Solving the Structural Modeling Problems for Tandem Repeat Proteins

Over the last decade, numerous studies have demonstrated fundamental importance of tandem repeat proteins (TRP) in many biological processes (Andrade, Perez-Iratxeta, and Ponting 2001). Repeat proteins are a widespread class of non-globular proteins carrying heterogeneous functions involved in several diseases. One of the most frequent problems in the study of biology is the functional characterization of a protein. This problem is usually solved by analyzing the three-dimensional (3D) structure. The experimental determination of the 3D structure is time consuming and technically difficult. For this reason structure prediction by homology modeling offers a fast alternative to experimental approaches. However homology modeling is not feasible for tandem repeat proteins because it is difficult to infer homology due to a high degree of sequence degeneration. In this thesis, I focused on algorithms oriented toward repeat unit prediction, and characterization. I developed an innovative approach, Repeat Protein Unit Predictor (ReUPred), for fast automatic prediction of repeat units and repeat classification, exploiting a Structure Repeat Unit Library (SRUL) derived from RepeatsDB, the core database of TRP. ReUPred is based on the Victor C++ library, an open source platform dedicated to protein structure manipulation. To prove the accuracy of the predictor, we ran it against all the entries in the PDB database and the resulting predictions allowed us to improve and increase RepeatsDB annotation twenty times. During my PhD I have integrated ReUPred prediction into the new version of RepeatsDB (release 2.0) that now features information on start and end positions for the repeat regions and units for all entries. The updated web interface includes a new search engine for complex queries and a fully re-designed entry page for a better overview of structural data. To further improve RepeatsDB quality we decided to provide a finer classification at the subclass level based on the structural conformation of the repeated units. We hypothesized that inside these ensembles it is possible to find subgroups of proteins sharing the same unit type. To prove it, we performed a detailed structural analysis. We created a network where nodes are the units and arcs represent structural similarity. The network can be partitioned in 7 different clusters. For each cluster, it was possible to create a Hidden Markov Model similar to those representing Pfam domains. This analysis is an unpublished work but it already helped to improve ReUPred accuracy and RepeatsDB annotation. To summarize, this work is a partial answer to the problems of TRP modeling and might be helpful during future investigations such as drug design and disease studies

Aerospace medicine and biology: A continuing bibliography with indexes (supplement 326)

This bibliography lists 108 reports, articles and other documents introduced into the NASA Scientific and Technical Information System during July, 1989. Subject coverage includes: aerospace medicine and psychology, life support systems and controlled environments, safety equipment, exobiology and extraterrestrial life, and flight crew behavior and performance

Aerospace medicine and biology: A continuing bibliography with indexes (supplement 338)

This bibliography lists 139 reports, articles and other documents introduced into the NASA Scientific and Technical Information System during June 1990. Subject coverage includes: aerospace medicine and psychology, life support systems and controlled environments, safety equipment, exobiology and extraterrestrial life, and flight crew behavior and performance

Aerospace Medicine and Biology

This bibliography lists 184 reports, articles and other documents introduced into the NASA Scientific and Technical Information System during October 1989. Subject coverage includes: aerospace medicine and psychology, life support systems and controlled environments, safety equipment, exobiology and extraterrestrial life, and flight crew behavior and performance

Event program

UNLV Undergraduates from all departments, programs and colleges participated in a campus-wide symposium on April 16, 2011. Undergraduate posters from all disciplines and also oral presentations of research activities, readings and other creative endeavors were exhibited throughout the festival

Interface: Technology & Portraiture

In Interface, five Kentucky-area artists explore a new language of representation with the aid of digital tools like Artificial Intelligence (AI) and Automatic Facial Recognition Software (AFR). Some artists use algorithms to alter celebrity faces beyond recognition, others feed data sets of existing art to AI models in an attempt to generate portraits of no one in particular. Others still create tools for understanding the very act of facial recognition or obfuscation. All have one thing in common: they wish to stretch the limits of and critique the genre of portraiture, as well as to cause viewers to question their assumptions about the genre’s scope and function.https://uknowledge.uky.edu/art_exhibitioncat_2023/1001/thumbnail.jp

Structure-guided evolution of antigenically distinct adeno-associated virus variants for immune evasion

Preexisting neutralizing antibodies (NAbs) against adeno-associated viruses (AAVs) pose a major, unresolved challenge that restricts patient enrollment in gene therapy clinical trials using recombinant AAV vectors. To tackle this problem, we developed a structure-guided approach to evolve AAV variants with altered antigenic footprints that cannot be recognized by preexisting antibodies. These proof-of-principle studies demonstrate that synthetic AAV variants can be evolved to evade neutralizing sera from different species—mice, nonhuman primates, and humans—without compromising yield and transduction efficiency or altering tropism. Our approach provides a roadmap for engineering any AAV strain to evade NAbs in prospective patients for human gene therapy

Marine Biotechnology: A New Vision and Strategy for Europe

Marine Board-ESF The Marine Board provides a pan-European platform for its member organisations to develop common priorities, to advance marine research, and to bridge the gap between science and policy in order to meet future marine science challenges and opportunities. The Marine Board was established in 1995 to facilitate enhanced cooperation between European marine science organisations (both research institutes and research funding agencies) towards the development of a common vision on the research priorities and strategies for marine science in Europe. In 2010, the Marine Board represents 30 Member Organisations from 19 countries. The Marine Board provides the essential components for transferring knowledge for leadership in marine research in Europe. Adopting a strategic role, the Marine Board serves its Member Organisations by providing a forum within which marine research policy advice to national agencies and to the European Commission is developed, with the objective of promoting the establishment of the European Marine Research Area

Focal Spot, Fall/Winter 1988

https://digitalcommons.wustl.edu/focal_spot_archives/1050/thumbnail.jp