Identification of shared neoantigens in esophageal carcinoma by the combination of comprehensive analysis of genomic data and in silico neoantigen prediction.

Neoantigens are attractive targets for cancer immunotherapy. The identification of neoantigens shared by different patients could promote the broad application of neoantigen-based immunotherapy. This study aimed to investigate shared neoantigens in esophageal carcinoma.

Constructing N-doping biomass-derived carbon with hierarchically porous architecture to boost fast reaction kinetics for higfh-performance lithium storage.

Active biomass-derived carbons are brought into focus on boosting high-performance lithium storage. However, their low electric conductivity and poor ion diffusion kinetics during the lithium storage reactions remain confusing topics. This study demonstrates a novel and effective strategy of dual system activation process to construct the nitrogen-doped biomass-derived carbon with hierarchically porous architecture (HNBC), which is composed of the three-dimensional porous networks connected by carbon nanorods and the flake-like edges constructed by carbon nanosheets.

ADAR1-Dependent RNA Editing Promotes MET and iPSC Reprogramming by Alleviating ER Stress.

RNA editing of adenosine to inosine (A to I) is catalyzed by ADAR1 and dramatically alters the cellular transcriptome, although its functional roles in somatic cell reprogramming are largely unexplored. Here, we show that loss of ADAR1-mediated A-to-I editing disrupts mesenchymal-to-epithelial transition (MET) during induced pluripotent stem cell (iPSC) reprogramming and impedes acquisition of induced pluripotency. Using chemical and genetic approaches, we show that absence of ADAR1-dependent RNA editing induces aberrant innate immune responses through the double-stranded RNA (dsRNA) sensor MDA5, unleashing endoplasmic reticulum (ER) stress and hindering epithelial fate acquisition.

Optical sensitivity enhancement in grating based micromechanical accelerometer by reducing non-parallelism error.

We report on optical sensitivity enhancement in a grating-based micromechanical accelerometer, which was achieved by reducing the non-parallelism error between the grating and reflected mirror. Based on the multi-slit Fraunhofer diffraction theory, an equivalent optical model is proposed in order to discuss the non-parallelism induced error that is caused by the residual stress in material and fabrication. An integrated fabrication flow with optimized quartz based and silicon based procedure is then presented to improve the parallelism between the grating and mirror, and to realize a hermetic package using silicon islands for the electrical interconnection.

RED-ML: a novel, effective RNA editing detection method based on machine learning.

With the advancement of second generation sequencing techniques, our ability to detect and quantify RNA editing on a global scale has been vastly improved. As a result, RNA editing is now being studied under a growing number of biological conditions so that its biochemical mechanisms and functional roles can be further understood. However, a major barrier that prevents RNA editing from being a routine RNA-seq analysis, similar to gene expression and splicing analysis, for example, is the lack of user-friendly and effective computational tools.

Characterization of RNA editome in primary and metastatic lung adenocarcinomas.

RNA editing results in post-transcriptional modification and could potentially contribute to carcinogenesis. However, RNA editing in advanced lung adenocarcinomas has not yet been studied. Based on whole genome and transcriptome sequencing data, we identified 1,071,296 RNA editing events from matched normal, primary and metastatic samples contributed by 24 lung adenocarcinoma patients, with 91.

Single-cell RNA sequencing reveals dynamic changes in A-to-I RNA editome during early human embryogenesis.

Background: A-to-I RNA-editing mediated by ADAR (adenosine deaminase acting on RNA) enzymes that converts adenosine to inosine in RNA sequence can generate mutations and alter gene regulation in metazoans. Previous studies have shown that A-to-I RNA-editing plays vital roles in mouse embryogenesis. However, the RNA-editing activities in early human embryonic development have not been investigated.

Spatial features for Escherichia coli genome organization.

Background: In bacterial genomes, the compactly encoded genes and operons are well organized, with genes in the same biological pathway or operons in the same regulon close to each other on the genome sequence. In addition, the linearly close genes have a higher probability of co-expression and their protein products tend to form protein-protein interactions. However, the organization features of bacterial genomes in a three-dimensional space remain elusive.

Sequence determinants of prokaryotic gene expression level under heat stress.

Prokaryotic gene expression is environment-dependent and temperature plays an important role in shaping the gene expression profile. Revealing the regulation mechanisms of gene expression pertaining to temperature has attracted tremendous efforts in recent years particularly owning to the yielding of transcriptome and proteome data by high-throughput techniques. However, most of the previous works concentrated on the characterization of the gene expression profile of individual organism and little effort has been made to disclose the commonality among organisms, especially for the gene sequence features.