Epithelial protein lost in neoplasm-α (EPLIN-α) is a potential prognostic marker for the progression of epithelial ovarian cancer

Epithelial protein lost in neoplasm-α (EPLIN-α) is a cytoskeletal protein whose expression is often lost or is aberrant in cancerous cells and tissues and whose loss is believed to be involved in aggressive phenotypes. This study examined this molecule in human epithelial ovarian tissues and investigated the cellular impact of EPLIN-α on ovarian cancer cells (EOC), SKOV3 and COV504. The expression of EPLIN-α in human ovarian tissues and EOC was assessed at both the mRNA and protein levels using reverse transcription-PCR (RT-PCR) and immunohistochemistry, respectively. In vitro assays for cellular matrix adhesion and migration (confirmed by an electrical cell substrate impedance sensing (ECIS) based method), invasion and cell growth were employed in order to assess the biological influence of EPLIN-α expression on EOC cells. Immunohistochemical analysis of ovarian cancer samples demonstrated that only a small number expressed EPLIN-α protein. Downregulation of EPLIN-α protein in EOC cell lines increased the growth, invasion, adhesion and migration in vitro. This EPLIN-α downregulation may have a prognostic value. From these data, we conclude that downregulation of EPLIN-α may be associated with poorer patient prognosis, and that this molecule appears to play a tumour suppressor role by inhibition of EOC growth and migration

A new reference genome assembly for the microcrustacean Daphnia pulex

Comparing genomes of closely related genotypes from populations with distinct demographic histories can help reveal the impact of effective population size on genome evolution. For this purpose, we present a high quality genome assembly of Daphnia pulex (PA42), and compare this with the first sequenced genome of this species (TCO), which was derived from an isolate from a population with >90% reduction in nucleotide diversity. PA42 has numerous similarities to TCO at the gene level, with an average amino acid sequence identity of 98.8 and >60% of orthologous proteins identical. Nonetheless, there is a highly elevated number of genes in the TCO genome annotation, with similar to 7000 excess genes appearing to be false positives. This view is supported by the high GC content, lack of introns, and short length of these suspicious gene annotations. Consistent with the view that reduced effective population size can facilitate the accumulation of slightly deleterious genomic features, we observe more proliferation of transposable elements (TEs) and a higher frequency of gained introns in the TCO genome

A computationally engineered RAS rheostat reveals RAS-ERK signaling dynamics.

Synthetic protein switches controlled with user-defined inputs are powerful tools for studying and controlling dynamic cellular processes. To date, these approaches have relied primarily on intermolecular regulation. Here we report a computationally guided framework for engineering intramolecular regulation of protein function. We utilize this framework to develop chemically inducible activator of RAS (CIAR), a single-component RAS rheostat that directly activates endogenous RAS in response to a small molecule. Using CIAR, we show that direct RAS activation elicits markedly different RAS-ERK signaling dynamics from growth factor stimulation, and that these dynamics differ among cell types. We also found that the clinically approved RAF inhibitor vemurafenib potently primes cells to respond to direct wild-type RAS activation. These results demonstrate the utility of CIAR for quantitatively interrogating RAS signaling. Finally, we demonstrate the general utility of our approach in design of intramolecularly regulated protein tools by applying it to the Rho family of guanine nucleotide exchange factors

Facial phenotypes in subgroups of prepubertal boys with autism spectrum disorders are correlated with clinical phenotypes

<p>Abstract</p> <p>Background</p> <p>The brain develops in concert and in coordination with the developing facial tissues, with each influencing the development of the other and sharing genetic signaling pathways. Autism spectrum disorders (ASDs) result from alterations in the embryological brain, suggesting that the development of the faces of children with ASD may result in subtle facial differences compared to typically developing children. In this study, we tested two hypotheses. First, we asked whether children with ASD display a subtle but distinct facial phenotype compared to typically developing children. Second, we sought to determine whether there are subgroups of facial phenotypes within the population of children with ASD that denote biologically discrete subgroups.</p> <p>Methods</p> <p>The 3dMD cranial System was used to acquire three-dimensional stereophotogrammetric images for our study sample of 8- to 12-year-old boys diagnosed with essential ASD (<it>n </it>= 65) and typically developing boys (<it>n </it>= 41) following approved Institutional Review Board protocols. Three-dimensional coordinates were recorded for 17 facial anthropometric landmarks using the 3dMD Patient software. Statistical comparisons of facial phenotypes were completed using Euclidean Distance Matrix Analysis and Principal Coordinates Analysis. Data representing clinical and behavioral traits were statistically compared among groups by using χ²tests, Fisher's exact tests, Kolmogorov-Smirnov tests and Student's <it>t</it>-tests where appropriate.</p> <p>Results</p> <p>First, we found that there are significant differences in facial morphology in boys with ASD compared to typically developing boys. Second, we also found two subgroups of boys with ASD with facial morphology that differed from the majority of the boys with ASD and the typically developing boys. Furthermore, membership in each of these distinct subgroups was correlated with particular clinical and behavioral traits.</p> <p>Conclusions</p> <p>Boys with ASD display a facial phenotype distinct from that of typically developing boys, which may reflect alterations in the prenatal development of the brain. Subgroups of boys with ASD defined by distinct facial morphologies correlated with clinical and behavioral traits, suggesting potentially different etiologies and genetic differences compared to the larger group of boys with ASD. Further investigations into genes involved in neurodevelopment and craniofacial development of these subgroups will help to elucidate the causes and significance of these subtle facial differences.</p

A Crosslingual Investigation of Conceptualization in 1335 Languages

Languages differ in how they divide up the world into concepts and words; e.g., in contrast to English, Swahili has a single concept for ‘belly’ and ‘womb’. We investigate these differences in conceptualization across 1,335 languages by aligning concepts in a parallel corpus. To this end, we propose Conceptualizer, a method that creates a bipartite directed alignment graph between source language concepts and sets of target language strings. In a detailed linguistic analysis across all languages for one concept (‘bird’) and an evaluation on gold standard data for 32 Swadesh concepts, we show that Conceptualizer has good alignment accuracy. We demonstrate the potential of research on conceptualization in NLP with two experiments. (1) We define crosslingual stability of a concept as the degree to which it has 1-1 correspondences across languages, and show that concreteness predicts stability. (2) We represent each language by its conceptualization pattern for 83 concepts, and define a similarity measure on these representations. The resulting measure for the conceptual similarity between two languages is complementary to standard genealogical, typological, and surface similarity measures. For four out of six language families, we can assign languages to their correct family based on conceptual similarity with accuracies between 54% and 87

QMCPACK: Advances in the development, efficiency, and application of auxiliary field and real-space variational and diffusion Quantum Monte Carlo

We review recent advances in the capabilities of the open source ab initio Quantum Monte Carlo (QMC) package QMCPACK and the workflow tool Nexus used for greater efficiency and reproducibility. The auxiliary field QMC (AFQMC) implementation has been greatly expanded to include k-point symmetries, tensor-hypercontraction, and accelerated graphical processing unit (GPU) support. These scaling and memory reductions greatly increase the number of orbitals that can practically be included in AFQMC calculations, increasing accuracy. Advances in real space methods include techniques for accurate computation of band gaps and for systematically improving the nodal surface of ground state wavefunctions. Results of these calculations can be used to validate application of more approximate electronic structure methods including GW and density functional based techniques. To provide an improved foundation for these calculations we utilize a new set of correlation-consistent effective core potentials (pseudopotentials) that are more accurate than previous sets; these can also be applied in quantum-chemical and other many-body applications, not only QMC. These advances increase the efficiency, accuracy, and range of properties that can be studied in both molecules and materials with QMC and QMCPACK

Quantum Efficiency of Charge Qubit Measurements Using a Single Electron Transistor

The quantum efficiency, which characterizes the quality of information gain against information loss, is an important figure of merit for any realistic quantum detectors in the gradual process of collapsing the state being measured. In this work we consider the problem of solid-state charge qubit measurements with a single-electron-transistor (SET). We analyze two models: one corresponds to a strong response SET, and the other is a tunable one in response strength. We find that the response strength would essentially bound the quantum efficiency, making the detector non-quantum-limited. Quantum limited measurements, however, can be achieved in the limits of strong response and asymmetric tunneling. The present study is also associated with appropriate justifications for the measurement and backaction-dephasing rates, which were usually evaluated in controversial methods.Comment: 10 pages, 2 figure