Characterization of the Aspartate Transcarbamoylase that is Found in the pyrBC Complex of Bordetella Pertussis

An aspartate transcarbamoylase (ATCase) gene from Bordetella pertussis was amplified by PCR and ligated into pT-ADV for expression in Escherichia coli. This particular ATCase (pyrB) was an inactive gene found adjacent to an inactive dihydroorotase (DHOase) gene (pyrC'). This experiment was undertaken to determine whether this pyrB gene was capable of expression alone or if it was capable of expression only when cotransformed with a functional pyrC'. When transformed into E. coli TB2 pyrB-, the gene did not produce any ATCase activity. The gene was then co-transformed into E. coli TB2 pyrB- along with a plasmid containing the pyrC' gene from Pseudomonas aeruginosa and assayed for ATCase activity. Negative results were again recorded

Distribution of DDS-cerberus Authenticated Facial Recognition Streams

Successful missions in the field often rely upon communication technologies for tactics and coordination. One middleware used in securing these communication channels is Data Distribution Service (DDS) which employs a publish-subscribe model. However, researchers have found several security vulnerabilities in DDS implementations. DDS-Cerberus (DDS-C) is a security layer implemented into DDS to mitigate impersonation attacks using Kerberos authentication and ticketing. Even with the addition of DDS-C, the real-time message sending of DDS also needs to be upheld. This paper extends our previous work to analyze DDS-C’s impact on performance in a use case implementation. The use case covers an artificial intelligence (AI) scenario that connects edge sensors across a commercial network. Specifically, it characterizes how DDS-C performs between unmanned aerial vehicles (UAV), the cloud, and video streams for facial recognition. The experiments send a set number of video frames over the network using DDS to be processed by AI and displayed on a screen. An evaluation of network traffic using DDS-C revealed that it was not statistically significant compared to DDS for the majority of the configuration runs. The results demonstrate that DDS-C provides security benefits without significantly hindering the overall performance

Quantifying DDS-cerberus Network Control Overhead

Securing distributed device communication is critical because the private industry and the military depend on these resources. One area that adversaries target is the middleware, which is the medium that connects different systems. This paper evaluates a novel security layer, DDS-Cerberus (DDS-C), that protects in-transit data and improves communication efficiency on data-first distribution systems. This research contributes a distributed robotics operating system testbed and designs a multifactorial performance-based experiment to evaluate DDS-C efficiency and security by assessing total packet traffic generated in a robotics network. The performance experiment follows a 2:1 publisher to subscriber node ratio, varying the number of subscribers and publisher nodes from three to eighteen. By categorizing the network traffic from these nodes into either data message, security, or discovery+ with Quality of Service (QoS) best effort and reliable, the mean security traffic from DDS-C has minimal impact to Data Distribution Service (DDS) operations compared to other network traffic. The results reveal that applying DDS-C to a representative distributed network robotics operating system network does not impact performance

Protein phosphatase 2A promotes hepatocellular carcinogenesis in the diethylnitrosamine mouse model through inhibition of p53

Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide. Most HCCs develop in cirrhotic livers. Alcoholic liver disease, chronic hepatitis B and chronic hepatitis C are the most common underlying liver diseases. Hepatitis C virus (HCV)-specific mechanisms that contribute to HCC are presently unknown. Transgenic expression of HCV proteins in the mouse liver induces an overexpression of the protein phosphatase 2A catalytic subunit (PP2Ac). We have previously reported that HCV-induced PP2Ac overexpression modulates histone methylation and acetylation and inhibits DNA damage repair. In this study, we analyze tumor formation and gene expression using HCV transgenic mice that overexpress PP2Ac and liver tissues from patients with HCC. We demonstrate that PP2Ac overexpression interferes with p53-induced apoptosis. Injection of the carcinogen, diethylnitrosamine, induced significantly more and larger liver tumors in HCV transgenic mice that overexpress PP2Ac compared with control mice. In human liver biopsies from patients with HCC, PP2Ac expression was significantly higher in HCC tissue compared with non-tumorous liver tissue from the same patients. Our findings demonstrate an important role of PP2Ac overexpression in liver carcinogenesis and provide insights into the molecular pathogenesis of HCV-induced HC

NUAK2 is a critical YAP target in liver cancer

Hippo-YAP pathway plays an important role in cancers; however the in vivo relevance of YAP/TAZ target genes is unclear. Here, the authors show that NUAK2 is a target of YAP and participates in a feedback loop to maximize YAP activity. Inhibition of NUAK2 suppresses YAP-driven hepatomegaly and liver cancer growth, offering a new target for cancer therapy

The Energy Computation Paradox and ab initio Protein Folding

The routine prediction of three-dimensional protein structure from sequence remains a challenge in computational biochemistry. It has been intuited that calculated energies from physics-based scoring functions are able to distinguish native from nonnative folds based on previous performance with small proteins and that conformational sampling is the fundamental bottleneck to successful folding. We demonstrate that as protein size increases, errors in the computed energies become a significant problem. We show, by using error probability density functions, that physics-based scores contain significant systematic and random errors relative to accurate reference energies. These errors propagate throughout an entire protein and distort its energy landscape to such an extent that modern scoring functions should have little chance of success in finding the free energy minima of large proteins. Nonetheless, by understanding errors in physics-based score functions, they can be reduced in a post-hoc manner, improving accuracy in energy computation and fold discrimination

Platform Dependent Verification: On Engineering Verification Tools for 21st Century

The paper overviews recent developments in platform-dependent explicit-state LTL model checking.Comment: In Proceedings PDMC 2011, arXiv:1111.006

Stromal Vascular Fraction Transplantation as an Alternative Therapy for Ischemic Heart Failure: Anti-inflammatory Role

<p>Abstract</p> <p>Background</p> <p>The aims of this study were: (1) to show the feasibility of using adipose-derived stromal vascular fraction (SVF) as an alternative to bone marrow mono nuclear cell (BM-MNC) for cell transplantation into chronic ischemic myocardium; and (2) to explore underlying mechanisms with focus on anti-inflammation role of engrafted SVF and BM-MNC post chronic myocardial infarction (MI) against left ventricular (LV) remodelling and cardiac dysfunction.</p> <p>Methods</p> <p>Four weeks after left anterior descending coronary artery ligation, 32 Male Lewis rats with moderate MI were divided into 3 groups. SVF group (n = 12) had SVF cell transplantation (6 × 10⁶cells). BM-MNC group (n = 12) received BM-MNCs (6 × 10⁶) and the control (n = 10) had culture medium. At 4 weeks, after the final echocardiography, histological sections were stained with Styrus red and immunohistochemical staining was performed for α-smooth muscle actin, von Willebrand factor, CD3, CD8 and CD20.</p> <p>Results</p> <p>At 4 weeks, in SVF and BM-MNC groups, LV diastolic dimension and LV systolic dimension were smaller and fractional shortening was increased in echocardiography, compared to control group. Histology revealed highest vascular density, CD3+ and CD20+ cells in SVF transplanted group. SVF transplantation decreased myocardial mRNA expression of inflammatory cytokines TNF-α, IL-6, MMP-1, TIMP-1 and inhibited collagen deposition.</p> <p>Conclusions</p> <p>Transplantation of adipose derived SVF cells might be a useful therapeutic option for angiogenesis in chronic ischemic heart disease. Anti-inflammation role for SVF and BM transplantation might partly benefit for the cardioprotective effect for chronic ischemic myocardium.</p

Automated Alphabet Reduction for Protein Datasets

<p>Abstract</p> <p>Background</p> <p>We investigate automated and generic alphabet reduction techniques for protein structure prediction datasets. Reducing alphabet cardinality without losing key biochemical information opens the door to potentially faster machine learning, data mining and optimization applications in structural bioinformatics. Furthermore, reduced but informative alphabets often result in, e.g., more compact and human-friendly classification/clustering rules. In this paper we propose a robust and sophisticated alphabet reduction protocol based on mutual information and state-of-the-art optimization techniques.</p> <p>Results</p> <p>We applied this protocol to the prediction of two protein structural features: contact number and relative solvent accessibility. For both features we generated alphabets of two, three, four and five letters. The five-letter alphabets gave prediction accuracies statistically similar to that obtained using the full amino acid alphabet. Moreover, the automatically designed alphabets were compared against other reduced alphabets taken from the literature or human-designed, outperforming them. The differences between our alphabets and the alphabets taken from the literature were quantitatively analyzed. All the above process had been performed using a primary sequence representation of proteins. As a final experiment, we extrapolated the obtained five-letter alphabet to reduce a, much richer, protein representation based on evolutionary information for the prediction of the same two features. Again, the performance gap between the full representation and the reduced representation was small, showing that the results of our automated alphabet reduction protocol, even if they were obtained using a simple representation, are also able to capture the crucial information needed for state-of-the-art protein representations.</p> <p>Conclusion</p> <p>Our automated alphabet reduction protocol generates competent reduced alphabets tailored specifically for a variety of protein datasets. This process is done without any domain knowledge, using information theory metrics instead. The reduced alphabets contain some unexpected (but sound) groups of amino acids, thus suggesting new ways of interpreting the data.</p

The RSPO–LGR4/5–ZNRF3/RNF43 module controls liver zonation and size

LGR4/5 receptors and their cognate RSPO ligands potentiate Wnt/β-catenin signalling and promote proliferation and tissue homeostasis in epithelial stem cell compartments. In the liver, metabolic zonation requires a Wnt/β-catenin signalling gradient, but the instructive mechanism controlling its spatiotemporal regulation is not known. We have now identified the RSPO-LGR4/5-ZNRF3/RNF43 module as a master regulator of Wnt/β-catenin-mediated metabolic liver zonation. Liver-specific LGR4/5 loss of function (LOF) or RSPO blockade disrupted hepatic Wnt/β-catenin signalling and zonation. Conversely, pathway activation in ZNRF3/RNF43 LOF mice or with recombinant RSPO1 protein expanded the hepatic Wnt/β-catenin signalling gradient in a reversible and LGR4/5-dependent manner. Recombinant RSPO1 protein increased liver size and improved liver regeneration, whereas LGR4/5 LOF caused the opposite effects, resulting in hypoplastic livers. Furthermore, we show that LGR4(+) hepatocytes throughout the lobule contribute to liver homeostasis without zonal dominance. Taken together, our results indicate that the RSPO-LGR4/5-ZNRF3/RNF43 module controls metabolic liver zonation and is a hepatic growth/size rheostat during development, homeostasis and regeneration