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THE BIOLOGY GENOME Portland State University - Department of Biology

What’s in this issue…

From the Chair’s Desk

Meet our Newest Faculty Member

Research In Focus

ResearchNOW

Shout-Outs!

Herpetology

Summer 2016 VOL 1., ISSUE 4. College of Liberal Arts & Sciences

From the Chair’s Desk - Dr. Jason Podrabsky

[Congratulation Biology Class of 2016!] As we put another academic year behind us and look forward to the next one, I wanted to

take a minute to reflect on the end of the year celebrations. First, the 2015 departmental

graduation ceremony was a great success thanks to the efforts of the Research and Devel-

opment Committee, our incredible staff, and our graduate student volunteers. We had 94

students attend and they brought with them over 400 friends and family – it was quite an

event! We were also honored by the attendance of long-time departmental supporters and

alumni Marcia Schulmerich and John Salmon, and more recent supporters of the depart-

ment Vincent and Zeny Seid. It was also great to have Dean Karen Marrongelle attend and

address the students. My favorite part of the ceremony was hearing the great things that

our students have to say about the support they received from family, friends and the de-

partment during their time at PSU! The gathering after the ceremony was also quite a suc-

cess with great food and exhibits of our museum collections and student art (our students

and students from the College of the Arts). I am continually inspired by hearing the impact

that our program has on our students, and I love that our ceremony is one way that we can

let the graduates know what a huge impact they have on us. I look forward to continuing

this tradition in the future.

The end of each academic year is also a time that we celebrate excellence in research and instruction through College and

University awards that recognize faculty achievements. This year, the John Eliot Allen Outstanding Teaching award for Biology

went to Dr. Radhika Reddy. On the research side, Dr. Daniel Ballhorn was awarded the Junior Research Faculty Excellence

Award. Congratulations to both Daniel and Radhika!

I hope that everyone is having a great summer and getting a chance to enjoy the beautiful outdoors in Oregon, or wherev-

er you find yourself.

To Contribute to the Biology Department

If you would like to support the important activities of the Depart-

ment of Biology, please donate to the PSU Foundation specifying the

name of the account you wish to support. Alumni and friend dona-

tions have made a tremendous impact on our ability to serve the stu-

dents, and we are very grateful for your generosity. Thanks you!

http://www.pdx.edu/biology/give-biology

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Research In Focus [Brown Lab]

The over-

arching re-

search goal

in the

Brown Lab

is the study

on how en-

vironmental

contami-

nants affect

the struc-

ture of indi-

vidual’s ge-

nomes.

Many

chemicals

found in the environment are either known to, or suspect-

ed to have, the ability to alter genome sequences. Many of

these chemicals are common and we are exposed to them

on a daily basis. One category of special concern are

chemicals known as Environmental Estrogens. These are

compounds that mimic or alter the effects of normal estro-

gens and can cause significant issues in exposed popula-

tions. Many of these issues are seen in fishes, including

extreme examples of intersex individuals (containing both

sperm and eggs within single gonads) and complete sex

reversal. Despite our understanding of the potential effects

of these compounds, we still lack a complete understand-

ing of the mechanisms under which they act. To under-

stand how these chemicals change genomic sequences

we utilize cutting edge genomic techniques and have de-

veloped novel tools for analyzing individual sequences.

To assess large scale genomic changes we utilize com-

parative genomic hybridization (cgh) to evaluate genomes

for copy number variants, i.e., the addition or loss of ge-

nomic segments ranging from 1,000 to 1 million nucleo-

tide bases and next generation DNA sequencing. Using

our model, zebrafish, we have determined the rate at

which novel copy number variants appear in the genome.

This will provide a baseline for us to assess whether dif-

ferent toxicants increase or decrease the generation rate

of copy number variants, given new copy number variants

can have detrimental effects on organism physiology and

development. We also have developed a new bioinfor-

matics tool to assess genomic sequences that fail to map

within any completed genome and tested this using

zebrafish and human genome sequences. Using this

method we identified over 220 Million bases of sequence

not previously mapped in the zebrafish genome and over

195 Million bases not previously mapped in the human

genome. We were able to map a substantial number of

these sequences in the human genome and were able to

identify several novel gene sequences and several popu-

lation specific genomic regions located within known can-

cer genes. These findings have clearly demonstrated that

even in the most complete vertebrate genome available,

unknown regions remain that have the potential to affect

physiology, development, and disease.

In addition to nuclear changes, we have also evaluated

the effects of environmental estrogens on mitochondrial

DNA stability. For this work we have exposed zebrafish to

human birth control and evaluated to determine whether

exposure changes the level of mitochondrial DNA hetero-

plasmy. Heteroplasmy is a unnatural condition where

multiple mitochondrial DNA sequences are found within a

single individual. Individuals with increased rates of heter-

oplasmy are

known to ex-

hibit diseases

including blind-

ness, diabetes,

muscle diseas-

es and others.

Our work clear-

ly demon-

strates that ex-

posures to

these chemi-

cals at levels of

only 10 parts

per billion can

significantly

alter levels of

heteroplasmy

after only 6 weeks of exposure (Fig. 1). Ongoing research

will assess the effects of prolonged exposure and seek to

determine the mechanism(s) through which these chemi-

cals affect mitochondrial DNA.

Continued page 3...

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Shout-Outs! Dr. Radhika Reddy was awarded this

year’s John Eliot Allen teaching award

for Biology.

Lindsay Holden was awarded the

Dean's Award for University Services at

the Doctoral level for the College of

Liberal Arts and Sciences

Alicia Chivers was awarded the

Dean's Award for Academic Achieve-

ment at the Master's level for the Col-

lege of Liberal Arts and Sciences.

James Powell (PhD candidate, Duf-

field Lab) has been awarded an EPA

STAR fellowship to continue and ex-

pand his doctoral research on bone

density in bottlenose dolphins.

Portland State University Biolo-

gy student John Donaho helped re-

searchers in Texas make a discovery

about the Deepwater Horizon Oil Spill

that is shaping how scientists look at

bacteria. His work was published in a

recent article in Nature Microbiology.

Congratulations Portland State Univer-

sity graduate student Jess Millar! Jess,

who is pursuing dual master's degrees

in Biology and Statistics , recently won a

graduate research fellowship from the

National Science Foundation (NSF)!

Dr. Anna-Louise Reysenbach and her

collegues at Oakridge National Re-

search lab have been awarded a $640K

research grant studying the evolution

and diversification of hyperthermo-

philic Archaea!

Jess Millar (Raghavan Lab) has been

awarded an NSF Graduate Research

Fellowship! Congrats Jess!!!!!!!

Amie Romney, PhD candidate in the

Podrabsky Lab presented her poster at

Sigma Xi NW/SW + AAAS Pacific Divi-

sion Annual Meeting at the University

of San Diego titled: Epigenetic regula-

tion of alternative developmental tra-

jectories in an annual killifish. She was

awarded first place in Cell and Molecu-

lar Biology, plus the President's Award.

Scorpions in the Columbia River Gorge!

Dr. Susan Masta gave a great inter-

view about a native species of scorpion

on KATU News!

Dr. Michael Murphy was Science

Advisor/Field Facilitator for a recently

episode of Nature on PBS/BBC. The

program was titled SuperNature - Wild

Fliers, Crowded Skies.

[Brown Lab]

Squid

Hatching [Dr. Masta’s Invertebrate Zoolo-

gy course found a squid egg

sack washed ashore. They

brought it back to the lab and

they hatched!]

Other topics of interest in

my lab include the physio-

logical effects of different

intestinal microbiomes. He

have recently completed

preliminary analysis of dif-

ferent populations of hatch-

ery Steelhead trout to de-

termine the core microbi-

ome within the species.

Our findings indicate a sig-

nificant level of diversity

between populations, with

the greatest diversity found

across the major phyloge-

netic divide within the spe-

cies, the Cascade Range (Fig. 2). Future work in this area will help to establish whether

differences between hatchery and wild populations can account for differences in return

rates among the two groups and how rapid changes in diet affect the physiological out-

put of individuals.

Lindsay Holden, Phd Student Candidate Christina Yildirimer, M.S. Student

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ResearchNOW [Papers published last Quarter]

G. .S. Diemer and K.M. Stedman. Modeling Microvirus Capsid Protein Evolution Utilizing Metagenomic Sequence Data. (2016) Journal of Molecular Evolution, published online, 6 July, 2016. DOI 10.1007/s00239-016-9751-y

Workman, R.E. and M.B. Cruzan. 2016. Mycelial networks impact competition in an invasive grass. American Journal of Botany (doi: 10.3732/ajb.1600142)

Marchini, M.L, N. Cole Sherlock, A.P. Ramakrishnan, D.M. Rosenthal, and M.B. Cruzan. 2016. Rapid purging of genetic load in a metapopu-lation and consequences for range expansion in an invasive plant. Biological Invasions 18:183-196. (doi: 10.1007/s10530-015-1001-5)

Cruzan, M.B. and S.C.H. Barrett. 2016. Post-pollination discrimination between self- and outcross-pollen covaries with the mating system of a self-compatible flowering plant. American Journal of Botany 103:568-576. (doi:10.3732/ajb.1500139)

JJ Faber-Hammond and KH Brown. Anchored pseudo-de novo assem-bly of human genomes identifies extensive sequence variation from unmapped sequence reads. Human genetics 135 (7), 727-740.

Stark, L. R., McLetchie, D. N., Greenwood, J. L., and Eppley, S. M. 2016. Moss antheridia are desiccation tolerant: rehydration dynam-ics influence sperm release in Bryum argenteum. American Journal of Botany 103: 856-864.

Llaneza Garcia, E., Rosenstiel, T. N., Graves, C., Shortlidge, E. E., and Eppley, S. M. 2016. Distribution drivers and physiological responses in geothermal bryophyte communities. American Journal of Bota-ny 103: 625-634.

Wurch, Louie, Giannone, Richard J., Belisle, Bernard S., Swift, Car-olyn, Utturkar, Sagar, Hettich, Robert L., Reysenbach, Anna-Louise, Podar, Mircea (2016) Genomics-informed isolation and characteriza-tion of a symbiotic Nanoarchaeota system from a terrestrial geother-mal environment, Nature Communications. 2016/07/05/online, http://dx.doi.org/10.1038/ncomms12115

Paths of heritable mitochondrial DNA mutation and heteroplasmy in reference and gas-1 strains of Caenorhabditis elegans, by Riana Wer-nick, Dana Howe, Suzanne Estes, Dee Denver, published in Frontiers in Genetics, http://dx.doi.org/10.3389/fgene.2016.00051.

Taylor, Laura A. V., undergraduate student Hasenkopf, Erik A.; and professor Cruzan, Mitchell B. published a paper in Biological Inva-sions : Barriers to invasive infilling by Brachypodium sylvaticum in Pacific Northwest forests. BIOLOGICAL INVA-SIONS Volume: 17 Issue: 8 Pages: 2247-2260 Published: AUG 2015

Shortlidge, Erin E., Gita Bangera, and Sara E. Brownell. “Faculty Per-spectives on Developing and Teaching Course-Based Undergraduate Research Experiences.” BioScience 66.1 (2016): 54-62.

Biology Professor, Todd Rosenstiel (with Graduate Student Will Por-ter, Physics) published "Reducing the negative human health impacts of bioenergy crop emissions through region-specific crop selection" In Environmental Research Letters

Anna Coleman-Hulbert, Ph.D. student in the Biology Department and Suzanne Estes, Associate Professor in the Biology department pub-lished a paper in Genome Biology and Evolution : Selfish mitochon-drial DNA proliferates and diversifies in small, but not large, experi-mental populations of Caenorhabditis briggisae. W.S. Phillips, A. Coleman-Hubbert, E.S. Weiss, D. K. Howe, S. Ping, R. I. Wernick, S. Estes, D. R. Denver. Doi: 10.1093/gbe/evv116

Biology professor Ken Stedman published an article in Annual Re-views in Virology: Deep Recombination : RNA and ssDNA virus genes in DNA virus and host genomes. Annu. Rev. Virol. 2:10.1-10.15. Doi: 1-/1146/annurev-virology-100114-055127

Ballhorn DJ, Schadler M, Elias JD, Millar JA, Kautz S. “Friend or foe - Light 2016 availability determines the relationship between mycor-rhizal fungi, rhizobia and lima bean (Phaseolus lunatus L.).” PLoS ONE. 11(5):e0154116.

Daniel J. Ballhorn , Martin Schadler (2016) Beneficial Soil Microbiota as Mediators of the Plant Defensive Phenotype and Aboveground Plant-Herbivore Interactions. Progress in Botany (Book Chapter). Springer International Publishing Switzerland DOI 10.1007/124_2016_13

2016-2017 Lester Newman Seminar Series

For more information and a list of next year’s seminars please visit:

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John Eliot Allen Outstanding Teaching Award

The Biology Department is now publishing the following

information on our website:

Faculty Office Hours

Office hours for faculty is now posted online and updated

each term.

Current & Past Term Syllabi

Starting Summer 2015 term course syllabi are being post-

ed online for your convenience!

Current Term TA assignments

Can’t remember your TAs name? TA assignments are

now posted on our website!

Complete List of upcoming Seminar Talks!

A complete list of Spring seminar is available on our website.

www.pdx.edu/biology

Undergraduate Web Resources

Herpetology, basking in the summer sun.

The summer class of Herpetology had an excellent trip to Ne-

vada and Southern Oregon last week. The class finished their

lab practical and final exams and packed to leave the next day

to apply their newly learned knowledge and techniques in the

field. A combination of day time hikes and evening road run-

ning trips yielded great returns for the students wherein they

identified among the desert plants, mammals, and birds; sev-

en lizard species, four species of snakes, and the local toad.

Focus was given to the herpetofauna, but students also dis-

cussed the natural history and geology of the region, success-

fully digging for fossils and the Oregon state rock, the thun-

deregg.

Instructor: Dr. Ed DeGrauw, TA: Kyle Tidwell

Top Left: Herpetology student Thomas Munger with the Great Basin Spadefoot Toad (Spea intermontana). Bottom Left: Part of the herpetology crew in a cave over-

looking the Alvord desert. Right: Student Kelsey Sandoval with a Gopher Snake (Pituophis catenifer).

Congratulations to Dr. Radhika Reddy as this year's recipient of the John

Eliot Allen teaching award for Biology!

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Meeting Biology’s Newest Faculty Member [Dr. Anne Thompson]

Dr. Anne Thomp-

son is a new re-

search assistant

professor in the

Biology Depart-

ment with a re-

search focus on

microbial ecology.

Specifically, her

research will focus

on the most abun-

dant photosyn-

thetic cells on

Earth, phytoplank-

ton. These incredibly abundant and diverse microbial popula-

tions impact global carbon cycles and oxygen production on

the same scale as terrestrial plants. Much remains to be dis-

covered about their ecology.

Dr. Thompson comes to PSU from a senior research

scientist position at the Institute for Systems Biology in Se-

attle where she studied microbial ecology in biological sys-

tems including the open ocean, coastal ocean, and groundwa-

ter. Most recently, she has examined single cell genomes and

gene expression to test the role of population heterogeneity

in the survival of microbial populations in fluctuating condi-

tions. Previously, Dr. Thompson worked with the Advanced

Cytometry Group at BD Biosciences to develop new methods

for analysis of phytoplankton and anaerobic microbial com-

munities using flow cytometric analysis and cell sorting. Dr.

Thompson completed a postdoctoral scholarship in Marine

Sciences at University of California, Santa Cruz in the lab of

Dr. Jonathan Zehr where she discovered a symbiosis between

a globally abundant marine cyanobacterium and a single-

celled eukaryotic phytoplankton that impacts how we under-

stand the link between carbon and nitrogen cycles on a global

level. She received her Ph.D. through the MIT-Woods Hole

Oceanographic Institution Joint Program studying the role of

iron in the ecology of cyanobacteria under the mentorship of

Dr. Penny Chisholm and Dr. Mak Saito.

At Portland State, Dr. Thompson’s lab will focus on

the relationship between genetic diversity, community struc-

ture, and ecosystem function in an open ocean phytoplank-

ton community. Specifically, through a grant from the Nation-

al Science Foundation, her group will study the cyanobacte-

rium Prochlorococcus, which is extremely abundant and di-

verse in the vast open ocean. There are twelve know lineages

of Prochlorococcus that respond in different ways to seasonal

cycles and gradients within the ocean. However, there is

much we do not understand about how these abundant cells

run Earth’s carbon cycles. Deciphering the ecological proper-

ties of these microbial communities is critical to understand-

ing and forecasting changes to the Earth System. Thompson’s

lab will run experiments and collect samples on board re-

search cruises in the North Pacific Ocean, where these cells

are abundant. Dr. Thompson is looking forward to engaging

PSU students in research at this exciting frontier. Also, over

the next three years, Dr. Thompson will be collaborating with

the Systems Education Experiences (SEE) program at the Insti-

tute for Systems Biology, high school teachers, and high

school students to develop a freely available on-line educa-

tional module to teach K-12 students about microbial ocean-

ography and the importance of this field to life on Earth as we

know it.

Finally, Dr. Thompson looks forward to building col-

laborations with other researchers at PSU, especially offering

expertise in single cell analysis and cell sorting via flow cytom-

etry to address questions in Biology. Thompson welcomes

any students or researchers to contact her to discuss oppor-

tunities and areas of overlapping interest.

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CONTACT US: Portland State University Department of Biology 1719 SW 10th Avenue SRTC, Room 246 Portland, Oregon. 97201 503-725-8757 biology@pdx.edu www.pdx.edu/biology Editor: Ian Garrett

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Congratulation Biology Class of 2016!!!

All the photos from the 2016 Biology Department Graduation Ceremony can be downloaded here:

2016 Biology Department Graduations Photos