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Advances in single-cell and -nucleus transcriptomics have enabled generation of increasingly large-scale datasets from hundreds of subjects and millions of cells. These studies promise to give unprecedented insight into the cell type specific biology of human disease. Yet performing differential expression analyses across subjects remains difficult due to challenges in statistical modeling of these complex studies and scaling analyses to large datasets. Our open-source R package dreamlet (DiseaseNeurogenomics.github.io/dreamlet) uses a pseudobulk approach based on precision-weighted linear mixed models to identify genes differentially expressed with traits across subjects for each cell cluster. Designed for data from large cohorts, dreamlet is substantially faster and uses less memory than existing workflows, while supporting complex statistical models and controlling the false positive rate. We demonstrate computational and statistical performance on published datasets, and a novel dataset of 1.4M single nuclei from postmortem brains of 150 Alzheimer’s disease cases and 149 controls.

The gas cluster ion beam (GCIB) is a valuable tool for surface analysis, providing new 3D mass analysis equipment possibilities. The main feature of the GCIB is that many particles are involved during the collision of the cluster ion beam with a sample surface. Studying the characteristics of the GCIB is essential for improving the performance of the analysis equipment. We evaluated the efficiency of the GCIB using a mixed-gas of Ar and CO2 as a primary ion beam for time-of-flight secondary ion mass spectrometry. We measured the characteristic factors and composition of the cluster ion beam depending on the mole fraction ratio of CO2/Ar. We measured that the CO2 composition of the output cluster ion beam rapidly increases to over 95% when the mole fraction ratio of CO2 increases by more than 10% in the injected mixed gas. Nevertheless, the optimal ratio of the CO2/Ar mole fraction (%) to increase the secondary ion efficiency was 96% CO2, which more than doubled the secondary ion efficiency over that of pure Ar clusters. The beam spot size began rapidly decreasing from 95% CO2, and it was reduced by up to 0.67 times at 100% CO2. According to the mixed-gas ratio, the sputtering yield of the Si wafer was 8 times lower than that of pure Ar clusters.

The induced circular dichroism (ICD) of phenol complexed with (

When an insulator sample is analyzed via time-of-flight secondary ion mass spectrometry (ToF-SIMS), charges accumulate on the sample surface due to the primary ion beam. These local surface charges and surface potentials cause many problems during analysis. A Kelvin probe was used to measure the surface potentials of the insulator sample. The surface potential induced on the surface of the sample and its temporal change was measured following the irradiation of the gas cluster ion beam. It was confirmed that the estimated surface potential value is affected by the high vacuum gauge, and there is an inflow of charges that possess polarities opposite to that of the surface potential. The amount of current flowing from the high vacuum gauge was calculated using the surface potential data that was measured. The amount of charge flowing onto the surface of the insulator was varied from several tens of fA to several fA, which was depended on its vacuum degree and position of high vacuum ion gauge. Additionally, neutralization of surface charges by the neutral gas effect was also weakly observed. This leaked current from the high vacuum gauges is likely to have a small but lasting impact on the ToF-SIMS insulator analysis.

Tolvaptan is the only drug approved to slow cyst growth and preserve kidney function in patients with autosomal dominant polycystic kidney disease (ADPKD). However, its limited efficacy combined with significant side effects underscores the need to identify new and safe therapeutic drug targets to slow progression to end stage kidney disease. We identified Discoidin Domain Receptor 1 (DDR1) as receptor tyrosine kinase upregulated in vivo in 3 mouse models of ADPKD using a novel mass spectrometry approach to identify kinases upregulated in ADPKD. Previous studies demonstrating critical roles for DDR1 to cancer progression, its potential role in the pathogenesis of a variety of other kidney disease, along with the possibility that DDR1 could provide new insight into how extracellular matrix impacts cyst growth led us to study the role of DDR1 in ADPKD pathogenesis. However, genetic deletion of DDR1 using CRISPR/Cas9 failed to slow cyst growth or preserve kidney function in both a rapid and slow mouse model of ADPKD demonstrating that DDR1 does not play a role in PKD pathogenesis and is thus a not viable drug target. In spite of the negative results, our studies will be of interest to the nephrology community as it will prevent others from potentially conducting similar experiments on DDR1 and reinforces the potential of performing unbiased screens coupled with in vivo gene editing using CRISPR/Cas9 to rapidly identify and confirm new potential drug targets for ADPKD.

The resonant two-photon ionization circular dichroism (R2PICD) spectrum represents the cumulative circular dichroism (CD) of one-photon excitation and the subsequent one-photon ionization, whereas the fluorescence-detected circular dichroism (FDCD) spectra exhibit only the CD of one-photon excitation, similar to conventional CD spectra. We obtained the FDCD spectra of jet-cooled ephedrine (EPD) near the origin band of the S0-S1 transition to measure the CD of one-photon absorption and thus the CD of the ionization process in R2PI in comparison with the R2PICD spectra. The CD effects of the ionization following excitation of the A (0-0) and C (930 cm(-1)) bands in the spectrum are small, whereas those of the B band (530 cm(-1)) are anomalously large, leading to opposite CD signs for the FDCD and R2PICD spectra. Based on the intermediate state-selective fragmentation patterns in the R2PI spectra, this large CD effect is attributed to the state-selective isomerization that occurs after excitation of the B band. By comparing the experimental and theoretical spectra, we determined that the B band corresponds to an asymmetric ring distortion mode that involves torsional motions of the side chain, which may facilitate the isomerization process. This study demonstrates that FDCD spectroscopy combined with R2PICD spectroscopy provides a powerful tool to measure the CD effects of the excitation and ionization processes separately in R2PI and thus probe the structural changes that occur during the ionization process following excitation to an intermediate state.

Induced circular dichroism (ICD) is the CD observed in the absorption of an achiral molecule bound to a transparent chiral molecule through noncovalent interactions. ICD spectroscopy has been used to probe the binding between molecules, such as protein–ligand interactions. However, most ICD spectra have been measured in solution, which only exhibit the averaged CD values of all conformational isomers in solution. Here, we obtained the first isomer-selective ICD spectra by applying resonant two-photon ionization CD spectroscopy to jet-cooled phenol complexes with (−)-methyl l-lactate (PhOH-(−)ML). The well-resolved CD bands in the spectra were assigned to two conformers, which contained different types of hydrogen-bonding interactions between PhOH and (−)ML. The ICD values of the two conformers have different signs and magnitudes, which were explained by differences both in the geometrical asymmetries of PhOH bound to (−)ML and in the electronic coupling strengths between PhOH and (−)ML.

We obtained resonant two-photon ionization circular dichroism (R2PICD) spectra of jet-cooled phenylalanine (Phe) and its hydrated clusters (Phe(H2O)n, n = 1–2) near the origin band of the S0–S1 transition. The R2PICD spectra of Phe exhibit well-resolved CD bands of six different conformers present in the jet, which vary in sign and magnitude depending on their conformations. We revised the previous structural assignments of the Phe conformers based on the comparison between the experimental and theoretical CD signs, infrared spectra, and rotational band contours. The R2PICD spectra of Phe(H2O)n reveal that hydration with one or two water molecule(s) does not affect the CD signs of Phe conformers but significantly increases their CD magnitudes. Furthermore, conformational selection by solvation alters relative populations of Phe conformers, leading to a sign inversion in the CD spectra of Phe(H2O)n compared with that of Phe monomer.