Regulatory transposable elements in the encyclopedia of DNA elements.

Transposable elements (TEs) comprise ~50% of our genome, but knowledge of how TEs affect genome evolution remains incomplete. Leveraging ENCODE4 data, we provide the most comprehensive study to date of TE contributions to the regulatory genome. We find 236,181 (~25%) human candidate cis-regulatory elements (cCREs) are TE-derived, with over 90% lineage-specific since the human-mouse split, accounting for 8-36% of lineage-specific cCREs.

Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome.

Recent studies have shown that the noncoding genome can produce unannotated proteins as antigens that induce immune response. One major source of this activity is the aberrant epigenetic reactivation of transposable elements (TEs). In tumors, TEs often provide cryptic or alternate promoters, which can generate transcripts that encode tumor-specific unannotated proteins.

Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser.

Genome browsers have become an intuitive and critical tool to visualize and analyze genomic features and data. Conventional genome browsers display data/annotations on a single reference genome/assembly; there are also genomic alignment viewer/browsers that help users visualize alignment, mismatch, and rearrangement between syntenic regions. However, there is a growing need for a comparative epigenome browser that can display genomic and epigenomic data sets across different species and enable users to compare them between syntenic regions.

Functional characterization of enhancer activity during a long terminal repeat's evolution.

Many transposable elements (TEs) contain transcription factor binding sites and are implicated as potential regulatory elements. However, TEs are rarely functionally tested for regulatory activity, which in turn limits our understanding of how TE regulatory activity has evolved. We systematically tested the human LTR18A subfamily for regulatory activity using massively parallel reporter assay (MPRA) and found AP-1- and CEBP-related binding motifs as drivers of enhancer activity.

Isolation and characterization of a γ-carbonic anhydrase localized in the mitochondria of Saccharina japonica.

Saccharina japonica is an ecologically and economically important seaweed that is dominant in the rocky shores of cold-temperate regions, forms the major component of productive beds, and affects marine environments. S. japonica exhibits a high photosynthetic efficiency in natural seawater with low dissolved CO concentration, thus suggesting the presence of its carbon-concentrating mechanism (CCM).

Epigenomic differences in the human and chimpanzee genomes are associated with structural variation.

Structural variation (SV), including insertions and deletions (indels), is a primary mechanism of genome evolution. However, the mechanism by which SV contributes to epigenome evolution is poorly understood. In this study, we characterized the association between lineage-specific indels and epigenome differences between human and chimpanzee to investigate how SVs might have shaped the epigenetic landscape.

Probing the Open Global Health Chemical Diversity Library for Multistage-Active Starting Points for Next-Generation Antimalarials.

Most phenotypic screens aiming to discover new antimalarial chemotypes begin with low cost, high-throughput tests against the asexual blood stage (ABS) of the malaria parasite life cycle. Compounds active against the ABS are then sequentially tested in more difficult assays that predict whether a compound has other beneficial attributes. Although applying this strategy to new chemical libraries may yield new leads, repeated iterations may lead to diminishing returns and the rediscovery of chemotypes hitting well-known targets.

An Autonomous Path Planning Model for Unmanned Ships Based on Deep Reinforcement Learning.

Deep reinforcement learning (DRL) has excellent performance in continuous control problems and it is widely used in path planning and other fields. An autonomous path planning model based on DRL is proposed to realize the intelligent path planning of unmanned ships in the unknown environment. The model utilizes the deep deterministic policy gradient (DDPG) algorithm, through the continuous interaction with the environment and the use of historical experience data; the agent learns the optimal action strategy in a simulation environment.

Author Correction: Transposable elements drive widespread expression of oncogenes in human cancers.

In the version of this article initially published, grant PF-17-201-01-TBG from the American Cancer Society to author Erica C. Pehrsson was not included in the Acknowledgements. The error has been corrected in the HTML and PDF versions of the article.

Transposable elements drive widespread expression of oncogenes in human cancers.

Transposable elements (TEs) are an abundant and rich genetic resource of regulatory sequences. Cryptic regulatory elements within TEs can be epigenetically reactivated in cancer to influence oncogenesis in a process termed onco-exaptation. However, the prevalence and impact of TE onco-exaptation events across cancer types are poorly characterized.

[Effect of Modified Danggui Yinzi on Delayed Allergy in Model Mice with Qi-Blood Deficiency Syndrome].

Objective: To explore the effect of Danggui Yinzi (DY) on delayed allergy in model mice with qi-blood deficiency syndrome (QBDS).

Methods: QBDS model was established in 48 Kuming mice of SPF grade by using reserpine and acetophenone hydrazine. Forty of them were then randomly divided into the model group, the loratadine group, the high dose DY group, the middle dose DY group, and the low dose DY group, 8 in each group.

High-Throughput Assay and Discovery of Small Molecules that Interrupt Malaria Transmission.

Preventing transmission is an important element of malaria control. However, most of the current available methods to assay for malaria transmission blocking are relatively low throughput and cannot be applied to large chemical libraries. We have developed a high-throughput and cost-effective assay, the Saponin-lysis Sexual Stage Assay (SaLSSA), for identifying small molecules with transmission-blocking capacity.

Professional and geographical network effects on healthcare information exchange growth: does proximity really matter?

Background And Objective: We postulate that professional proximity due to common patients and geographical proximity among practice locations are significant factors influencing the adoption of health information exchange (HIE) services by healthcare providers. The objective of this study is to investigate the direct and indirect network effects of these drivers on HIE diffusion.

Design: Multi-dimensional scaling and clustering are first used to create different clusters of physicians based on their professional and geographical proximities.

Induction of a 55 kDa acetylcholinesterase protein during apoptosis and its negative regulation by the Akt pathway.

Acetylcholinesterase (AChE) is emerging as an important contributor to apoptosis in various cell types. However, overexpression of AChE does not initiate apoptosis, and cells which express AChE at basal levels grow normally, suggesting that AChE may function differently between normal and apoptotic conditions. In this study, we determined that an AChE-derived protein (∼55 kDa) positively correlated with cellular apoptotic levels.

Crystalline amorphous semiconductor superlattice.

A new class of superlattice, crystalline amorphous superlattice (CASL), by alternatively depositing two semiconductor materials, is proposed. CASL displays three states depending on the component materials' phase: both polycrystalline phases, both amorphous phases, and one polycrystalline phase while another amorphous phase. Using materials capable of reversible phase transition, CASL can demonstrate reversibility among three states.

Discovery of a novel small molecule, 1-ethoxy-3-(3,4-methylenedioxyphenyl)-2-propanol, that induces apoptosis in A549 human lung cancer cells.

A novel small molecule, 1-ethoxy-3-(3,4-methylenedioxyphenyl)-2-propanol (EOD), was synthesized in our laboratory. Previously, we reported pharmacological properties of EOD, triggering apoptosis in Human umbilical vein endothelial cells (HUVECs). Here, we further investigated the effects of EOD on the growth of A549 human lung cancer cells.

Effects of novel safrole oxide derivatives, 1-methoxy-3-(3,4-methylenedioxyphenyl)-2-propanol and 1-ethoxy-3-(3,4-methylenedioxyphenyl)-2-propanol, on apoptosis induced by deprivation of survival factors in vascular endothelial cells.

Two safrole oxide derivatives, 1-methoxy-3-(3,4-methylenedioxyphenyl)-2-propanol (MOD) and 1-ethoxy-3-(3,4-methylenedioxyphenyl)-2-propanol (EOD), were newly synthesized as promoters of apoptosis in vascular endothelial cells (VECs). The purpose of this study was to investigate the effects of these two safrole oxide derivatives on cell growth and apoptosis induced by deprivation of survival factors (serum and fibroblast growth factors, aFGF and bFGF) in VECs. Morphological changes were observed with light microscopy.

Cross-sectional transmission electron microscopy of silicon LSI circuits and Josephson junction devices.

Cross-sectional transmission electron microscopy (XTEM) has been used to diagnose silicon LSI circuits and Josephson junction devices. For LSI circuits, some typical failure problems have been presented. For Nb-Si-Nb Josephson junction, microholes in the thin silicon layer have observed, and they are responsible for the short circuiting of these devices.