoric be-10 mixing in fluvial sediment collected from small catchments in China. Chemical Geology, 471, 119-130. 

Friday, October 20, 2017

Estrogens and the Cognitive Symptoms of Schizophrenia

New publication from Professor of Neuroscience Jan Thornton:

McGregor, Claire, Alexander Riordan, and Janice Thornton. "Estrogens and the Cognitive Symptoms of Schizophrenia: Possible Neuroprotective Mechanisms." Frontiers in Neuroendocrinology, vol. 47, 2017, pp. 19-33, doi:10.1016/j.yfrne.2017.06.003.

From the abstract: "We review the relationship between estrogens and brain derived neurotrophic factor, neuroinflammation, NMDA receptors, GABA receptors, and luteinizing hormone. Exploring these pathways may enable novel treatments for schizophrenia and a greater understanding of this devastating disease."

https://www.journals.elsevier.com/frontiers-in-neuroendocrinology

Thursday, September 28, 2017

Translating Science Symposium, Friday September 29

The libraries have been highlighting science journalism, science writing, and science media all week long, to promote the symposium happening tomorrow.  Take a look at the science library tumblr and the main library twitter #translatingsciencesymopsium - so many good resources to feature, one week certainly can't do justice to the abundance of great science writing available online and in print.

Here is one more recommendation that can't fail to please: The Best American Science and Nature Writing, an annual series that can be found in the science library.  Check out a volume!
http://www.hmhco.com/at-home/featured-shops/popular-series/best-american-series/ba-science-nature

Published by HMH LOGO

Tuesday, September 12, 2017

New faculty publications from Mike Moore (Biology) and Lisa Ryno (Chemistry)

New publications from Michael Moore and Lisa Ryno, as found in the Web of Science.

Guo, Rui, Jacob B. Landis, Michael J. Moore, Aiping Meng, Shuguang Jian, Xiaohong Yao, and Hengchang Wang. 2017. Development and application of transcriptome-derived microsatellites in actinidia eriantha (actinidiaceae). Frontiers in Plant Science 8: 1383.

Ryno, Lisa M., Emma R. Brezel, Sarel J. Loewus, and Erica J. Zheng. 2017. Targeting sigma factor controlled signaling pathways to modulate biofilm growth and composition. FASEB Journal 31, 939.5 (conference presentation).

Sun, Yanxia, Michael J. Moore, Nan Lin, Kole F. Adelalu, Aiping Meng, Shuguang Jian, Linsen Yang, Jianqiang Li, and Hengchang Wang. 2017. Complete plastome sequencing of both living species of circaeasteraceae (ranunculales) reveals unusual rearrangements and the loss of the ndh gene family. BMC Genomics 18: 592.

Zheng, Erica J., Eric W. Bell, and Lisa M. Ryno. 2017. Exploring inhibitors of the periplasmic chaperone SurA using fluorescence anisotropy. FASEB Journal 31, 939.4 (conference presentation)

Thursday, July 27, 2017

Kwakye on dopaminergic cell model of Parkinson's; Moore publishes on carnivorous caryophyllales


New publications from Gunner Kwakye, Neuroscience and Michael Moore, Biology. Student co-authors (now alumni) include Weelic Chong, Jessica Jimenez and Jessica Mikenas.

Chong, Weelic, Jessica Jimenez, Matthew McIIvin, Mak A. Saito, and Gunnar F. Kwakye. 2017. Alpha-synuclein enhances cadmium uptake and neurotoxicity via oxidative stress and caspase activated cell death mechanisms in a dopaminergic cell model of Parkinson's disease. Neurotoxicity Research 32, no. 2: 231-246.  Online access for subscribers


http://www.amjbot.org/ 
Walker, Joseph F., Ya Yang, Michael J. Moore, Jessica Mikenas, Alfonso Timoneda, Samuel F. Brockington, and Stephen A. Smith. 2017. Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous caryophyllales. American Journal of Botany 104, no. 6: 858-867.  Open Access article

Tuesday, July 18, 2017

Neuronal metal manganese effect on arginase activity implicated in Huntington's disease

Assistant Professor of Neuroscience Gunnar Kwakye is one of 22 collaborators in this research, from institutions in England, Illinois, Italy, Michigan, New York, Ohio, Pennsylvania, Tennessee and Texas.

Bichell TJV, Wegrzynowicz M, Tipps KG, Bradley EM, Uhouse MA, Bryan M, Horning K, Fisher N, Dudek K, Halbesma T, et al. 2017.

Reduced bioavailable manganese causes striatal urea cycle pathology in Huntington's disease mouse model. Biochimica Et Biophysica Acta-Molecular Basis of Disease 1863(6):1596-604

http://www.sciencedirect.com/science/journal/09254439
sciencedirect.com/science/journal/09254439
Huntington's disease (HD) is caused by a mutation in the huntingtin gene (HIT), resulting in profound striatal neurodegeneration through an unknown mechanism. Perturbations in the urea cycle have been reported in HD models and in HD patient blood and brain. In neurons, arginase is a central urea cycle enzyme, and the metal manganese (Mn) is an essential cofactor. Deficient biological responses to Mn, and reduced Mn accumulation have been observed in HD striatal mouse and cell models. Here we report in vivo and ex vivo evidence of a urea cycle metabolic phenotype in a prodromal HD mouse model. Further, either in vivo or in vitro Mn supplementation reverses the urea-cycle pathology by restoring arginase activity. We show that Arginase 2 (ARG2) is the arginase enzyme present in these mouse brain models, with ARG2 protein levels directly increased by Mn exposure. ARG2 protein is not Teduced in the prodromal stage, though enzyme activity is reduced, indicating that altered Mn bioavailability as a cofactor leads to the deficient enzymatic activity. These data support a hypothesis that mutant HIT leads to a selective deficiency of neuronal Mn at an early disease stage, contributing to HD striatal urea-cycle pathophysiology through an effect on arginase activity. (C) 2017 The Author(s). Published by Elsevier B.V.

Open Access at Sciencedirect

Thursday, July 13, 2017

"Web app for population viability and harvesting analyses." Co-authored by Rich Salter

New publication from Professor Emeritus Richard Salter:
Official Journal of the Resource Modeling Association

Getz WM, Muellerklein OC, Salter RM, Carlson CJ, Lyons AJ, Seidel DP. 2017. A web app for population viability and harvesting analyses. Natural Resource Modeling 30(2):e12120

Abstract:
Population viability analysis (PVA) is used to assess the probability that a biological population will persist for a specified period of time. Such models are typically cast as Markov processes that may include age, stage, sex and metapopulation structures, density-dependence and ecological interaction processes. They may also include harvesting, stocking, and thresholds that trigger interventions. Here we present a PVA web app that includes extensible user-selected options. Specifically, this PVA web app allows for the specification of one to ten age classes, one or two sexes, single population or metapopulation configurations with 2 or 3 subpopulations, as well as density-dependent settings for inducing region-specific carrying capacities. Movement among subpopulations can be influenced by age, metapopulation connectivity, and attractivity of regions based on the relative fitness of the youngest age classes in each region. Simulations can be carried out deterministically or stochastically, with a user-specified combination of demographic and environmental processes. This PVA web app is freely available at http://www.numerusinc.com/webapps/pva for running directly on any browser and device. It is easily modified by users familiar with the NovaModeler Software Platform.

Subscriber access on Wiley Online Library.

Friday, July 07, 2017

Oxidative stress and neurotoxicity in Huntington's disease: publication by G. Kwakye

About NeuroToxicology
New publication from Assistant Professor of Neuroscience Gunnar Kwakye and students in the Kwakye lab:

"Acute exposure to chlorpyrifos caused NADPH oxidase mediated oxidative stress and neurotoxicity in a striatal cell model of Huntington's disease."
Authors:
Gifty A. Dominah, OC'15.; Rachel A. McMinimy, OC'17; Sallay Kallon, OC'17; Gunnar F. Kwakye.
Source:
NeuroToxicology, vol. 60, pp 54-69;  MAY 2017

Subscriber Access on ScienceDirect
Abstract and indexing on PubMed
About NeuroToxicology

Wednesday, June 07, 2017

Plant systematics & evolution of Potentilleae and Sibbalidia: new publication from Mike Moore

A new publication by Michael Moore, Associate Professor of Botany, and collaborators in China.

Feng T, Moore, Michael J, Yan M, Sun Y, Zhang H, Meng A, Li X, Jian S, Li J, Wang H. 2017. Phylogenetic study of the tribe Potentilleae (Rosaceae), with further insight into the disintegration of Sibbaldia. Journal of Systematics and Evolution 55(3):177-91.

Sibbaldia procumbens (5066467208)
Potentilleae, one of 10 tribes of the Rosaceae, are mainly distributed in alpine regions of the Northern Hemisphere. The taxonomy of Potentilleae has been challenging due to extensive hybridization, polyploidization, and/or apomixis characterizing several genera of Potentilleae, such as Alchemilla, Argentina, and Potentilla. To help clarify relationships within Potentilleae, a phylogenetic analysis of the tribe with an emphasis on the polyphyletic genus Sibbaldia was carried out using nuclear ribosomal internal and external transcribed spacer regions and the plastid trnL-F and trnS-G spacer regions. In agreement with previous phylogenetic analyses, three major clades were identified in the present study: the subtribe Fragariinae, the genera Argentina, and Potentilla. The 15 species of Sibbaldia were recovered in five distinct clades: three in subtribe Fragariinae, one in Argentina, and the last in Potentilla. The recently established genus Chamaecallis, comprising a single species formerly treated in Sibbaldia that has intermediate floral character states with respect to Fragariinae and Potentilla, was recovered as sister to Drymocallis. Morphological character state reconstruction indicated that a reduction in the number of stamens (10) is a derived character state that has arisen multiple times in Potentilleae. Molecular dating analyses agreed with previously published estimates and suggested that crown group Potentilleae arose in the Middle to Late Eocene, with most generic-level divergences occurring in the Oligocene and Miocene.  (from the publisher's website)

Thursday, May 25, 2017

Environmental Dashboard and Ground-state rotational constants examined: two very different areas of study by Oberlin researchers

Recent publications from faculty and staff (Oberlin affiliated authors are in bold font):

https://doi.org/10.1371/journal.pone.0176322

Clark, Shane; Petersen, John E; Frantz, Cindy M; Roose, Deborah; Ginn, Joel; Daneri DR. 2017. Teaching systems thinking to 4th and 5th graders using environmental dashboard display technology. Plos One 12(4):e0176322
Tackling complex environmental challenges requires the capacity to understand how relationships and interactions between parts result in dynamic behavior of whole systems. There has been convincing research that these "systems thinking" skills can be learned. However, there is little research on methods for teaching these skills to children or assessing their impact. The Environmental Dashboard is a technology that uses "sociotechnical" feedback-information feedback designed to affect thought and behavior. Environmental Dashboard (ED) combines real-time information on community resource use with images and words that reflect pro-environmental actions of community members. Prior research indicates that ED supports the development of systems thinking in adults. To assess its impact on children, the technology was installed in a primary school and children were passively exposed to ED displays. This resulted in no measurable impact on systems thinking skills. The next stage of this research examined the impact of actively integrating ED into lessons on electricity in 4th and 5th grade. This active integration enhanced both content-related systems thinking skills and content retention.

Demaison J, Craig Norman C, Gurusinghe R, Tubergen MJ, Rudolph HD, Coudert LH, Szalay PG, Csaszar AG. 2017. Fourier transform microwave spectrum of propene-3-d(1) (CH2=CHCH2D), quadrupole coupling constants of deuterium, and a semiexperimental equilibrium structure of propene. Journal of Physical Chemistry A 121(16):3155-66
The ground-state rotational spectrum of propene-3-d(1), CH2=CHCH2D, was measured by Fourier transform microwave spectroscopy. Transitions were assigned for the two conformers, one with the D atom in the symmetry plane (S) and the other with the D atom out of the plane (A). The energy difference between the two conformers was calculated to be 6.5 cm(-1), the S conformer having lower energy. The quadrupole hyperfine structure due to deuterium was resolved and analyzed for both conformers. The experimental quadrupole coupling and the centrifugal distortion constants compared favorably to their ab initio counterparts. Ground-state rotational constants, for the S conformer are 40582.157(9), 9067.024(1), and 7766.0165(12) MHz. Ground-state rotational constants for the A Conformer are 43403.75(3), 8658.961(2), and 7718.247(2) MHz. For the A conformer, a small tunneling splitting (19 MHz) due to internal rotation was observed and analyzed. Using the new rotational constants of this work as well as those previously determined for the C-13 species and for some deuterium-substituted species from the literature, a new semiexperimental equilibrium structure was determined and its high accuracy was confirmed. The difficulty in obtaining accurate coordinates for the out-of-plane hydrogen atom is discussed.

Tuesday, April 25, 2017

Deep learning discussed on the TED Radio Hour

Deep Learning / Ian Goodfellow, Joshua Bengio and
Aaron Courville.  MIT Press, 2016.
The TED Radio Hour on Friday, April 21, 2017 was titled The Digital Industrial Revolution, followed by the question, "As machine learning surpasses human intelligence, where does that leave us?"

During the session, TED speakers explored "ideas about the exciting — and terrifying — future of human-robot collaboration."

One of the speakers referenced deep learning, which immediately brought to mind this book on our new book shelf.  It defines deep learning as a "form of machine learning that enables computers to learn from experience and understand the work in terms of a hierarchy of concepts."  Seemingly benign, and the book's cover is soothing at first glance, with its profusion of blossoms.  On close examination, the cover art work has multiple layers of meaning, and it is this multiplicity of issues surrounding deep learning and neural networks that the TED Radio Hour speakers address.  It makes for fascinating listening!  The four talks are linked here:

Monday, April 17, 2017

Hormones at the hippocampus, caffeine cocrystals, lateral roots, and transcirptome: new publications

Four recent publications from Oberlin College science faculty (names indicated in bold). Student or alumni co-authors in the list below include Veronica Burnham, Christopher Sunday, Abigail Laman-Magarg, and Nicolas Vigilante.

As indexed in Web of Science
Burnham, Veronica, Christopher Sundby, Abigail Laman-Maharg, and Janice Thornton. 2017. Luteinizing hormone acts at the hippocampus to dampen spatial memory. Hormones and Behavior 89, : 55-63. Download: OhioLINK Electronic Journal Center

Laskowski, Marta and Kirsten H. ten Tusscher. 2017. Periodic lateral root priming: What makes it tick? Plant Cell 29, no. 3: 432-444. Download, open access, at Plant Cell

Vigilante, Nicolas J. and Manish A. Mehta. 2017. A C-13 solid-state NMR investigation of four cocrystals of caffeine and theophylline. Acta Crystallographica Section C-Structural Chemistry 73, : 234-243. Read the abstract online at publisher's site

Yang, Ya, Michael J. Moore, Samuel F. Brockington, Alfonso Timoneda, Tao Feng, Hannah E. Marx, Joseph F. Walker, and Stephen A. Smith. 2017. An efficient field and laboratory workflow for plant phylotranscriptomic projects. Applications in Plant Sciences 5, no. 3: 1600128. Download: BioOne

Monday, April 10, 2017

Happy National Library Week! Come get a book...

What better way to celebrate National Library Week than with a new good read?  Check out a book - enjoy your library.  We have a (very small) sweet treat for everyone who checks out a science library book (and reads it, we trust!).  Reserve materials don't count, despite how essential they are for your coursework, so find something great from a display or in the stacks of bookshelves in the middle of the library.

We've received hundreds of new books in the past three months - something is surely of interest to you!  We would be so happy to help you find your perfect read.

There are thousands and thousands of books online, too, beautifully cataloged in OBIS.  Click on the E-BOOKS tab for an easy way to limit your search to online books.


Friday, April 07, 2017

Unintended side effects of conservation: case study in China.

New publication from Assistant Professor of Geology Amanda Schmidt

Schmidt, Amanda H., Yongxian Li, and Ya Tang. 2017. Unintended side effects of conservation: A case study of changing land use in Jiuzhaigou, Sichuan, China. Mountain Research and Development 37, no. 1: 56-65.

Mountain Research and Development is an open access journal.

Partial abstract and conclusions of the study:

Photos by Amanda Schmidt showing
treeless areas of the JNNR
"Toward the goals of returning the landscape of Jiuzhaigou National Nature Reserve (JNNR) to a perceived “natural” state and protecting the environment, the Reserve in 1998–2002 implemented forest preservation policies that included restrictions on forestry, agriculture, and animal herding practiced by resident Tibetans. ...As argued in prior studies in JNNR (Trac et al 2013; Urgenson et al 2014; Harrell et al 2016), we suggest that land managers carefully consider the baseline conditions to which they are trying to restore landscapes. If, as is the case in JNNR, landscapes have been altered by human activity for millennia (eg d'Alpoim Guedes et al 2015), it may not make sense to aim for restoration to a “natural” landscape that does not include people. Likewise, if management policies and changing economic conditions result in people relocating from traditional villages, complete assessments of natural hazards would enable those making relocation decisions to make informed choices about where to situate new developments."

Thursday, April 06, 2017

How to Spot Fake News - with thanks to IFLA and FactCheck.org

Read the story behind the infographic.  IFLA is the International Federation of Library Associations and Institutions.  
How to Spot Fake News
IFLA infographic based on FactCheck.org’s 2016 article "How to Spot Fake News"
Source: 
https://www.ifla.org/publications/node/11174

Monday, March 27, 2017

Leslie Kwakye publishes in Frontiers in Integrative Neuroscience, with six student researchers

Members of the Kwakye lab recently published an article in this highly-regarded open access journal.  View the abstract and link to similar articles and reviews (such a helpful feature!) in PubMed.

http://home.frontiersin.org/
Kyla D. Gibney, Enimielen Aligbe, Brady A. Eggleston, Sarah R. Nunes, Willa G. Kerkhoff, Cassandra L. Dean and Leslie D. Kwakye.
Visual Distractors Disrupt Audiovisual Integration Regardless of Stimulus Complexity.

Frontiers in Integrative Neuroscience, vol. 11, article number 1.  Jan. 20, 2017.
DOI: 10.3389/fnint.2017.00001
As of today, the article has been viewed 1,135 times, including 72 downloads.

Partial abstract:
"The intricate relationship between multisensory integration and attention has been extensively researched in the multisensory field; however, the necessity of attention for the binding of multisensory stimuli remains contested. In the current study, we investigated whether diverting attention from well-known multisensory tasks would disrupt integration and whether the complexity of the stimulus and task modulated this interaction. A secondary objective of this study was to investigate individual differences in the interaction of attention and multisensory integration... The results of this study indicate that attention plays a crucial role in multisensory integration for both highly complex and simple multisensory tasks and that attention may interact differently with multisensory processing in individuals who do not strongly integrate multisensory information."

Monday, March 20, 2017

Award honors the legacy of Dr. Eugene Garfield

We were pleased to learn of this new award from Clarivate Analytics:

"To honor the legacy of Dr. Eugene Garfield, the visionary founder of the Web of Science and a pioneer of Information Science, Clarivate Analytics created the “Eugene Garfield Information Sciences Pioneer Award.” The award will be given annually to at least one promising information scientist, selected by a board of prominent scientometricians.

"Clarivate Analytics, the home of the Web of Science and Journal Impact Factor, supports innovative research by individuals in the scientometric community through a thought leadership program, which gives researchers access to Web of Science data, as well as to scholarships such as the American Society of Information Science & Technology’s Outstanding Teacher Award and Dissertation Proposal Award. Both awards were created in the early 1980s by Dr. Garfield. This new award will enable additional researchers to advance the field and build on Dr. Garfield’s legacy.

"At least one prize will be given annually for the most innovative research in scientometrics, which can be applied to the field globally. It will be awarded to an early-career researcher (i.e., no more than PhD + 10 years) and based on the application criteria and on the researcher’s needs. In addition to the award, Clarivate Analytics will provide the successful applicant with in-kind support and access to Web of Science data."

Thursday, March 16, 2017

Communicating Science: more than just the facts, please

The library is celebrating great science writers with a display of engaging, delightful to read, fact-based books that draw in the reader with compelling stories.  
It will become a rotating display (figuratively and literally, once the new display rack arrives) of new books on science topics, written for a general audience.

The Internet abounds with wonderful science writing as well, of course.  Sean Carroll speaks to this very persuasively in his 2014 blog post, "Twenty-First Century Science Writers."

In 2015, Columbia Journalism Review highlighted "Six great pieces of science writing you may have missed this year."

The description of our book display (Oberlin College Libraries tumblr, March 15) includes a long list of recommended articles - to that list, we add two by Dyani Sabin '14 (former Science Library Student Assistant):

Hawaii Could Become an All-Renewable All-Electric Car Paradise by 2045
Dyani Sabin Clean Energy February 21, 2017

The Blue Collar Job of the Future Is Solar Panel Installer
Dyani Sabin Solar Energy February 22, 2017.

It's remarkable how much one can learn (even those who are reluctant to approach science in any manner) when a good writer weaves the facts with an interesting story that brings home a strong message.

Thursday, March 09, 2017

Senior Ryanna Fossum co-authors a paper in Lithos

Oberlin College geology major Ryanna Fossum worked with researchers from the American Museum of Natural History and Rutgers State University Wright Rieman Labs on this project:

Zirakparvar, N. Alex; Setera, Jacob; Mathez, Edmond; Vantongeren, Jill; Fossum, Ryanna.  2017. The pre-Atlantic Hf isotope evolution of the east Laurentian continental margin: Insights from zircon in basement rocks and glacial tillites from northern New Jersey and southeastern New York. Lithos 272, : 69-83. 

From the Abstract:
This paper presents laser ablation U–Pb age and Hf isotope data for zircons from basement rocks and glacial deposits in northern New Jersey and southeastern New York. The purpose is to understand the eastern Laurentian continental margin's Hf isotope record in relation to its geologic evolution prior to the opening of the Atlantic Ocean.  
 
Access this at sciencdirect.com or the OhioLINK EJC.

Thursday, March 02, 2017

Brad Carter publishes in the journal Zebrafish

New publication from Brad Carter, Visiting Assistant Professor in Neuroscience, from research completed at the Whitehead Institute for Biomedical Research, Cambridge, Massachusetts.

Validation of Protein Knockout in Mutant Zebrafish Lines Using In Vitro Translation Assays.
Bradley S. Carter, Christian Cortés-Campos, Xiao Chen, Jasmine M. McCammon, and Hazel L. Sive.
Zebrafish. February 2017, 14(1): 73-76. doi:10.1089/zeb.2016.1326.  (full-text access for subscribers)

Abstract:
Advances in genome-editing technology have made creation of zebrafish mutant lines accessible to the community. Experimental validation of protein knockout is a critical step in verifying null mutants, but this can be a difficult task. Absence of protein can be confirmed by Western blotting; however, this approach requires target-specific antibodies that are generally not available for zebrafish proteins. We address this issue using in vitro translation assays, a fast and standard procedure that can be easily implemented.

Publication by Matthew Elrod and current students, alumnus

New publication from the Elrod lab, as indexed in the Web of Science
Authors:  William C. Thomas, Class of 2015; William D. Dresser, junior; Diego A. Cortés, senior; Matthew J. Elrod, Associate Professor of Chemistry and Biochemistry.
Gas Phase Oxidation of Campholenic Aldehyde and Solution Phase Reactivity of its Epoxide Derivative.
The Journal of Physical Chemistry A 2017 121 (1), 168-180
DOI: 10.1021/acs.jpca.6b08642  (access for American Chemical Society subscribers)

From the abstract: "On the basis of the rate constants determined for CA and CAE, it is likely that these species are reactive on atmospherically relevant time scales in the gas and aerosol phases, respectively. The results of the present study largely support a previous supposition that a-pinene-derived secondary organic aerosol may be influenced by the multiphase processing of various intermediate species, including those with epoxide functionality."

Tuesday, February 28, 2017

Eugene Garfield Obituary: Scientometrics Pioneer | The Scientist Magazine®

Eugene Garfield Obituary: Scientometrics Pioneer | The Scientist Magazine®: Eugene Garfield, founder of the Institute for Scientific Information and The Scientist, has passed away at age 91.

The only evidence of the once imposing wall of volumes -
our neglected shelf list card for Science Citation Index.
I was sorry to read the news today of Dr. Garfield's passing.  It was an honor to meet Eugene Garfield when I was invited to participate in a users group forum at the Institute for Scientific Information in the mid-1980s.  He was very kind and welcoming, and surprised us with his self-deprecating humor in the face of our deference to his superior knowledge of citation metrics.  It seems like a life-time ago (and for the current generation of undergraduates, it is more than a life-time) that the science faculty here routed the library's copies of Current Contents, issued weekly, around each department as a way of keeping abreast of new research.  Likewise, the print volumes of Science Citation Index hit the recycling bin ages ago - perhaps directly to a landfill, in the pre-recycling era - and Web of Science competes mightily with Google Scholar and other databases for the same reliance from today's students as once shown by faculty to Current Contents.  Dr. Garfield's legacy is still very evident, even as formats and use patterns evolve.