CoolMPS for robust sequencing of single-nuclear RNAs captured by droplet-based method

Massively-parallel single-cell and single-nucleus RNA sequencing (scRNA-seq, snRNA-seq) requires extensive sequencing to achieve proper per-cell coverage, making sequencing resources and availability of sequencers critical factors for conducting deep transcriptional profiling. CoolMPS is a novel sequencing-by-synthesis approach that relies on nucleotide labeling by re-usable antibodies, but whether it is applicable to snRNA-seq has not been tested. Here, we use a low-cost and off-the-shelf protocol to chemically convert libraries generated with the widely-used Chromium 10X technology to be sequenceable with CoolMPS technology. To assess the quality and performance of converted libraries sequenced with CoolMPS, we generated a snRNA-seq dataset from the hippocampus of young and old mice. Native libraries were sequenced on an Illumina Novaseq and libraries that were converted to be compatible with CoolMPS were sequenced on a DNBSEQ-400RS. CoolMPS-derived data faithfully replicated key characteristics of the native library dataset, including correct estimation of ambient RNA-contamination, detection of captured cells, cell clustering results, spatial marker gene expression, inter- and intra-replicate differences and gene expression changes during aging. In conclusion, our results show that CoolMPS provides a viable alternative to standard sequencing of RNA from droplet-based libraries

Ab initio study of the volume dependence of dynamical and thermodynamical properties of silicon

Motivated by the negative thermal expansion observed for silicon between 20 K and 120 K, we present first an ab initio study of the volume dependence of interatomic force constants, phonon frequencies of TA(X) and TA(L) modes, and of the associated mode Gruneisen parameters. The influence of successive nearest neighbors shells is analysed. Analytical formulas, taking into account interactions up to second nearest neighbors, are developped for phonon frequencies of TA(X) and TA(L) modes and the corresponding mode Gruneisen parameters. We also analyze the volume and pressure dependence of various thermodynamic properties (specific heat, bulk modulus, thermal expansion), and point out the effect of the negative mode Gruneisen parameters of the acoustic branches on these properties. Finally, we present the evolution of the mean square atomic displacement and of the atomic temperature factor with the temperature for different volumes, for which the anomalous effects are even greater.Comment: 24 pages, Revtex 3.0, 11 figures, accepted for publication in Phys. Rev.

First Principles Phase Diagram Calculations for the Octahedral-Interstitial System ZrOX_{X}, 0≤X≤1/20 \leq X \leq 1/2

First principles based phase diagram calculations were performed for the octahedral-interstitial solid solution system \alpha ZrOX (\alpha Zr[ ]_(1-X)OX; [ ]=Vacancy; 0 \leq X \leq 1/2). The cluster expansion method was used to do a ground state analysis, and to calculate the phase diagram. The predicted diagram has four ordered ground-states in the range 0 \leq X \leq 1/2, but one of these, at X=5/12, is predicted to disproportionate at T \approx 20K, well below the experimentally investigated range T \approx 420K. Thus, at T \succeq 420K, the first-principles based calculation predicts three ordered phases rather than the four that have been reported by experimentalists

Hypoxic gene expression in chronic hepatitis B virus infected patients is not observed in state-of-the-art in vitro and mouse infection models

Hepatitis B virus (HBV) is the leading cause of hepatocellular carcinoma (HCC) worldwide. The prolyl hydroxylase domain (PHD)-hypoxia inducible factor (HIF) pathway is a key mammalian oxygen sensing pathway and is frequently perturbed by pathological states including infection and inflammation. We discovered a significant upregulation of hypoxia regulated gene transcripts in patients with chronic hepatitis B (CHB) in the absence of liver cirrhosis. We used state-of-the-art in vitro and in vivo HBV infection models to evaluate a role for HBV infection and the viral regulatory protein HBx to drive HIF-signalling. HBx had no significant impact on HIF expression or associated transcriptional activity under normoxic or hypoxic conditions. Furthermore, we found no evidence of hypoxia gene expression in HBV de novo infection, HBV infected human liver chimeric mice or transgenic mice with integrated HBV genome. Collectively, our data show clear evidence of hypoxia gene induction in CHB that is not recapitulated in existing models for acute HBV infection, suggesting a role for inflammatory mediators in promoting hypoxia gene expression

Thermostable DNA Polymerase from a Viral Metagenome Is a Potent RT-PCR Enzyme

Viral metagenomic libraries are a promising but previously untapped source of new reagent enzymes. Deep sequencing and functional screening of viral metagenomic DNA from a near-boiling thermal pool identified clones expressing thermostable DNA polymerase (Pol) activity. Among these, 3173 Pol demonstrated both high thermostability and innate reverse transcriptase (RT) activity. We describe the biochemistry of 3173 Pol and report its use in single-enzyme reverse transcription PCR (RT-PCR). Wild-type 3173 Pol contains a proofreading 3′-5′ exonuclease domain that confers high fidelity in PCR. An easier-to-use exonuclease-deficient derivative was incorporated into a PyroScript RT-PCR master mix and compared to one-enzyme (Tth) and two-enzyme (MMLV RT/Taq) RT-PCR systems for quantitative detection of MS2 RNA, influenza A RNA, and mRNA targets. Specificity and sensitivity of 3173 Pol-based RT-PCR were higher than Tth Pol and comparable to three common two-enzyme systems. The performance and simplified set-up make this enzyme a potential alternative for research and molecular diagnostics

Measurement of Z0 decays to hadrons, and a precise determination of the number of neutrino species

We have made a precise measurement of the cross section for e+e--->Z0-->hadrons with the L3 detector at LEP, covering the range from 88.28 to 95.04 GeV. From a fit to the Z0 mass, total width, and the hadronic cross section to be MZ0=91.160 +/- 0.024 (experiment) +/-0.030(LEP) GeV, [Gamma]Z0=2.539+/-0.054 GeV, and [sigma]h(MZ0)=29.5+/-0.7 nb. We also used the fit to the Z0 peak cross section and the width todetermine [Gamma]invisible=0.548+/-0.029 GeV, which corresponds to 3.29+/-0.17 species of light neutrinos. The possibility of four or more neutrino flavors is thus ruled out at the 4[sigma] confidence level.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/28683/3/0000500.pd

Measurement of electroweak parameters from hadronic and leptonic decays of the Z 0

We have studied the reactions e + e − →hadrons, e + e − , μ + μ − and τ + τ − , in the energy range 88.2 GeV. A total luminosity of 5.5 pb −1 , corresponding to approximately 115000 hadronic and 10000 leptonic Z 0 decays, has been recorded with the L3 detector. From a simultaneous fit to all of our measured cross section data, we obtain assuming lepton universality:Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47890/1/10052_2005_Article_BF01475788.pd

Управление системой электрохимической защиты магистрального газопровода в условиях вечной мерзлоты

Объектом исследования подсистема коррозионного мониторинга электрохимической зашиты магистрального газопровода. Цель работы – проанализировать управление системой электрохимической зашиты магистрального газопровода в условиях вечной мерзлоты. В результате анализа установлено, что ПКМ-ТСТ-КонтКорр удовлетворяет требованиям системы управления техническим состоянием и целостностью площадных объектов организации.The object of study is the subsystem of corrosion monitoring of electrochemical protection of the main gas pipeline. The purpose of the work is to analyze the management of the system of electrochemical protection of the main gas pipeline in permafrost conditions. As a result of the analysis, it was established that PKM-TST-KontKorr satisfies the requirements of the system for managing the technical condition and integrity of the organization’s area facilities