Browsing School of Systems Biology by Issue Date

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Oxidized Extracellular DNA as a Stress Signal in Human Cells

Ermakov, Aleksei V.; Konkova, Marina S.; Kostyuk, Svetlana V.; Izevskaya, Vera L.; Baranova, Ancha; Veiko, Natalya N. (Hindawi Publishing Corporation, 2013-01)

The term “cell-free DNA” (cfDNA) was recently coined for DNA fragments from plasma/serum, while DNA present in in vitro cell culture media is known as extracellular DNA (ecDNA). Under oxidative stress conditions, the levels ...
Knowledge-Based Identification of Soluble Biomarkers: Hepatic Fibrosis in NAFLD as an Example

Page, Sandra; Birerdinc, Aybike; Estep, Michael; Stepanova, Maria; Afendy, Arian; Petricoin, Emanuel; Younossi, Zobair; Chandhoke, Vikas; Baranova, Ancha (Public Library of Science, 2013-02-06)

The discovery of biomarkers is often performed using high-throughput proteomics-based platforms and is limited to the molecules recognized by a given set of purified and validated antigens or antibodies. Knowledge-based, ...
Functional Genomic Analyses of Two Morphologically Distinct Classes of Drosophila Sensory Neurons: Post-Mitotic Roles of Transcription Factors in Dendritic Patterning

Iyer, Eswar Prasad R.; Iyer, Srividya Chandramouli; Sullivan, Luis; Wang, Dennis; Meduri, Ramakrishna; Graybeal, Lacey L.; Cox, Daniel N. (Public Library of Science, 2013-08-15)

Background Neurons are one of the most structurally and functionally diverse cell types found in nature, owing in large part to their unique class specific dendritic architectures. Dendrites, being highly specialized ...
Sequence and structure based models of HIV-1 protease and reverse transcriptase drug resistance

Masso, Majid; Vaisman, Iosif I. (BioMed Central, 2013-10-01)

Background Successful management of chronic human immunodeficiency virus type 1 (HIV-1) infection with a cocktail of antiretroviral medications can be negatively affected by the presence of drug resistant mutations in the ...
Knowledge-based compact disease models identify new molecular players contributing to early-stage Alzheimer’s disease

Mayburd, Anatoly; Baranova, Ancha (BioMed Central, 2013-11-07)

Background High-throughput profiling of human tissues typically yield as results the gene lists comprised of a mix of relevant molecular entities with multiple false positives that obstruct the translation of such results ...
Four-body atomic potential for modeling protein-ligand binding affinity: application to enzyme-inhibitor binding energy prediction

Masso, Majid (BioMed Central, 2013-11-08)

Background : Models that are capable of reliably predicting binding affinities for protein-ligand complexes play an important role the field of structure-guided drug design. Methods : Here, we begin by applying the ...
The Role of IKKβ in Venezuelan Equine Encephalitis Virus Infection

Amaya, Moushimi; Voss, Kelsey; Sampey, Gavin; Senina, Svetlana; de la Fuente, Cynthia; Mueller, Claudius; Calvert, Valerie; Kehn-Hall, Kylene; Carpenter, Calvin; Kashanchi, Fatah; Bailey, Charles; Mogelsvang, Soren; Petricoin, Emanuel; Narayanan, Aarthi (Public Library of Science, 2014-02-19)

Venezuelan equine encephalitis virus (VEEV) belongs to the genus Alphavirus, family Togaviridae. VEEV infection is characterized by extensive inflammation and studies from other laboratories implicated an involvement of ...
Multi-Faceted Proteomic Characterization of Host Protein Complement of Rift Valley Fever Virus Virions and Identification of Specific Heat Shock Proteins, Including HSP90, as Important Viral Host Factors

Nuss, Jonathan E.; Kehn-Hall, Kylene; Benedict, Ashwini; Costantino, Julie; Ward, Michael; Peyser, Brian D.; Retterer, Cary J.; Tressler, Lyal E.; Wanner, Laura M.; McGovern, Hugh F.; Zaidi, Anum; Anthony, Scott M.; Kota, Krishna P.; Bavari, Sina; Hakami, Ramin M. (Public Library of Science, 2014-05-08)

Rift Valley fever is a potentially fatal disease of humans and domestic animals caused by Rift Valley fever virus (RVFV). Infection with RVFV in ruminants can cause near 100% abortion rates and recent outbreaks in naïve ...
Whole Proteome Analysis of Mouse Lymph Nodes in Cutaneous Anthrax

Popova, Taissia G.; Espina, Virginia; Zhou, Weidong; Mueller, Claudius; Liotta, Lance; Popov, Serguei G. (Public Library of Science, 2014-10-20)

This study aimed to characterize a soluble proteome of popliteal lymph nodes during lymphadenitis induced by intradermal injection of Bacillus anthracis Sterne spores in mice using tandem LC-MS/MS and reverse-phase protein ...
Cranberry proanthocyanidins have anti-biofilm properties against Pseudomonas aeruginosa

Ulrey, Robert K.; Barksdale, Stephanie M.; Zhou, Weidong; van Hoek, Monique L. (BioMed Central, 2014-12-16)

Background Bacteria within a biofilm are phenotypically more resistant to antibiotics, desiccation, and the host immune system, making it an important virulence factor for many microbes. Cranberry juice has long been used ...
Age-Independent Rise of Inflammatory Scores May Contribute to Accelerated Aging in Multi-Morbidity

Stepanova, Maria; Rodriguez, Edgar; Birerdinc, Aybike; Baranova, Ancha (Impact Journals, LLC, 2015-02-10)

Aging is associated with an increase in a chronic, low-grade inflammation. This phenomenon, termed “inflammaging” is also a risk factor for both morbidity and mortality in the elderly. Frequent co-occurrence of chronic ...
Host response during Yersinia pestis infection of human bronchial epithelial cells involves negative regulation of autophagy and suggests a modulation of survival-related and cellular growth pathways

Alem, Farhang; Yao, Kuan; Lane, Douglas; Calvert, Valerie; Petricoin, Emanuel F.; Kramer, Liana; Hale, Martha L.; Bavari, Sina; Panchal, Rekha G.; Hakami, Ramin M. (Frontiers Media, 2015-02-13)

Yersinia pestis (Yp) causes the re-emerging disease plague, and is classified by the CDC and NIAID as a highest priority (Category A) pathogen. Currently, there is no approved human vaccine available and advances in early ...
Chemokine-Releasing Nanoparticles for Manipulation of the Lymph Node Microenvironment

Popova, Taissia G.; Teunis, Allison; Magni, Ruben; Luchini, Alessandra; Espina, Virginia; Liotta, Lance A.; Popov, Serguei G. (Multidisciplinary Digital Publishing Institute, 2015-03-05)

Chemokines (CKs) secreted by the host cells into surrounding tissue establish concentration gradients directing the migration of leukocytes. We propose an in vivo CK gradient remodeling approach based on sustained release ...
BRCA1 functions as a novel transcriptional cofactor in HIV-1 infection

Guendel, Irene; Meltzer, Beatrix W.; Baer, Alan; Dever, Seth M.; Valerie, Kristoffer; Guo, Jia; Wu, Yuntao; Kehn-Hall, Kylene (BioMed Central, 2015-03-06)

Background Viruses have naturally evolved elegant strategies to manipulate the host’s cellular machinery, including ways to hijack cellular DNA repair proteins to aid in their own replication. Retroviruses induce DNA ...
In silico prediction of phosphorylation of NS3 as an essential mechanism for Dengue virus replication and the antiviral activity of Quercetin

Alomair, Lamya Abdulaziz; Almsned, Fahad; Ullah, Aman; Jafri, M. Saleet (Biology, 2019)

Infection by Dengue virus is a global health problem for which there have been challenges to obtaining a cure. Current vaccines can only be narrowly applied in ongoing clinical trials. We employed computational methods to ...
X-ROS Signaling Depends on Length-Dependent Calcium Buffering by Troponin

Limbu, Sarita; Prosser, Benjamin L.; Lederer, W. Jonathan; Ward, Christopher W.; Jafri, M. Saleet (2021)
Machine Learning-Based Prediction of Drug and Ligand Binding in BCL-2 Variants Through Molecular Dynamics

Hamre, John III; Klimov, Dimitri K.; McCoy, Mathew D.; Jafri, M. Saleet (2021)

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