Identification of protein coding genes in genomes with statistical functions based on the circular code

A new statistical approach using functions based on the circular code classifies correctly more than 93 % of bases in protein (coding) genes and non-coding genes of human sequences. Based on this statistical study, a research software called "Analysis of Coding Genes" (ACG) has been developed for identifying protein genes in the genomes and for determining their frame. Furthermore, the software ACG also allows an evaluation of the length of protein genes, their position in the genome, their relative position between themselves, and the prediction of internal frames in protein genes

TGFβ signaling regulates Epithelial-mesenchymal plasticity in ovarian cancer ascites-derived spheroids

Epithelial-mesenchymal transition (EMT) serves as a key mechanism driving tumor cell migration, invasion, and metastasis in many carcinomas. Transforming growth factor-beta (TGFβ) signaling is implicated in several steps during cancer pathogenesis and acts as a classical inducer of EMT. Since epithelial ovarian cancer (EOC) cells have the potential to switch between epithelial and mesenchymal states during metastasis, we predicted that modulation of TGFβ signaling would significantly impact EMT and the malignant potential of EOC spheroid cells. Ovarian cancer patient ascites-derived cells naturally underwent an EMT response when aggregating into spheroids, and this was reversed upon spheroid re-attachment to a substratum. CDH1/E-cadherin expression was markedly reduced in spheroids compared with adherent cells, in concert with an up-regulation of several transcriptional repressors, i.e., SNAI1/Snail, TWIST1/2, and ZEB2. Treatment of EOC spheroids with the TGFβ type I receptor inhibitor, SB-431542, potently blocked the endogenous activation of EMT in spheroids. Furthermore, treatment of spheroids with SB-431542 upon re-attachment enhanced the epithelial phenotype of dispersing cells and significantly decreased cell motility and Transwell migration. Spheroid formation was significantly compromised by exposure to SB-431542 that correlated with a reduction in cell viability particularly in combination with carboplatin treatment. Thus, our findings are the first to demonstrate that intact TGFb signaling is required to control EMT in EOC ascites-derived cell spheroids, and it promotes the malignant characteristics of these structures. As such, we show the therapeutic potential for targeted inhibition of this pathway in ovarian cancer patients with late-stage disease

Increased ice flow in Western Palmer Land linked to ocean melting

A decrease in the mass and volume of Western Palmer Land has raised the prospect that ice speed has increased in this marine-based sector of Antarctica. To assess this possibility, we measure ice velocity over 25 years using satellite imagery and an optimized modeling approach. More than 30 unnamed outlet glaciers drain the 800 km coastline of Western Palmer Land at speeds ranging from 0.5 to 2.5 m/d, interspersed with near-stagnant ice. Between 1992 and 2015, most of the outlet glaciers sped up by 0.2 to 0.3 m/d, leading to a 13% increase in ice flow and a 15 km3/yr increase in ice discharge across the sector as a whole. Speedup is greatest where glaciers are grounded more than 300 m below sea level, consistent with a loss of buttressing caused by ice shelf thinning in a region of shoaling warm circumpolar water

Intact LKB1 activity is required for survival of dormant ovarian cancer spheroids

Metastatic epithelial ovarian cancer (EOC) cells can form multicellular spheroids while in suspension and disperse directly throughout the peritoneum to seed secondary lesions. There is growing evidence that EOC spheroids are key mediators of metastasis, and they use specific intracellular signalling pathways to control cancer cell growth and metabolism for increased survival. Our laboratory discovered that AKT signalling is reduced during spheroid formation leading to cellular quiescence and autophagy, and these may be defining features of tumour cell dormancy. To further define the phenotype of EOC spheroids, we have initiated studies of the Liver kinase B1 (LKB1)-5′-AMP-activated protein kinase (AMPK) pathway as a master controller of the metabolic stress response. We demonstrate that activity of AMPK and its upstream kinase LKB1 are increased in quiescent EOC spheroids as compared with proliferating adherent EOC cells. We also show elevated AMPK activity in spheroids isolated directly from patient ascites. Functional studies reveal that treatment with the AMP mimetic AICAR or allosteric AMPK activator A-769662 led to a cytostatic response in proliferative adherent ovarian cancer cells, but they fail to elicit an effect in spheroids. Targeted knockdown of STK11 by RNAi to reduce LKB1 expression led to reduced viability and increased sensitivity to carboplatin treatment in spheroids only, a phenomenon which was AMPK-independent. Thus, our results demonstrate a direct impact of altered LKB1-AMPK signalling function in EOC. In addition, this is the first evidence in cancer cells demonstrating a pro-survival function for LKB1, a kinase traditionally thought to act as a tumour suppressor

Combination of AKT inhibition with autophagy blockade effectively reduces ascites-derived ovarian cancer cell viability

Recent genomics analysis of the high-grade serous subtype of epithelial ovarian cancer (EOC) show aberrations in the phosphatidylinositol 3-kinase (PI3K)/AKT pathway that result in upregulated signaling activity. Thus, the PI3K/AKT pathway represents a potential therapeutic target for aggressive high-grade EOC. We previously demonstrated that treatment of malignant ascites-derived primary human EOC cells and ovarian cancer cell lines with the allosteric AKT inhibitor Akti-1/2 induces a dormancy-like cytostatic response but does not reduce cell viability. In this report, we show that allosteric AKT inhibition in these cells induces cytoprotective autophagy. Inhibition of autophagy using chloroquine (CQ) alone or in combination with Akti-1/2 leads to a significant decrease in viable cell number. In fact, Akti-1/2 sensitizes EOC cells to CQ-induced cell death by exhibiting markedly reduced EC50 values in combination-treated cells compared with CQ alone. In addition, we evaluated the effects of the novel specific and potent autophagy inhibitor-1 (Spautin-1) and demonstrate that Spautin-1 inhibits autophagy in a Beclin-1-independent manner in primary EOC cells and cell lines. Multicellular EOC spheroids are highly sensitive to Akti-1/2 and CQ/Spautin-1 cotreatments, but resistant to each agent alone. Indeed, combination index analysis revealed strong synergy between Akti-1/2 and Spautin-1 when both agents were used to affect cell viability; Akti-1/2 and CQ cotreatment also displayed synergy in most samples. Taken together, we propose that combination AKT inhibition and autophagy blockade would prove efficacious to reduce residual EOC cells for supplying ovarian cancer recurrence. © The Author 2014. Published by Oxford University Press. All rights reserved

Review of gasless pyrotechnic time delays

Gasless pyrotechnic delay compositions for time‐sequencing energetic events are reviewed. They are mixtures of powdered fuels and oxidants capable of a highly exothermic oxidation‐reduction reaction. Trends favor ‘green’ compositions targeted to replace compositions containing perchlorates, chromates, lead and barium. Thermite‐based reactions dominate but intermetallics (especially multi‐layered versions) and hybrids appear promising considering progress in self‐propagating high temperature synthesis technology. Improving computer modelling will require better description of condensed phase reactions. Progress was made with the development of “hot spot” models and expressing reactivity in terms of the number of contact points (or contact surface area) between particles. Promising processing advances include mechanochemical synthesis of reactive particle composites by arrested milling or comminution of cold‐rolled multilayer intermetallics. Dry mixing of reactive powders has made way for slurry mixing followed by spray drying.AEL Mining Services (AEL/UP‐4400021845) and by the National Research Foundation (NRF) of South Africa (Grant 83874).http://www.pep.wiley-vch.de2020-01-01hj2019Chemical Engineerin

Accuracy and repeatability of wrist joint angles in boxing using an electromagnetic tracking system

© 2019, The Author(s). The hand-wrist region is reported as the most common injury site in boxing. Boxers are at risk due to the amount of wrist motions when impacting training equipment or their opponents, yet we know relatively little about these motions. This paper describes a new method for quantifying wrist motion in boxing using an electromagnetic tracking system. Surrogate testing procedure utilising a polyamide hand and forearm shape, and in vivo testing procedure utilising 29 elite boxers, were used to assess the accuracy and repeatability of the system. 2D kinematic analysis was used to calculate wrist angles using photogrammetry, whilst the data from the electromagnetic tracking system was processed with visual 3D software. The electromagnetic tracking system agreed with the video-based system (paired t tests) in both the surrogate ( 0.9). In the punch testing, for both repeated jab and hook shots, the electromagnetic tracking system showed good reliability (ICCs > 0.8) and substantial reliability (ICCs > 0.6) for flexion–extension and radial-ulnar deviation angles, respectively. The results indicate that wrist kinematics during punching activities can be measured using an electromagnetic tracking system

Comparative Study With New Accuracy Metrics for Target Volume Contouring in PET Image Guided Radiation Therapy

[EN] The impact of positron emission tomography (PET) on radiation therapy is held back by poor methods of defining functional volumes of interest. Many new software tools are being proposed for contouring target volumes but the different approaches are not adequately compared and their accuracy is poorly evaluated due to the ill-definition of ground truth. This paper compares the largest cohort to date of established, emerging and proposed PET contouring methods, in terms of accuracy and variability. We emphasize spatial accuracy and present a new metric that addresses the lack of unique ground truth. Thirty methods are used at 13 different institutions to contour functional volumes of interest in clinical PET/CT and a custom-built PET phantom representing typical problems in image guided radiotherapy. Contouring methods are grouped according to algorithmic type, level of interactivity and how they exploit structural information in hybrid images. Experiments reveal benefits of high levels of user interaction, as well as simultaneous visualization of CT images and PET gradients to guide interactive procedures. Method-wise evaluation identifies the danger of over-automation and the value of prior knowledge built into an algorithm.For retrospective patient data and manual ground truth delineation, the authors wish to thank S. Suilamo, K. Lehtio, M. Mokka, and H. Minn at the Department of Oncology and Radiotherapy, Turku University Hospital, Finland. This study was funded by the Finnish Cancer Organisations.Shepherd, T.; Teräs, M.; Beichel, RR.; Boellaard, R.; Bruynooghe, M.; Dicken, V.; Gooding, MJ.... (2012). Comparative Study With New Accuracy Metrics for Target Volume Contouring in PET Image Guided Radiation Therapy. IEEE Transactions on Medical Imaging. 31(12):2006-2024. doi:10.1109/TMI.2012.2202322S20062024311

Evidence of pervasive biologically functional secondary structures within the Genomes of Eukaryotic Single-Stranded DNA Viruses

Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here.Department of HE and Training approved lis

On the Evolution of the Standard Genetic Code: Vestiges of Critical Scale Invariance from the RNA World in Current Prokaryote Genomes

Herein two genetic codes from which the primeval RNA code could have originated the standard genetic code (SGC) are derived. One of them, called extended RNA code type I, consists of all codons of the type RNY (purine-any base-pyrimidine) plus codons obtained by considering the RNA code but in the second (NYR type) and third (YRN type) reading frames. The extended RNA code type II, comprises all codons of the type RNY plus codons that arise from transversions of the RNA code in the first (YNY type) and third (RNR) nucleotide bases. In order to test if putative nucleotide sequences in the RNA World and in both extended RNA codes, share the same scaling and statistical properties to those encountered in current prokaryotes, we used the genomes of four Eubacteria and three Archaeas. For each prokaryote, we obtained their respective genomes obeying the RNA code or the extended RNA codes types I and II. In each case, we estimated the scaling properties of triplet sequences via a renormalization group approach, and we calculated the frequency distributions of distances for each codon. Remarkably, the scaling properties of the distance series of some codons from the RNA code and most codons from both extended RNA codes turned out to be identical or very close to the scaling properties of codons of the SGC. To test for the robustness of these results, we show, via computer simulation experiments, that random mutations of current genomes, at the rates of 10−10 per site per year during three billions of years, were not enough for destroying the observed patterns. Therefore, we conclude that most current prokaryotes may still contain relics of the primeval RNA World and that both extended RNA codes may well represent two plausible evolutionary paths between the RNA code and the current SGC