Deep learning allows genome-scale prediction of Michaelis constants from structural features

AU The:Michaelis Pleaseconfirmthatallheadinglevelsarerepresentedcorrectly constant KM describes the affinity of an enzyme : for a specific substrate and is a central parameter in studies of enzyme kinetics and cellular physiology. As measurements of KM are often difficult and time-consuming, experimental estimates exist for only a minority of enzyme–substrate combinations even in model organisms. Here, we build and train an organism-independent model that successfully predicts KM values for natural enzyme–substrate combinations using machine and deep learning methods. Predictions are based on a task-specific molecular fingerprint of the substrate, generated using a graph neural network, and on a deep numerical representation of the enzyme’s amino acid sequence. We provide genome-scale KM predictions for 47 model organisms, which can be used to approximately relate metabolite concentrations to cellular physiology and to aid in the parameterization of kinetic models of cellular metabolism

A novel small molecule that selectively inhibits glioblastoma cells expressing EGFRvIII

BACKGROUND: Mutations of the epidermal growth factor receptor (EGFR) are a possible molecular target for cancer therapy. EGFR is frequently amplified in glioblastomas and 30 to 40% of glioblastomas also express the deletion mutation EGFRvIII. This frequent oncogenic mutation provides an opportunity for identifying new anti-glioblastoma therapies. In this study, we sought small molecule inhibitors specific for cancer cells expressing EGFRvIII, using isogenic parental cells without EGFRvIII as a control. RESULTS: A screen of the NCI small molecule diversity set identified one compound, NSC-154829, which consistently inhibited growth of different human glioblastoma cells expressing EGFRvIII, but permitted normal growth of matched control cells. NSC-154829 had no previously established medicinal use, but has a purine-like structural component. Further experiments showed this compound increased apoptosis in cells with EGFRvIII, and moderately affected the expression of p21, independent of any changes in p53 levels or in Akt phosphorylation. CONCLUSION: These initial results suggest that NSC-154829 or a closely related structure might be further investigated for its potential as an anti-glioblastoma drug, although its precise molecular mechanism is still undefined

Scaling of Selfavoiding Tethered Membranes: 2-Loop Renormalization Group Results

The scaling properties of selfavoiding polymerized membranes are studied using renormalization group methods. The scaling exponent \nu is calculated for the first time at two loop order. \nu is found to agree with the Gaussian variational estimate for large space dimension d and to be close to the Flory estimate for d=3.Comment: 4 pages, RevTeX + 20 .eps file

Queen Conch (Strombus gigas) Testis Regresses during the Reproductive Season at Nearshore Sites in the Florida Keys

BACKGROUND: Queen conch (Strombus gigas) reproduction is inhibited in nearshore areas of the Florida Keys, relative to the offshore environment where conchs reproduce successfully. Nearshore reproductive failure is possibly a result of exposure to environmental factors, including heavy metals, which are likely to accumulate close to shore. Metals such as Cu and Zn are detrimental to reproduction in many mollusks. METHODOLOGY/PRINCIPAL FINDINGS: Histology shows gonadal atrophy in nearshore conchs as compared to reproductively healthy offshore conchs. In order to determine molecular mechanisms leading to tissue changes and reproductive failure, a microarray was developed. A normalized cDNA library for queen conch was constructed and sequenced using the 454 Life Sciences GS-FLX pyrosequencer, producing 27,723 assembled contigs and 7,740 annotated transcript sequences. The resulting sequences were used to design the microarray. Microarray analysis of conch testis indicated differential regulation of 255 genes (p<0.01) in nearshore conch, relative to offshore. Changes in expression for three of four transcripts of interest were confirmed using real-time reverse transcription polymerase chain reaction. Gene Ontology enrichment analysis indicated changes in biological processes: respiratory chain (GO:0015992), spermatogenesis (GO:0007283), small GTPase-mediated signal transduction (GO:0007264), and others. Inductively coupled plasma-mass spectrometry analysis indicated that Zn and possibly Cu were elevated in some nearshore conch tissues. CONCLUSIONS/SIGNIFICANCE: Congruence between testis histology and microarray data suggests that nearshore conch testes regress during the reproductive season, while offshore conch testes develop normally. Possible mechanisms underlying the testis regression observed in queen conch in the nearshore Florida Keys include a disruption of small GTPase (Ras)-mediated signaling in testis development. Additionally, elevated tissue levels of Cu (34.77 ng/mg in testis) and Zn (831.85 ng/mg in digestive gland, 83.96 ng/mg in testis) nearshore are similar to reported levels resulting in reproductive inhibition in other gastropods, indicating that these metals possibly contribute to NS conch reproductive failure

Contrasting microfossil preservation and lake chemistries within the 1200–1000 Ma Torridonian Supergroup of NW Scotland

We acknowledge the Australian Microscopy & Microanalysis Research Facility at the Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, a facility funded by the University, State and Commonwealth Governments. DW acknowledges funding from the European Commission and the Australian Research Council. This is publication number 838 from the Australian Research Council Centre of Excellence for Core to Crust Fluid Systems.Publisher PD

The Statistical Mechanics of Membranes

The fluctuations of two-dimensional extended objects membranes is a rich and exciting field with many solid results and a wide range of open issues. We review the distinct universality classes of membranes, determined by the local order, and the associated phase diagrams. After a discussion of several physical examples of membranes we turn to the physics of crystalline (or polymerized) membranes in which the individual monomers are rigidly bound. We discuss the phase diagram with particular attention to the dependence on the degree of self-avoidance and anisotropy. In each case we review and discuss analytic, numerical and experimental predictions of critical exponents and other key observables. Particular emphasis is given to the results obtained from the renormalization group epsilon-expansion. The resulting renormalization group flows and fixed points are illustrated graphically. The full technical details necessary to perform actual calculations are presented in the Appendices. We then turn to a discussion of the role of topological defects whose liberation leads to the hexatic and fluid universality classes. We finish with conclusions and a discussion of promising open directions for the future.Comment: 75 LaTeX pages, 36 figures. To appear in Physics Reports in the Proceedings of RG2000, Taxco, 199

STAT3 Induction of miR-146b Forms a Feedback Loop to Inhibit the NF-kB to IL-6 Signaling Axis and STAT3-Driven Cancer Phenotypes

Interleukin-6 (IL-6)–mediated activation of signal transducer and activator of transcription 3 (STAT3) is a mechanism by which chronic inflammation can contribute to cancer and is a common oncogenic event. We discovered a pathway, the loss of which is associated with persistent STAT3 activation in human cancer. We found that the gene encoding the tumor suppressor microRNA miR-146b is a direct STAT3 target gene, and its expression was increased in normal breast epithelial cells but decreased in tumor cells. Methylation of the miR-146b promoter, which inhibited STAT3-mediated induction of expression, was increased in primary breast cancers. Moreover, we found that miR-146b inhibited nuclear factor kB (NF-kB)–dependent production of IL-6, subsequent STAT3 activation, and IL-6/STAT3–driven migration and invasion in breast cancer cells, thereby establishing a negative feedback loop. In addition, higher expression of miR-146b was positively correlated with patient survival in breast cancer subtypes with increased IL6 expression and STAT3 phosphorylation. Our results identify an epigenetic mechanism of crosstalk between STAT3 and NF-kB relevant to constitutive STAT3 activation in malignancy and the role of inflammation in oncogenesis

Optimal Renormalization Scale and Scheme for Exclusive Processes

We use the BLM method to fix the renormalization scale of the QCD coupling in exclusive hadronic amplitudes such as the pion form factor and the photon-to-pion transition form factor at large momentum transfer. Renormalization-scheme-independent commensurate scale relations are established which connect the hard scattering subprocess amplitudes that control exclusive processes to other QCD observables such as the heavy quark potential and the electron-positron annihilation cross section. The commensurate scale relation connecting the heavy quark potential, as determined from lattice gauge theory, to the photon-to-pion transition form factor is in excellent agreement with $\gamma e \to \pi^0 e$ data assuming that the pion distribution amplitude is close to its asymptotic form $\sqrt{3}f_\pi x(1-x)$. We also reproduce the scaling and normalization of the $\gamma \gamma \to \pi^+ \pi^-$ data at large momentum transfer. Because the renormalization scale is small, we argue that the effective coupling is nearly constant, thus accounting for the nominal scaling behavior of the data. However, the normalization of the space-like pion form factor $F_\pi(Q^2)$ obtained from electroproduction experiments is somewhat higher than that predicted by the corresponding commensurate scale relation. This discrepancy may be due to systematic errors introduced by the extrapolation of the $\gamma^* p \to \pi^+ n$ electroproduction data to the pion pole.Comment: 22 pages, Latex, 7 Latex figures. Several references added, discussion of scale fixing revised for clarity. Final version to appear in Phys. Rev.

Changes in serogroup and genotype prevalence among carried meningococci in the United Kingdom during vaccine implementation.

BACKGROUND: Herd immunity is important in the effectiveness of conjugate polysaccharide vaccines against encapsulated bacteria. A large multicenter study investigated the effect of meningococcal serogroup C conjugate vaccine introduction on the meningococcal population. METHODS: Carried meningococci in individuals aged 15-19 years attending education establishments were investigated before and for 2 years after vaccine introduction. Isolates were characterized by multilocus sequence typing, serogroup, and capsular region genotype and changes in phenotypes and genotypes assessed. RESULTS: A total of 8462 meningococci were isolated from 47 765 participants (17.7%). Serogroup prevalence was similar over the 3 years, except for decreases of 80% for serogroup C and 40% for serogroup 29E. Clonal complexes were associated with particular serogroups and their relative proportions fluctuated, with 12 statistically significant changes (6 up, 6 down). The reduction of ST-11 complex serogroup C meningococci was probably due to vaccine introduction. Reasons for a decrease in serogroup 29E ST-254 meningococci (from 1.8% to 0.7%) and an increase in serogroup B ST-213 complex meningococci (from 6.7% to 10.6%) were less clear. CONCLUSIONS: Natural fluctuations in carried meningococcal genotypes and phenotypes a can be affected by the use of conjugate vaccines, and not all of these changes are anticipatable in advance of vaccine introduction

A simple and effective F0 knockout method for rapid screening of behaviour and other complex phenotypes.

Hundreds of human genes are associated with neurological diseases, but translation into tractable biological mechanisms is lagging. Larval zebrafish are an attractive model to investigate genetic contributions to neurological diseases. However, current CRISPR-Cas9 methods are difficult to apply to large genetic screens studying behavioural phenotypes. To facilitate rapid genetic screening, we developed a simple sequencing-free tool to validate gRNAs and a highly effective CRISPR-Cas9 method capable of converting >90% of injected embryos directly into F0 biallelic knockouts. We demonstrate that F0 knockouts reliably recapitulate complex mutant phenotypes, such as altered molecular rhythms of the circadian clock, escape responses to irritants, and multi-parameter day-night locomotor behaviours. The technique is sufficiently robust to knockout multiple genes in the same animal, for example to create the transparent triple knockout crystal fish for imaging. Our F0 knockout method cuts the experimental time from gene to behavioural phenotype in zebrafish from months to one week