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NCASD, Martin Labs Apply Network Analysis and Molecular Modeling to Chitinases

Published on March 20, 2017 by

Chitin, the polysaccharide-based material from which insects make their exoskeletons, is tough stuff – and digesting it is a tall order, especially for a plant.  Nevertheless, some carnivorous plants, like the Cape Sundew, Drosera Capensis, are able to do just that.  In a recent paper in Biochemica et Biophysica Acta, NCASD Lab PI Butts and members of the Martin Lab model the structures of 11 novel chitinases from D. Capensis, whose genome was published as part of the same collaborative effort this past year.  Applying a combination of bioinformatics, molecular modeling, and techniques adapted from social network analysis, the team was able to predict the three-dimensional structure of each enzyme and gain insights into potential functional differences.  Among the discoveries is a novel chitinase with two active domains that closely resembles a protein seen in microorganisms, but never before found in plants.  These new enzymes can do more than bite bugs: chitin is also the essential component of fungal cell walls, and these molecules may hold promise for combating fungal growth on food or even fungal infections in humans.  This work demonstrates the potential for fusing computational and data analytic techniques with biological know-how to quickly move from genomic “source code” to potentially valuable biomolecules.

 
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Dr. Gianmarc Grazioli to Join NCASD Lab

Published on March 17, 2017 by

The NCASD Lab is pleased to welcome Dr. Gianmarc Grazioli, who will be joining as a postdoctoral scholar as of spring quarter, 2017.  Dr. Grazioli, who obtained his Ph.D. in the Andricioaei lab before a one-year stint in the Paesani lab at UCSD, brings with him a wealth of expertise in molecular modeling, particularly the use of modified potentials for importance sampling of trajectories in order to explore rare transitions.  In his new position, Dr. Grazioli will contribute to the team’s work on modeling of protein aggregation, statistical methods for prediction of structural and functional properties of biological macromolecules, and the development of network analytic methods for the study of biological systems.  A computational chemist by training, Grazioli adds to the lab’s diverse mix of disciplinary expertise (currently spanning sociology, statistics, electrical engineering, and computer science), and deepens the group’s bench in expertise related to simulation and sampling techniques.

 
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CNRA Fellow and Lab Member Phillips Heading to Harvard

Published on March 15, 2017 by

CNRA Graduate Fellow and NCASD Lab Member Nolan Phillips has accepted a position as a postdoctoral scholar at Harvard University, starting in fall 2018.  Phillips, who is completing his dissertation work on network comparison, model evaluation, and the dynamics of technology adoption by government agencies, will join the group of Professor Robert Sampson, where he will be working on an ambitious new project involving neighborhood ecology and community outcomes.  This project is part of a broader interdisciplinary collaboration among researchers in the Boston area, including researchers at Harvard and Northeastern universities, to which Phillips will bring his experience with social network analysis, modeling, and the use of archival data.

 
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Lab Alumna Liana Landivar Joins NSF

Published on December 6, 2016 by

Lab alumna Liana Landivar, formerly statistician at the US Department of the Census, has now accepted a position as survey statistician at the National Science Foundation.  In her capacity at the Census, Landivar played a key role in managing the Census’s measurement and categorization of occupations – a complex task that supplies vital information on the health of the US economy and labor force for use by government, industry, and research entities.  She was also active in helping to craft Federal guidelines for determining the occupations considered to be part of the science, technology, engineering, and mathematics (STEM) field.  At NSF, Landivar will be leveraging her experience and expertise with occupations to help study the evolution of America’s science and technology labor force, including the changing demographics of workers in STEM fields.  Her work there will provide insights to inform science and education policy, and to better assess occupational fields that are central to US competitiveness and economic growth.

 
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NCASD, Martin Lab Publish Carnivorous Plant Genome

Published on July 12, 2016 by

NCASD lab members Butts and Zhang, in collaboration with Alfredo Freites and the Martin lab (UCI Chemistry and MB&B) are pleased to announce two forthcoming papers on the genome of the Cape sundew (Drosera Capensis), a widely cultivated carnivorous plant.  The team’s sequencing of D. Capensis marks the first published genome in the family Caryophyllales, and the third carnivorous plant to be sequenced.  In their forthcoming work, Butts, Martin, and colleagues identify and model a large number of novel proteases from the Capensis genome, identifying promising targets for biotechnological applications such as the preparation of samples for mass spectrometry or attacking bacterial biofilms on sensitive medical devices.  The team has also identified a new “enzyme within an enzyme” with potential uses as an antifungal agent.  In the spirit of UCI’s growing commitment to convergnce science, this research fuses state-of-the-art computational methods (including structure prediction, docking, and molecular dynamics), methods adapted from social network analysis, and traditional genomic and biophysical techniques to move from genomic “source code” to useful biomolecules in a fraction of the time and cost of conventional approaches.  The team’s work is forthcoming at Proteins and the Computational and Structural Biotechnology Journal.

 
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Fitzhugh, Gibson, Spiro, and Butts published in Social Science Research

Published on June 8, 2016 by

Lab alum Sean Fitzhugh, along with lab member Ben Gibson, lab alum Emma Spiro, and lab PI Carter Butts, have published their article “Spatio-temporal Filtering Techniques for the Detection of Disaster-related Communication” in an upcoming special issue of Social Science Research on big data. This paper develops a family of techniques for filtering large streams of communication across time and space in order to detect signals of hazard-related rumoring. They reliably detect signal of rumoring activity across a variety of disasters affecting a wide range of populations, from dense urban areas to sparse rural areas. The results highlight spatio-temporal variation of rumoring activity in response to impending and realized disasters. Additionally, they illustrate a case study of how message content varies across time and space during a disaster.

The article can be found online here.

 
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Lab alum Almquist recognized as distinguished UCI alumni

Published on June 7, 2016 by

Zack Almquist, lab alumni and assistant professor at the University of Minnesota, has recently been recognized as one of the top 50 graduate and postdoc alumni from UCI for its 50th year celebration. Selected nominees represent five decades of graduate program impact and some of our most successful graduate and postdoctoral scholar alumni. Congratulations, Zack!

 
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Lab alum Marcum wins award from the NIH

Published on June 7, 2016 by

Lab alum Christopher Marcum was the recipient of the Matilda White Riley Early Stage Investigator Honors from the NIH, a paper competition for Early Stage Investigators. The selected paper, which is on triadic models of intergenerational exchanges, was co-authored Laura Koehly and published in Advances in Life Course Research last year. Visit here to learn more about this recognition. Congratulations, Chris!

 
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HEROIC Project Published in Proceedings of the National Academy of Sciences (PNAS)

Published on November 25, 2015 by

A HEROIC-funded paper entitled “A cross-hazard analysis of terse message retransmission on Twitter” was published in Proceedings of the National Academy of Sciences (PNAS) last week.  This research provides the first systematic study of the factors predicting the social amplification of risk communication in OSNs by examining the retransmission of official messages across five hazards. Our findings demonstrate the respective impacts of sender characteristics, message content, and message style in determining whether an official message will be passed on during an emergency, as well whether these vary across hazards. These results contribute to the evidence base for policies guiding the delivery by emergency management organizations of lifesaving information to the public.

 
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NSF Grant Kick-Off Meeting

Published on November 25, 2015 by

We are excited to announce the kick-off of a new NSF funded effort by researchers at the University of Kentucky and the University of California-Irvine to better understand the dynamics of informal online communication in response to extreme events. Through a combination of data collection and modeling of conversation dynamics, the project team aims to understand the relationship between hazard events, informal communication and emergency response. The Project HEROIC Data Consortium is to be created to further the goals of this project and provide infrastructure for future data collection and analysis related to informal online communication and emergency response.

 

 
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