Separating Scarring Effect and Selection of Early-Life Exposures With Genetic Data.

Causal life course research examining consequences of early-life exposures has largely relied on associations between early-life environments and later-life outcomes using exogenous environmental shocks. Nonetheless, even with (quasi-)randomized early-life exposures, these associations may reflect not only causation ("scarring") but also selection (i.e., which members are included in data assessing later life). Investigating this selection and its impacts on estimated effects of early-life conditions has, however, often been ignored because of a lack of pre-exposure data. This study proposes an approach for assessing and correcting selection, separately from scarring, using genetic measurements. Because genetic measurements are determined at the time of conception, any associations with early-life exposures should be interpreted as selection. Using data from the UK Biobank, we find that in utero exposure to a higher area-level infant mortality rate is associated with genetic predispositions correlated with better educational attainment and health. These findings point to the direction and magnitude of selection from this exposure. Corrections for this selection in examinations of effects of exposure on later educational attainment suggest underestimates of 26-74%; effects on other life course outcomes also vary across selection correction methods.

Optimization of Cas12a for multiplexed genome-scale transcriptional activation.

Cas12a CRISPR technology, unlike Cas9, allows for facile multiplexing of guide RNAs from a single transcript, simplifying combinatorial perturbations. While Cas12a has been implemented for multiplexed knockout genetic screens, it has yet to be optimized for CRISPR activation (CRISPRa) screens in human cells. Here, we develop a new Cas12a-based transactivation domain (TAD) recruitment system using the ALFA nanobody and demonstrate simultaneous activation of up to four genes. We screen a genome-wide library to identify modulators of growth and MEK inhibition, and we compare these results with those obtained with open reading frame (ORF) overexpression and Cas9-based CRISPRa. We find that the activity of multiplexed arrays is largely predictable from the best-performing guide and provide criteria for selecting active guides. We anticipate that these results will greatly accelerate the exploration of gene function and combinatorial phenotypes at scale.

Accounting for small variations in the tracrRNA sequence improves sgRNA activity predictions for CRISPR screening.

CRISPR technology is a powerful tool for studying genome function. To aid in picking sgRNAs that have maximal efficacy against a target of interest from many possible options, several groups have developed models that predict sgRNA on-target activity. Although multiple tracrRNA variants are commonly used for screening, no existing models account for this feature when nominating sgRNAs. Here we develop an on-target model, Rule Set 3, that makes optimal predictions for multiple tracrRNA variants. We validate Rule Set 3 on a new dataset of sgRNAs tiling essential and non-essential genes, demonstrating substantial improvement over prior prediction models. By analyzing the differences in sgRNA activity between tracrRNA variants, we show that Pol III transcription termination is a strong determinant of sgRNA activity. We expect these results to improve the performance of CRISPR screening and inform future research on tracrRNA engineering and sgRNA modeling.

Gene-by-peer-environment interaction effects on cigarette, alcohol, and marijuana use among US high school students of European Ancestry.

Research has shown that adolescents' substance use behavior is determined not only by individual characteristics but also by peer environments, and an emerging literature in social genomics has also found that individual genotypes moderate peer effects on egos' substance use. However, the previous literature on genetic by peer environment (GxPE) interaction effects is limited by the use of genetic measures with limited power and a lack of focus on causality. Based on a sample of about 4000 adolescents of European Ancestry from the National Longitudinal Study of Adolescent to Adult Health, this study utilizes polygenic scores to examine GxPE interactions between ego's genetics and peers' cigarette, alcohol, and marijuana use. The results show peers' cigarette and marijuana use positively affect ego's substance use, and peer effects are stronger when the ego is genetically predisposed to substance use. However, genetic propensities toward risk tolerance are found to weaken the peer effects on the ego's marijuana use. Overall, our findings provide new evidence for the existence of GxPE effects on adolescent substance use and reveal the multidimensional nature of GxPE effects.

The effects of education on cognition in older age: Evidence from genotyped Siblings.

A growing literature has sought to tie educational attainment with later-life cognition and Alzheimer's disease outcomes. This paper leverages sibling comparisons in educational attainment as well as genetic predictors (polygenic scores) for cognition, educational attainment, and Alzheimer's disease to estimate effects of educational attainment on cognition in older age in the United Kingdom. We find that the effects of education on cognition are confounded by family background factors (~40%) and by genetics (<10%). After adjustments, we continue to find large effects of education. College graduates have cognition scores that are approximately 0.75 SD higher than those who report no credentials. We also find evidence that educational effects on cognition are smaller for those with high polygenic scores for Alzheimer's disease.

Mosaic Immunoassays Integrated with Microfluidic Channels for High-Throughput Parallel Detection.

Using the ice-printing technique, we have integrated micromosaic immunoassays (µMIAs) with microfluidic channels, which reduces the sample consumption and response time and allows high-throughput parallel detection. The ice-printing method is a low-temperature and contaminant-free process, which is more convenient, precise, and biofriendly than the traditional fabrication method. Meanwhile, based on the ice-drying process, this method can obtain a uniform distribution of the residue protein patterns, which leads to a uniform fluorescence result. As a proof of concept, the test of stability, sensitivity, and specificity of µMIA based on one-step ELISA are demonstrated. In this device, immobilized antigens surrounded with ice could remain biological at -20 °C for months.

Inkjet printing-based fabrication of microscale 3D ice structures.

This study proposed a method for fabricating 3D microstructures of ice without a supporting material. The inkjet printing process was performed in a low humidity environment to precisely control the growth direction of the ice crystals. In the printing process, water droplets (volume = hundreds of picoliters) were deposited onto the previously formed ice structure, after which they immediately froze. Different 3D structures (maximum height = 2000 µm) could be formed by controlling the substrate temperature, ejection frequency and droplet size. The growth direction was dependent on the landing point of the droplet on the previously formed ice structure; thus, 3D structures could be created with high degrees of freedom.

Rapid Quantitative Fluorescence Detection of Copper Ions with Disposable Microcapsule Arrays Utilizing Functional Nucleic Acid Strategy.

In this work, an economical and easy-to-use microcapsule array fabricated by ice printing technique has been realized for ultrasensitive fluorescence quantification of copper ions employing functional nucleic acid strategy. With ice printing, the detection reagents are sealed by polystyrene (PS) film isolation and photopolymer, which guarantees a stable and contamination-free environment for functional nucleic acid reaction. Our microcapsule arrays have shown long-term stability (20 days) under -20 °C storage in frozen form before use. During the Cu2+ on-site detection, 1 µL sample is simply injected into the thawy microcapsule by a microliter syringe under room temperature, and after 20 minutes the fluorescence result can be obtained by an LED transilluminator. This method can realize the detection limit to 100 nM (100 fmol/µL) with high specificity.

Chitin and waste shrimp shells liquefaction and liquefied products/polyvinyl alcohol blend membranes.

Ball-milled chitin was liquefied with an optimal yield of 92% under sulfuric acid in diethylene glycol (DEG) at 160 °C for 120 min. The resulting liquid mixture was roughly separated into two portions: the real products of the reaction (liquefied ball-milled chitin, LBMC) and the remaining unreacted DEG. LBMC was further mingled with polyvinyl alcohol (PVA) to prepare LBMC/PVA blend membranes. To promote the direct utilization of shellfishery waste, raw shrimp shells were used to replace chitin for the liquefaction and membrane preparation operations. Liquefied ball-milled shrimp shells (LBMS) and the corresponding LBMS/PVA blend membranes were obtained. After adding LBMC or LBMS, the mechanical, thermal, water content and antibacterial performance of blend membranes were significantly improved compared to pure PVA membrane. Surprisingly, all the measured properties of LBMC/PVA and LBMS/PVA blend membranes were comparable, and even some properties of the latter were slightly superior than those of the former.

From functional structure to packaging: full-printing fabrication of a microfluidic chip.

This paper presents a concept of a full-printing methodology aiming at convenient and fast fabrication of microfluidic devices. For the first time, we achieved a microfluidic biochemical sensor with all functional structures fabricated by inkjet printing, including electrodes, immobilized enzymes, microfluidic components and packaging. With the cost-effective and rapid process, this method provides the possibility of quick model validation of a novel lab-on-chip system. In this study, a three-electrode electrochemical system was integrated successfully with glucose oxidase immobilization gel and sealed in an ice channel, forming a disposable microfluidic sensor for glucose detection. This fully-printed chip was characterized and showed good sensitivity and a linear section at a low-level concentration of glucose (0-10 mM). With the aid of automatic equipment, the fully-printed sensor can be massively produced with low cost.

Liquefied chitin/polyvinyl alcohol based blend membranes: Preparation and characterization and antibacterial activity.

To expand the applications of fishing industrial wastes, the liquefaction technique was employed to convert chitin into liquids, which were first further used for the modification of polymer materials. Ball-mill treated chitin was effectively liquefied into polyols in polyethylene glycol 400/glycerin mixed solvent. FTIR, 1H NMR and size exclusion chromatography analyses of liquefied chitin turned out that depolymerization and deacetylation reactions occurred during liquefaction process. The liquefied chitin/polyvinyl alcohol blend membranes with various mixing ratios were prepared and characterized by FTIR and SEM. In addition, transparency, tensile strength, elongation at break, water absorption, water retention and antibacterial properties were thoroughly discussed. The mechanical property and thermal stability were greatly enhanced under the optimized conditions of 25wt% liquefied chitin incorporation to polyvinyl alcohol. Moreover, the blend membranes showed improvements in water absorption and water retention capacity. In particular, the antibacterial activity was significantly improved after incorporation of liquefied chitin.