Optogenetic control of kinesin-1, -2, -3 and dynein reveals their specific roles in vesicular transport.

Each cargo in a cell employs a unique set of motor proteins for its transport. To dissect the roles of each type of motor, we developed optogenetic inhibitors of endogenous kinesin-1, -2, -3 and dynein motors and examined their effect on the transport of early endosomes, late endosomes, and lysosomes. While kinesin-1, -3, and dynein transport vesicles at all stages of endocytosis, kinesin-2 primarily drives late endosomes and lysosomes.

Tau differentially regulates the transport of early endosomes and lysosomes.

Microtubule-associated proteins (MAPs) modulate the motility of kinesin and dynein along microtubules to control the transport of vesicles and organelles. The neuronal MAP tau inhibits kinesin-dependent transport. Phosphorylation of tau at Tyr-18 by fyn kinase results in weakened inhibition of kinesin-1.

Benchmarking Single-Cell mRNA-Sequencing Technologies Uncovers Differences in Sensitivity and Reproducibility in Cell Types With Low RNA Content.

Single-cell RNA sequencing (scRNA-seq) has the ability to classify each cell and determine the transcriptomic profile of specific cell types and cells of a given disease state; however, sensitivity of the gene count for each cell can be a critical component to the success of a single-cell study. The recently introduced SMART-Seq Single Cell PLUS Kit (SSsc PLUS) claims to provide higher sensitivity and reproducibility versus popular methods for the sequencing analysis of single cells. Here, the cDNA-generation component of the kit, SMART-Seq Single Cell Kit (SSsc), was compared with the popular homebrew protocol, Smart-seq2, and its update, Smart-seq3.

RAGE Isoforms, its Ligands and their Role in Pathophysiology of Alzheimer's Disease.

Receptor for Advanced Glycation End product (RAGE) plays a crucial role in a variety of physiological and pathological processes due to its ability to bind a broad repertory of ligands. There are also multiple forms of RAGE that exist; some work on promoting feed-forward pathways while others perform inhibitory actions. This review focuses on the RAGE isoforms expression, its intracellular pathways activation via RAGE- ligand interaction, and its importance in the physiological and pathological process of the brain.

Massively parallel nanowell-based single-cell gene expression profiling.

Background: Technological advances have enabled transcriptome characterization of cell types at the single-cell level providing new biological insights. New methods that enable simple yet high-throughput single-cell expression profiling are highly desirable.

Results: Here we report a novel nanowell-based single-cell RNA sequencing system, ICELL8, which enables processing of thousands of cells per sample.

Enhanced prediction of conformational flexibility and phosphorylation in proteins.

Many sequence-based predictors of structural and functional properties of proteins have been developed in the past. In this study, we developed new methods for predicting measures of conformational flexibility in proteins, including X-ray structure-derived temperature (B-) factors and the variance within NMR structural ensemble, as effectively measured by the solvent accessibility standard deviations (SASDs). We further tested whether these predicted measures of conformational flexibility in crystal lattices and solution, respectively, can be used to improve the prediction of phosphorylation in proteins.

Artificial intelligence approaches for rational drug design and discovery.

Pattern recognition, machine learning and artificial intelligence approaches play an increasingly important role in rational drug design, screening and identification of candidate molecules and studies on quantitative structure-activity relationships (QSAR). In this review, we present an overview of basic concepts and methodology in the fields of machine learning and artificial intelligence (AI). An emphasis is put on methods that enable an intuitive interpretation of the results and facilitate gaining an insight into the structure of the problem at hand.