Genome-wide inhibition of pro-atherogenic gene expression by multi-STAT targeting compounds as a novel treatment strategy of CVDs

Cardiovascular diseases (CVDs), including atherosclerosis, are globally the leading cause of death. Key factors contributing to onset and progression of atherosclerosis include the pro-inflammatory cytokines Interferon (IFN)a and IFN? and the Pattern Recognition Receptor (PRR) Toll-like receptor 4 (TLR4). Together, they trigger activation of Signal Transducer and Activator of Transcription (STAT)s. Searches for compounds targeting the pTyr-SH2 interaction area of STAT3, yielded many small molecules, including STATTIC and STX-0119. However, many of these inhibitors do not seem STAT3-specific. We hypothesized that multi-STAT-inhibitors that simultaneously block STAT1, STAT2, and STAT3 activity and pro-inflammatory target gene expression may be a promising strategy to treat CVDs. Using comparative in silico docking of multiple STAT-SH2 models on multi-million compound libraries, we identified the novel multi-STAT inhibitor, C01L-F03. This compound targets the SH2 domain of STAT1, STAT2, and STAT3 with the same affinity and simultaneously blocks their activity and expression of multiple STAT-target genes in HMECs in response to IFNa. The same in silico and in vitro multi-STAT inhibiting capacity was shown for STATTIC and STX-0119. Moreover, C01L-F03, STATTIC and STX-0119 were also able to affect genome-wide interactions between IFN? and TLR4 by commonly inhibiting pro-inflammatory and pro-atherogenic gene expression directed by cooperative involvement of STATs with IRFs and/or NF-κB. Moreover, we observed that multi-STAT inhibitors could be used to inhibit IFN?+LPS-induced HMECs migration, leukocyte adhesion to ECs as well as impairment of mesenteric artery contractility. Together, this implicates that application of a multi-STAT inhibitory strategy could provide great promise for the treatment of CVDsThis publication was supported by grants UMO-2015/17/B/NZ2/00967 (HB) and UMO-2015/16/T/NZ2/00055 (MS) from National Science Centre Poland. This work was supported by the KNOW RNA Research Centre in Poznan (No. 01/KNOW2/2014) and in part by PL-Grid Infrastructure (MS

Multivariate Analysis in Management, Engineering and the Sciences

Recently statistical knowledge has become an important requirement and occupies a prominent position in the exercise of various professions. In the real world, the processes have a large volume of data and are naturally multivariate and as such, require a proper treatment. For these conditions it is difficult or practically impossible to use methods of univariate statistics. The wide application of multivariate techniques and the need to spread them more fully in the academic and the business justify the creation of this book. The objective is to demonstrate interdisciplinary applications to identify patterns, trends, association sand dependencies, in the areas of Management, Engineering and Sciences. The book is addressed to both practicing professionals and researchers in the field

Microbial lifestyle engineering

Using Pseudomonas putida KT2440 as a proof-of-concept organism, this thesis was aimed at microbial lifestyle engineering for industrial applications. In this thesis, a structured approach was applied by first determining what microbial improvements industry is looking for by conducting a series of interviews with both industry and academia. Besides pinpointing the fields of interest from an industrial perspective, the interviews also clarified the limitations of the actual implementation of novel or (synthetically) adapted strains developed. Strain safety being at the top of their list, we first checked the claimed GRAS safety level of P. putida KT2440. A major obstacle for the breakthrough of P. putida KT2440 to be widely used as a biotechnological host is its obligate aerobic metabolism. In silico-directed strain improvement were initiated by the adaptation of strict aerobic P. putida KT2440 to micro-oxic and anoxic conditions. Adaptation to micro-oxic levels was done by first creating a design for a recombinant strain capable of anaerobic fermentation. The bottlenecks uncovered were resolved by insertion of three genes, and the recombinant strains were monitored through an adaptive laboratory evolution method with oxygen gradients set up specifically for this purpose. Recombinant strains were able to grow under micro-oxic conditions. Strain performance did not improve compared to the negative control under anoxic conditions. A more elaborate in-silico analysis was performed, combining protein domain analysis, transcriptomic analysis and genome-scale metabolic models to design a recombinant P. putida KT2440 strain capable of anaerobic respiration. Another general limitation in strains is their limited thermo-tolerance. We discovered a strong universal connection between NAD+ availability and thermo-tolerance. By replacing one single gene for a thermophilic heterolog in mesophilic prokaryotes, both P. putida and E. coli showed instant improved thermo-tolerance. Insertion of the aspartate NAD+ biogeneration pathway in eukaryotic yeast S. cerevisiae resulted in a similar effect. To determine the value of this thermo-tolerance in industry, a down-scaled microfluidics system was developed to mimic temperature fluctuations occurring in large scale  bioreactors. The novel discovery between thermo-tolerance and NAD+ availabilty was patented

Dictyostelium discoideum as a model for the evaluation of teratogenic compounds

Before new chemicals can be put on the market, they must be evaluated for toxicological safety. Evaluating the safety of new chemicals, for either medical, cosmetic or environmental application, is tightly regulated by worldwide legislation. A critical aspect of toxicity evaluation is developmental and reproductive toxicity (DART) testing. Traditionally, DART testing has been conducted in vivo in mammalian model systems. In fact, current EU DART testing guidelines accounts for the majority of animals used and the financial costs of new compound compliance testing. Therefore, because of the need to reduce the financial and animal costs associated with DART testing, there is a growing demand for new alternative model systems for toxicity evaluation. Dictyostelium discoideum is a eukaryotic amoeba which due to its unique developmental cycle has the potential to serve as a non-animal alternative model in DART testing. However, for a new alternative model to be proven effective it must allow for high-throughput screening, whilst maintaining biological complexity; allowing developmental toxicity results to be predictive of mammalian systems. To address these concerns, we developed new high-throughput D. discoideum growth and developmental toxicity assays. We use the assays to characterise toxicity across a broad range of test compounds, thereby revealing a significant relationship between D. discoideum and mammalian toxicity values. Our data demonstrates that D. discoideum has the biological complexity necessary to be predictive of mammalian toxicity. We further assess whether D. discoideum could be used to genetically characterise developmentally toxic compounds. Using next generation functional genomic screens, we show how the developmentally toxicity compounds, lithium and VPA can be globally genetically phenotyped. Using this genetic phenotyping approach, we were also able to identify the biological targets and processes that mediate lithium and VPA toxicity. Together, these studies illustrate the potential of D. discoideum to be developed as a new alternative model in DART testing

Washington University Senior Undergraduate Research Digest (WUURD), Spring 2018

From the Washington University Office of Undergraduate Research Digest (WUURD), Vol. 13, 05-01-2018. Published by the Office of Undergraduate Research. Joy Zalis Kiefer, Director of Undergraduate Research and Associate Dean in the College of Arts & Scienc

Evolutionary genomics : statistical and computational methods

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward

Genome-Wide Inhibition of Pro-atherogenic Gene Expression by Multi-STAT Targeting Compounds as a Novel Treatment Strategy of CVDs

Cardiovascular diseases (CVDs), including atherosclerosis, are globally the leading cause of death. Key factors contributing to onset and progression of atherosclerosis include the pro-inflammatory cytokines Interferon (IFN)α and IFNγ and the Pattern Recognition Receptor (PRR) Toll-like receptor 4 (TLR4). Together, they trigger activation of Signal Transducer and Activator of Transcription (STAT)s. Searches for compounds targeting the pTyr-SH2 interaction area of STAT3, yielded many small molecules, including STATTIC and STX-0119. However, many of these inhibitors do not seem STAT3-specific. We hypothesized that multi-STAT-inhibitors that simultaneously block STAT1, STAT2, and STAT3 activity and pro-inflammatory target gene expression may be a promising strategy to treat CVDs. Using comparative in silico docking of multiple STAT-SH2 models on multi-million compound libraries, we identified the novel multi-STAT inhibitor, C01L_F03. This compound targets the SH2 domain of STAT1, STAT2, and STAT3 with the same affinity and simultaneously blocks their activity and expression of multiple STAT-target genes in HMECs in response to IFNα. The same in silico and in vitro multi-STAT inhibiting capacity was shown for STATTIC and STX-0119. Moreover, C01L_F03, STATTIC and STX-0119 were also able to affect genome-wide interactions between IFNγ and TLR4 by commonly inhibiting pro-inflammatory and pro-atherogenic gene expression directed by cooperative involvement of STATs with IRFs and/or NF-κB. Moreover, we observed that multi-STAT inhibitors could be used to inhibit IFNγ+LPS-induced HMECs migration, leukocyte adhesion to ECs as well as impairment of mesenteric artery contractility. Together, this implicates that application of a multi-STAT inhibitory strategy could provide great promise for the treatment of CVDs

East Carolina University: Creating a Better Tomorrow: 5th Annual Research & Creative Achievement Week

The Program of the 5th Annual Research and Creative Activity Week is available, with a schedule of events and abstracts for the lectures and presentations. These events took place from April 4-8, 2011, in Mendenhall Student Center on the campus of East Carolina University