Saturation profiling of drug-resistant genetic variants using prime editing.

Methods to characterize the functional effects of genetic variants of uncertain significance (VUSs) have been limited by incomplete coverage of the mutational space. In clinical oncology, drug resistance arising from VUSs can prevent optimal treatment. Here we introduce PEER-seq, a high-throughput method based on prime editing that can evaluate the functional effects of single-nucleotide variants (SNVs).

Near surface oxidation of elemental mercury leads to mercury exposure in the Arctic Ocean biota.

Atmospheric mercury (Hg(0), Hg(II)) and riverine exported Hg (Hg(II)) are proposed as important Hg sources to the Arctic Ocean. As plankton cannot passively uptake Hg(0), gaseous Hg(0) has to be oxidized to be bioavailable. Here, we measured Hg isotope ratios in zooplankton, Arctic cod, total gaseous Hg, sediment, seawater, and snowpack from the Bering Strait, the Chukchi Sea, and the Beaufort Sea.

Effects of different levels of organic chromium and selenomethionine cocktails in broilers.

Selenium (Se) is an essential trace mineral that plays an important role in physiological processes by regulating the antioxidant defense system and enhancing immunity. Chromium is an essential mineral involved in carbohydrate and lipid metabolism and also plays a role in maintaining normal insulin function. Based on these advantages, we hypothesized that the addition of selenomethionine (SeMet) and organic chromium (OC) to broiler diets would increase Se deposition, antioxidant capacity and immune response in meat.

High-throughput functional evaluation of human cancer-associated mutations using base editors.

Comprehensive phenotypic characterization of the many mutations found in cancer tissues is one of the biggest challenges in cancer genomics. In this study, we evaluated the functional effects of 29,060 cancer-related transition mutations that result in protein variants on the survival and proliferation of non-tumorigenic lung cells using cytosine and adenine base editors and single guide RNA (sgRNA) libraries. By monitoring base editing efficiencies and outcomes using surrogate target sequences paired with sgRNA-encoding sequences on the lentiviral delivery construct, we identified sgRNAs that induced a single primary protein variant per sgRNA, enabling linking those mutations to the cellular phenotypes caused by base editing.

Sequence-specific prediction of the efficiencies of adenine and cytosine base editors.

Base editors, including adenine base editors (ABEs) and cytosine base editors (CBEs), are widely used to induce point mutations. However, determining whether a specific nucleotide in its genomic context can be edited requires time-consuming experiments. Furthermore, when the editable window contains multiple target nucleotides, various genotypic products can be generated.

Assessment and source identification of As and Cd contamination in soil and plants in the vicinity of the Nui Phao Mine, Vietnam.

This study investigated the contamination levels and sources of As and Cd vicinity area from Nui Phao mine that is one of the largest tungsten (W) open pit mines in the world. Soil and plant samples were collected from the study area to identify the concentrations of As and Cd using aqua-regia or HNO digestion. According to the Vietnamese agricultural soil criteria, all soil samples were contaminated with As and Cd.

High-throughput analysis of the activities of xCas9, SpCas9-NG and SpCas9 at matched and mismatched target sequences in human cells.

The applications of clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing can be limited by a lack of compatible protospacer adjacent motifs (PAMs), insufficient on-target activity and off-target effects. Here, we report an extensive comparison of the PAM-sequence compatibilities and the on-target and off-target activities of Cas9 from Streptococcus pyogenes (SpCas9) and the SpCas9 variants xCas9 and SpCas9-NG (which are known to have broader PAM compatibility than SpCas9) at 26,478 lentivirally integrated target sequences and 78 endogenous target sites in human cells. We found that xCas9 has the lowest tolerance for mismatched target sequences and that SpCas9-NG has the broadest PAM compatibility.

SpCas9 activity prediction by DeepSpCas9, a deep learning-based model with high generalization performance.

We evaluated SpCas9 activities at 12,832 target sequences using a high-throughput approach based on a human cell library containing single-guide RNA-encoding and target sequence pairs. Deep learning-based training on this large dataset of SpCas9-induced indel frequencies led to the development of a SpCas9 activity-predicting model named DeepSpCas9. When tested against independently generated datasets (our own and those published by other groups), DeepSpCas9 showed high generalization performance.

Dual-line fabrication method in direct laser lithography to reduce the manufacturing time of diffractive optics elements.

To reduce the manufacturing time of DOEs (Diffractive Optics Elements) and POEs (Periodical Optics Elements), a new fabrication method in direct laser lithography is proposed based on the laser ablation phenomenon and the thermochemical effect of chrome. The basic mechanism of the proposed method and experimental results are also presented. It was found that when a 3 × 3 rectangular pattern is fabricated, the proposed method can reduce the total lithographic length by approximately 33%.

Deep learning improves prediction of CRISPR-Cpf1 guide RNA activity.

We present two algorithms to predict the activity of AsCpf1 guide RNAs. Indel frequencies for 15,000 target sequences were used in a deep-learning framework based on a convolutional neural network to train Seq-deepCpf1. We then incorporated chromatin accessibility information to create the better-performing DeepCpf1 algorithm for cell lines for which such information is available and show that both algorithms outperform previous machine learning algorithms on our own and published data sets.

Cognitive and Neuroanatomical Correlates in Early Versus Late Onset Parkinson's Disease Dementia.

Background: Aging is the most important risk factor of development of dementia in Parkinson's disease (PD), but there are no data on clinical and radiological heterogeneity of PD dementia (PDD) depending on age at onset.

Objectives: The goal of this study was to examine whether patients with PDD are clinically and radiologically heterogeneous depending on age at onset.

Methods: A total of 116 patients with PD dementia and 121 age- and sex-matched normal controls were enrolled.