EXPANSION: A Webserver to Explore the Functional Consequences of Protein-Coding Alternative Splice Variants in Cancer Genomics

EXPANSION (https://expansion.bioinfolab.sns.it/) is an integrated web-server to explore the functional consequences of protein-coding alternative splice (AS) variants. We combined information from Differentially Expressed (DE) protein-coding transcripts from cancer genomics, together with domain architecture, protein interaction network, and gene enrichment analysis to provide an easy-to-interpret view of the effects of protein-coding splice variants. We retrieved all the protein-coding Ensembl transcripts and mapped Interpro domains and Post-translational modifications (PTMs) on canonical sequences to identify functionally relevant splicing events. We also retrieved isoform-specific protein-protein interactions (PPIs) and binding regions from IntAct to uncover isoform-specific functions via gene-sets over-representation analysis. Through EXPANSION, users can analyse pre-calculated or user-inputted DE transcript datasets, to easily gain functional insights on any protein spliceform of interest

Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain.

Z-DNA and Z-RNA are functionally important left-handed structures of nucleic acids, which play a significant role in several molecular and biological processes including DNA replication, gene expression regulation and viral nucleic acid sensing. Most proteins that have been proven to interact with Z-DNA/Z-RNA contain the so-called Zα domain, which is structurally well conserved. To date, only eight proteins with Zα domain have been described within a few organisms (including human, mouse, Danio rerio, Trypanosoma brucei and some viruses). Therefore, this paper aimed to search for new Z-DNA/Z-RNA binding proteins in the complete PDB structures database and from the AlphaFold2 protein models. A structure-based similarity search found 14 proteins with highly similar Zα domain structure in experimentally-defined proteins and 185 proteins with a putative Zα domain using the AlphaFold2 models. Structure-based alignment and molecular docking confirmed high functional conservation of amino acids involved in Z-DNA/Z-RNA, suggesting that Z-DNA/Z-RNA recognition may play an important role in a variety of cellular processes

Design, Implementation, and Performance Analysis of In-Home Video based Monitoring System for Patients with Dementia

Dementia is a major public health problem affecting 35 million people in USA. The caregivers of dementia patients experience many types of physical and psychological stress while dealing with disruptive behaviors of dementia patients. This will also result in frequent hospitalizations and re-admissions. In this project we design, implement, and measure the performance of an advanced video based monitoring system to aide the caregivers in managing the behavioral symptoms of dementia patients. The caregivers will be able to easily capture and share the antecedents, consequences, and the function of behavior, through a video clip, and get the real-time feedback from clinical experts. Overall the system will help in reducing the hospital admission/readmission, improve the quality of life for caregivers, and in general result in reduced cost of health care systems. System is developed using python scripts, open source web frameworks, FFmpeg tool chain, and commercial off-the-shelf IP camera and mini-PC. WebRTC is used for video based coaching of caregivers. A framework has been developed to evaluate the storage and retrieval latency of video clips to public and On-premise clouds, video streaming performance in LAN and WLAN environments, and WebRTC performance in different types of access networks. InstaGENIrack, a GENI rack in KU is used as on-premise cloud infrastructure for the evaluation. OpenSSL utilities are employed for secured transport and storage of captured video clips. We conducted the trials in Google fiber ISP in Kansas city, and compared the performance with other traditional ISPs

Enabling End-To-End Orchestration of Multi-Cloud Applications

The orchestration of application components across heterogeneous cloud providers is a problem that has been tackled using various approaches, some of which led to the creation of cloud orchestration and management standards, such as TOSCA and CAMP. Standardization is a definitive method of providing an end-To-end solution capable of defining, deploying, and managing applications and their components across heterogeneous cloud providers. TOSCA and CAMP, however, perform different functions with regard to cloud applications. TOSCA is focused primarily on topology modeling and orchestration, whereas CAMP is focused on deployment and management of applications. This paper presents a novel solution that not only involves the combination of the emerging standards TOSCA and CAMP, but also introduces extensions to CAMP to allow for multi-cloud application orchestration through the use of declarative policies. Extensions to the CAMP platform are also made, which brings the standards closer together to enable a seamless integration. Our proposal provides an end-To-end cloud orchestration solution that supports a cloud application modeling and deployment process, allowing a cloud application to span and be deployed over multiple clouds. The feasibility and the benefit of our approach are demonstrated in our validation study

CCP4 Cloud for structure determination and project management in macromolecular crystallography

Nowadays, progress in the determination of three-dimensional macromolecular structures from diffraction images is achieved partly at the cost of increasing data volumes. This is due to the deployment of modern high-speed, high-resolution detectors, the increased complexity and variety of crystallographic software, the use of extensive databases and high-performance computing. This limits what can be accomplished with personal, offline, computing equipment in terms of both productivity and maintainability. There is also an issue of long-term data maintenance and availability of structure-solution projects as the links between experimental observations and the final results deposited in the PDB. In this article, CCP4 Cloud, a new front-end of the CCP4 software suite, is presented which mitigates these effects by providing an online, cloud-based environment for crystallographic computation. CCP4 Cloud was developed for the efficient delivery of computing power, database services and seamless integration with web resources. It provides a rich graphical user interface that allows project sharing and long-term storage for structure-solution projects, and can be linked to data-producing facilities. The system is distributed with the CCP4 software suite version 7.1 and higher, and an online publicly available instance of CCP4 Cloud is provided by CCP4.The following funding is acknowledged: Biotechnology and Biological Sciences Research Council (grant No. BB/L007037/1; grant No. BB/S007040/1; grant No. BB/S007083/1; grant No. BB/S005099/1; grant No. BB/S007105/1; award No. BBF020384/1); Medical Research Council (grant No.MC_UP_A025_1012; grant No. MC_U105184325); Ro¨ntgenA˚ ngstro¨m Cluster (grant No. 349-2013-597); Nederlandse Wetenschappelijke Organisatie (grant No. TKI 16219)

Structural alphabets derived from attractors in conformational space

Background: The hierarchical and partially redundant nature of protein structures justifies the definition of frequently occurring conformations of short fragments as 'states'. Collections of selected representatives for these states define Structural Alphabets, describing the most typical local conformations within protein structures. These alphabets form a bridge between the string-oriented methods of sequence analysis and the coordinate-oriented methods of protein structure analysis.Results: A Structural Alphabet has been derived by clustering all four-residue fragments of a high-resolution subset of the protein data bank and extracting the high-density states as representative conformational states. Each fragment is uniquely defined by a set of three independent angles corresponding to its degrees of freedom, capturing in simple and intuitive terms the properties of the conformational space. The fragments of the Structural Alphabet are equivalent to the conformational attractors and therefore yield a most informative encoding of proteins. Proteins can be reconstructed within the experimental uncertainty in structure determination and ensembles of structures can be encoded with accuracy and robustness.Conclusions: The density-based Structural Alphabet provides a novel tool to describe local conformations and it is specifically suitable for application in studies of protein dynamics. © 2010 Pandini et al; licensee BioMed Central Ltd

Understanding Multilevel Protein Communication of the Mitochondrial Carrier Family and the TIM23 Complex

Mitochondria are dynamic organelles that require an intricate network of protein communication that traverse multiple compartments and membrane bilayers but membrane proteins are notoriously difficult to study with traditional structure determination methods. This thesis investigates intra- and inter- membrane protein communication including residue-residue communications within a protein, between protein domains, as well as inter-protein communication between proteins of a complex and of the electron transport chain (ETC). The first part of this thesis utilizes coevolution analysis to determine novel insights into the structure and structural dynamics of the mitochondrial carrier family (MCF) and Tim23. The ADP/ATP Carrier (AAC) is the most abundant and widely studied transporter of the MCF and imports ADP into the mitochondrial matrix and exports ATP to the cytosol by an alternating access mechanism resulting in two alternate conformational states: one with the channel interior exposed to the cytosol and one exposed to the matrix. Coevolution analysis of the AAC identifies novel residue interactions integral to the transition and stabilization of the AAC. Tim23 is the core channel-forming protein of the translocase of the inner membrane (TIM23) complex that is responsible for the translocation and integration of approximately 70% of mitochondrial proteins. Tim23 is composed of a soluble N-terminal domain in the intermembrane space and a membrane bound channel domain. Although key structural regions for complex assembly and protein translocation have been identified there is no high-resolution structure of Tim23. The coevolution analysis presented here predicts the first model of the Tim23 channel domain and predicts residue interactions that suggest novel structural dynamics. The second part of this thesis investigates the inter-protein communication between subunits of the TIM23 complex. Assays of native protein assemblies, demonstrate how the lipid cardiolipin, supports proper TIM23 subunit association. The final part of this thesis focuses on understanding the effect of NAPQI, an acetaminophen metabolite, on the electron transport activity of complex II. A reductionist approach, in which complex II was reconstituted into model membrane systems, was necessary to determine the concentration dependent effect of NAPQI on complex II activity