GPSS Conference - BCB students Shine !

April 13, 2018
News

Several BCB students took part in the GPSS Conference held April 11 in the Memorial Union at Iowa State.  More information about the conference is below.

Congratulations to Sayane Shome from Robert Jernigan's lab, a BCB faculty member in the BBMB Department who won the Best Poster Award, and Carla Mann from Drena Dobbs' lab, a BCB faculty member in the GDCB Department who won first place in the 3MT presentations.  Gaurav Kandoi, from Julie Dickerson's lab, a BCB faculty member in ECPE, received a GPSS Leadership Award honoring his work as CIO of the GPSS organization.

Other BCB students who took part in presentations or posters included Vishnu Ramasubramanian in William Beavis lab, a BCB Facuty member in the Agronomy Department who presented in the 3MT competition, Sagnik Banerjee, from Roger Wise' lab, a BCB faculty member in Plant Path and Microbiology who presented a poster, and Lindsay Rutter, from Di Cook's lab in the Statistics Department, who gave an oral presentation and took the below picture.

Here are the abstracts of the talk and poster Carla and Sayane presented:

Carla Mann, pictured in the middle below, won the 3-Minute Presentation portion at the conference.  She presented on RNA protein interactions and her abstract follows:

RNA-protein interactions are implicated in a wide range of critical regulatory roles whose disruption can lead to cancer, neurodegenerative disorders such as Alzheimer’s Disease, and metabolic disorders. Due to the time and expense required to experimentally identify and characterize these interactions, computer-based methods for predicting them are valuable. Published prediction methods rely on various sequence and structural features, but their practical utility is limited by high false positive rates (FPRs) and/or limitations on the length of query sequences. Intrinsically disordered regions (IDRs) are highly flexible regions in proteins. IDRs are known to be abundant in RNA binding sites of proteins. We hypothesized that incorporating information about IDRs, in conjunction with RNA and protein sequence features, could improve machine learning prediction of RNA-protein interaction partners.

We developed a new machine learning method, RPIDisorder, which requires as input only the primary ribonucleotide and amino acid sequences of potential binding partners. RPIDisorder is a random forest classifier that uses both predicted IDR information and the relative frequencies of amino acid triads and ribonucleotide tetrads. On an independent test set of 11,281 interacting RNA-protein pairs and 971 non-interacting RNA-protein pairs, RPIDisorder had superior performance over our group's previously published method, RPISeq, achieving an FPR of 21% vs 55% for RPISeq and a Matthews Correlation Coefficient (MCC) of 0.68 (vs 0.47). 

In a case study, RPIDisorder outperformed RPISeq in predicting which RNAs bind the RGG RNA-binding domain of the Fragile X Mental Retardation Protein (FMRP). On a test set of 14 RNAs experimentally determined to bind to FMRP and 16 non-binding ncRNAs, RPIDisorder achieved an FPR of only 6.3%, compared to RPISeq’s 25%, and an MCC of 0.73 vs RPISeq’s 0.61.

These results indicate that incorporating IDR information can improve the reliability of RNA-protein partner prediction over sequence composition alone, and demonstrates that RPIDisorder can be utilized to make predictions for highly disordered proteins, which are otherwise difficult to characterize.

Sayane Shome, Carla Mann, Gaurav Kandoi

Sayane Shome, pictured on the left in the picture, presented her work at both the Biophysical Society Annual meeting as an oral presentation at the Molecular Dynamics Session. That meeting took place in San Francisco, California, February 19, 2018.  Sayane also co-chaired the session.

She presented the same abstract at the GPSS conference as poster presentation:

Transport Pathways in Membrane Transporters

Substrate transport through membrane transporters is critical for many biological processes. One of the most interesting questions is how to understand the substrate specificity of transporters. Due to the limitations of experimental methods, computational approaches can be applied advantageously to screen a large number of possible transported molecules. The experimental determination of the mechanistic details of transport is difficult. We have employed steered molecular dynamics simulations to determine the critical factors responsible for the transport and how they interact with protein components along the pathway.

 

Photo courtesy of Lindsay Rutter, BCB student

Abstracts for the GPSS conference were reviewed based on their clarity and impact. The following parameters were primarily considered by the review committee while reviewing the abstracts:

  • Is the problem or hypothesis identified clearly?
  • Are the methods clear and understandable to an educated lay person?
  • Did the author(s) use proper grammar and sentence structure?
  • Is a conclusion clearly summarized?
  • Did the author(s) establish implication of their research?

Details of the 5th Graduate and Professional Student Research Conference held Wednesday, April 11, 2018 at the Memorial Union follow:

The 5th Graduate and Professional Student Research Conference was held on April 11, 2018. The conference program included impactful innovation, 3-minute thesis, poster or oral presentation. This year Dr. Joel Best and Dr. Patrick Schnable were the keynote speakers!

Presentation Categories* include:

* Please click on the links above to know more about each presentation type.

Based on the abstract quality and the number of slots available for each category, the abstracts submitted for 3MT and/or oral session could be moved to the poster session. The decision of review committee will be final and binding in this regard.

PROGRAM OUTLINE

Time Event Speaker(s)

8:00 AM - Registration Starts - Great Hall Lobby

8.30- 10.45 AM -- Case Competition (College of Business) -- Room 3512, Memorial Union

8.30- 9.30 AM -- Oral Presentation (Sessions 1, 2, 3, 4) -- 3219, 3505, 3538, 3558

9.45- 10:45 AM -- Oral Presentation (Sessions 5, 6, 7, 8) -- 3219, 3505, 3538, 3558

9.00- 10.00 AM -- Want a Faculty Job? Prepare at ISU -- Holly Bender (CELT) -- Cardinal Room

9.00- 10.00 AM -- Issues Pertaining to International Student Wellness -- Jason Huntley (Student Wellness) -- Gold Room

10:00- 11:00 AM -- Composing an Impressive Research Statement -- Mitchell Stephenson; Beatrice Berzina (CCE) -- Cardinal Room

11:00-11:50 PM -- Lunch Break -- Oak Room

10.30- 11.50AM -- Poster session/ Impactful innovations -- Great Hall

12:00- 1:00 PM -- Keynote Speaker Patrick Schnable -- Sun Room

1:15- 2.15 PM -- Oral Presentation (Sessions 9, 10, 11, 12) -- 3219, 3505, 3538, 3558

2.30- 3.30 PM -- Oral Presentation (Sessions 13, 14, 15, 16) -- 3219, 3505, 3538, 3558

1.30- 2.30 PM -- Startup Factory and the Ecosystem -- Bill Adamowski (Startup Factory) -- Campanile Room

2.30- 3.30 PM -- Entrepreneurial Opportunities for Post-Docs -- Judi Eyles (PapaJohn Center) -- Cardinal Room

3.00- 4.00 PM -- The Importance of Retirement Savings -- Ann Doty (Human Resources) -- Gold Room

Eligibility:

  • Oral and Poster Presentation: All graduate students at Iowa State University are welcome to submit abstracts.
  • 3 Minute Thesis: All graduate students at Iowa State University who have passed their PhD Preliminary Examination and thus achieved PhD candidacy are welcome to submit abstracts for the 3MT.
  • Impactful Innovation: All graduate students at Iowa State University are welcome to submit abstracts. Each impactful innovation can be presented by a maximum of three people.
  • Case Competition: All graduate students from Ivy College of Business are welcome to submit their plans.

Submission Guidelines:

  1. The presenter of the abstract shall be a graduate or professional student.
  2. The abstract should be limited to maximum of 400 words. The abstract should not contain any tables, figures, or any other graphic files.
  3. All abstracts should have a clearly identifiable purpose, methods, results, and conclusion.
  4. All the abstracts will be submitted through online abstract submission process. Follow abstracts submission link on the website.
  5. The abstract should reflect the original work of the author(s). However the authors are welcome to submit previously published research.
  6. GPSRC will not publish the proceedings. The authors can still submit the abstract to GPSRC–2018, even if they plan to present or have presented it in any professional conference or journal.

Judging and Acceptance:

The abstracts submitted will undergo review process for acceptance. The abstracts will be reviewed based on their clarity and impact. Following parameters will primarily be considered by the review committee while reviewing the abstracts:

  • Is the problem or hypothesis identified clearly?
  • Are the methods clear and understandable to an educated lay person?
  • Did the author(s) use proper grammar and sentence structure?
  • Is a conclusion clearly summarized?
  • Did the author(s) establish implication of their research?
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