Predictive biomarker discovery through the parallel integration of clinical trial and functional genomics datasets

The European Union multi-disciplinary Personalised RNA interference to Enhance the Delivery of Individualised Cytotoxic and Targeted therapeutics (PREDICT) consortium has recently initiated a framework to accelerate the development of predictive biomarkers of individual patient response to anti-cancer agents. The consortium focuses on the identification of reliable predictive biomarkers to approved agents with anti-angiogenic activity for which no reliable predictive biomarkers exist: sunitinib, a multi-targeted tyrosine kinase inhibitor and everolimus, a mammalian target of rapamycin (mTOR) pathway inhibitor. Through the analysis of tumor tissue derived from pre-operative renal cell carcinoma (RCC) clinical trials, the PREDICT consortium will use established and novel methods to integrate comprehensive tumor-derived genomic data with personalized tumor-derived small hairpin RNA and high-throughput small interfering RNA screens to identify and validate functionally important genomic or transcriptomic predictive biomarkers of individual drug response in patients. PREDICT's approach to predictive biomarker discovery differs from conventional associative learning approaches, which can be susceptible to the detection of chance associations that lead to overestimation of true clinical accuracy. These methods will identify molecular pathways important for survival and growth of RCC cells and particular targets suitable for therapeutic development. Importantly, our results may enable individualized treatment of RCC, reducing ineffective therapy in drug-resistant disease, leading to improved quality of life and higher cost efficiency, which in turn should broaden patient access to beneficial therapeutics, thereby enhancing clinical outcome and cancer survival. The consortium will also establish and consolidate a European network providing the technological and clinical platform for large-scale functional genomic biomarker discovery. Here we review our current understanding of molecular mechanisms driving resistance to anti-angiogenesis agents, the current limitations of laboratory and clinical trial strategies and how the PREDICT consortium will endeavor to identify a new generation of predictive biomarkers

A multi-species evaluation of digital wildlife monitoring using the Sigfox IoT network

DATA AVAILABILITY : The Amazon rainforest datasets are publicly available at Movebank (www. movebank.org [26]) (Movebank study ID: 2122748764). The other datasets generated and or analysed during the current study are not publicly avail able due to ongoing studies and to protect animals from poaching but are almost entirely archived on Movebank (Movebank study IDs: 2155070222, 1409712816, 894254831, 1365616235, 1493312931, 1296030530, 1725249380, 1431850095, 1323242594, 1732512659, 1286005281, 1291290503, 1600771155, 1670322706, 1623175929, 1323163019, 1323668146, 2057805903, 2198940839), and can be made available by the authors upon reasonable request.Bio-telemetry from small tags attached to animals is one of the principal methods for studying the ecology and behaviour of wildlife. The field has constantly evolved over the last 80 years as technological improvement enabled a diversity of sensors to be integrated into the tags (e.g., GPS, accelerometers, etc.). However, retrieving data from tags on free-ranging animals remains a challenge since satellite and GSM networks are relatively expensive and or power hungry. Recently a new class of low-power communication networks have been developed and deployed worldwide to connect the internet of things (IoT). Here, we evaluated one of these, the Sigfox IoT network, for the potential as a real-time multi-sensor data retrieval and tag commanding system for studying fauna across a diversity of species and ecosystems. We tracked 312 individuals across 30 species (from 25 g bats to 3 t elephants) with seven different device concepts, resulting in more than 177,742 successful transmissions. We found a maximum line of sight communication distance of 280 km (on a flying cape vulture [Gyps coprotheres]), which sets a new documented record for animal-borne digital data transmission using terrestrial infrastructure. The average transmission success rate amounted to 68.3% (SD 22.1) on flying species and 54.1% (SD 27.4) on terrestrial species. In addition to GPS data, we also collected and transmitted data products from accelerometers, barometers, and thermometers. Further, we assessed the performance of Sigfox Atlas Native, a low-power method for positional estimates based on radio signal strengths and found a median accuracy of 12.89 km (MAD 5.17) on animals. We found that robust real-time communication (median message delay of 1.49 s), the extremely small size of the tags (starting at 1.28 g without GPS), and the low power demands (as low as 5.8 µAh per transmitted byte) unlock new possibilities for ecological data collection and global animal observation.The Deutsche Forschungsgemeinschaft (DFG, German Research Foundation). Open Access funding enabled and organized by Projekt DEAL.https://animalbiotelemetry.biomedcentral.comVeterinary Tropical Disease

anti-CD47 clone MIAP410 ELISA

ELISA performed at Stanford University with mouse anti-CD47, MIAP410 antibody. Antibody used for this project (https://osf.io/9pbos/

Pyrazolate-based cobalt(II)-containing metal-organic frameworks in heterogeneous catalytic oxidation reactions: elucidating the role of entatic states for biomimetic oxidation processes

Crystal structures of two metal–organic frameworks (MFU‐1 and MFU‐2) are presented, both of which contain redox‐active CoII centres coordinated by linear 1,4‐bis[(3,5‐dimethyl)pyrazol‐4‐yl] ligands. In contrast to many MOFs reported previously, these compounds show excellent stability against hydrolytic decomposition. Catalytic turnover is achieved in oxidation reactions by employing tert‐butyl hydroperoxide and the solid catalysts are easily recovered from the reaction mixture. Whereas heterogeneous catalysis is unambiguously demonstrated for MFU‐1, MFU‐2 shows catalytic activity due to slow metal leaching, emphasising the need for a deeper understanding of structure–reactivity relationships in the future design of redox‐active metal–organic frameworks. Mechanistic details for oxidation reactions employing tert‐butyl hydroperoxide are studied by UV/Vis and IR spectroscopy and XRPD measurements. The catalytic process accompanying changes of redox states and structural changes were investigated by means of cobalt K‐edge X‐ray absorption spectroscopy. To probe the putative binding modes of molecular oxygen, the isosteric heats of adsorption of O2 were determined and compared with models from DFT calculations. The stabilities of the frameworks in an oxygen atmosphere as a reactive gas were examined by temperature‐programmed oxidation (TPO). Solution impregnation of MFU‐1 with a co‐catalyst (N‐hydroxyphthalimide) led to NHPI@MFU‐1, which oxidised a range of organic substrates under ambient conditions by employing molecular oxygen from air. The catalytic reaction involved a biomimetic reaction cascade based on free radicals. The concept of an entatic state of the cobalt centres is proposed and its relevance for sustained catalytic activity is briefly discussed

Polypeptide-binding proteins mediate completion of co-translational protein translocation into the mammalian endoplasmic reticulum

The first step in the secretion of most mammalian proteins is their transport into the lumen of the endoplasmic reticulum (ER). Transport of pre-secretory proteins into the mammalian ER requires signal peptides in the precursor proteins and a protein translocase in the ER membrane. In addition, hitherto unidentified lumenal ER proteins have been shown to be required for vectorial protein translocation. This requirement was confirmed in this study by using proteoliposomes that were made from microsomal detergent extracts and contained either low or high concentrations of lumenal ER proteins. Furthermore, immunoglobulin-heavy-chain-binding protein (BiP) was shown to be able to substitute for the full set of lumenal proteins and, in the case of biotinylated precursor proteins, avidin was found to be able to substitute for lumenal proteins. Thus, the polypeptide-chain-binding protein BiP was identified as one lumenal protein that is involved in efficient vectorial protein translocation into the mammalian ER

CD14-expressing cancer cells establish the inflammatory and proliferative tumor microenvironment in bladder cancer.

Nonresolving chronic inflammation at the neoplastic site is consistently associated with promoting tumor progression and poor patient outcomes. However, many aspects behind the mechanisms that establish this tumor-promoting inflammatory microenvironment remain undefined. Using bladder cancer (BC) as a model, we found that CD14-high cancer cells express higher levels of numerous inflammation mediators and form larger tumors compared with CD14-low cells. CD14 antigen is a glycosyl-phosphatidylinositol (GPI)-linked glycoprotein and has been shown to be critically important in the signaling pathways of Toll-like receptor (TLR). CD14 expression in this BC subpopulation of cancer cells is required for increased cytokine production and increased tumor growth. Furthermore, tumors formed by CD14-high cells are more highly vascularized with higher myeloid cell infiltration. Inflammatory factors produced by CD14-high BC cells recruit and polarize monocytes and macrophages to acquire immune-suppressive characteristics. In contrast, CD14-low BC cells have a higher baseline cell division rate than CD14-high cells. Importantly, CD14-high cells produce factors that further increase the proliferation of CD14-low cells. Collectively, we demonstrate that CD14-high BC cells may orchestrate tumor-promoting inflammation and drive tumor cell proliferation to promote tumor growth

Isoaspartyl dipeptidase activity of plant-type asparaginases.

Recombinant plant-type asparaginases from the cyanobacteria Synechocystis sp. PCC (Pasteur culture collection) 6803 and Anabaena sp. PCC 7120, from Escherichia coli and from the plant Arabidopsis thaliana were expressed in E. coli with either an N-terminal or a C-terminal His tag, and purified. Although each of the four enzymes is encoded by a single gene, their mature forms consist of two protein subunits that are generated by autoproteolytic cleavage of the primary translation products at the Gly-Thr bond within the sequence GTI/VG. The enzymes not only deamidated asparagine but also hydrolysed a range of isoaspartyl dipeptides. As various isoaspartyl peptides are known to arise from proteolytic degradation of post-translationally altered proteins containing isoaspartyl residues, and from depolymerization of the cyanobacterial reserve polymer multi-L-arginyl-poly-L-aspartic acid (cyanophycin), plant-type asparaginases may not only function in asparagine catabolism but also in the final steps of protein and cyanophycin degradation. The properties of these enzymes are compared with those of the sequence-related glycosylasparaginases