The aggregation of proteins into oligomers and amyloid fibrils is characteristic of several neurodegenerative diseases, including Parkinson disease (PD). In PD, the process of aggregation of α-synuclein (α-syn) from monomers, via oligomeric intermediates, into amyloid fibrils is considered the disease-causative toxic mechanism. We developed α-syn mutants that promote oligomer or fibril formation and tested the toxicity of these mutants by using a rat lentivirus system to investigate loss of dopaminergic neurons in the substantia nigra. The most severe dopaminergic loss in the substantia nigra is observed in animals with the α-syn variants that form oligomers (i.e., E57K and E35K), whereas the α-syn variants that form fibrils very quickly are less toxic. We show that α-syn oligomers are toxic in vivo and that α-syn oligomers might interact with and potentially disrupt membranes. P arkinson disease (PD) is the most common movement disorder, currently affecting approximately 2% of the population older than age 60 y. Prominent neuropathological hallmarks of PD are the loss of dopaminergic neurons in the substantia nigra (SN) region of the midbrain (1) and the presence of α-syn-containing intracellular inclusions: Lewy bodies (LBs) and Lewy neurites (2). α-Syn, a 140-aa protein physiologically found in presynaptic terminals of neurons, is the major fibrillar protein in LBs and Lewy neurites in sporadic and inherited PD. Moreover, point mutations (A53T, A30P, E46K) and gene multiplications of human WT (hWT) α-syn are related to rare familial autosomal-dominant forms of early-onset PD (3-6), suggesting that increased gene dosage and aberrant protein structure may accelerate disease onset and progression.Recent reports indicate that the accumulation of α-syn can result in the formation of intermediate-state oligomers, and oligomers of different shapes and sizes have been described (7-10). These oligomers interact with lipids, disrupt membranes (7,8), and cause cell death in vitro (10, 11) and in nonmammalian models, such as Caenorhabditis elegans and Drosophila melanogaster (12). However, we are aware of no previous direct in vivo demonstration of the toxicity of α-syn oligomers in mammals.We aim to establish a model that allows specific testing of the effects of α-syn oligomerization in vitro and in vivo. To elucidate the causal structure-toxicity relationship of these oligomeric protein assemblies in a mammalian system, we designed "conformation-trapped" mutants based on structural modeling of α-syn fibrils (13, 14). Structurally, amyloid fibrils of α-syn are composed of cross-β-sheets (15). Residues from approximately 30 to 110 of α-syn form the core of the fibrils, whereas the approximately 30 N-terminal residues are heterogeneous and the approximately 30 C-terminal residues are flexible (13,14,16,17). Based on our structural model, recently developed from NMR data, the core of α-syn fibrils comprises five β-strands reminiscent of a five-layered "β-sandwich" (14). Several loops adjacent to and between the strands ar...

Article Methods Cell lines Cell lines were purchased from ATCC and were not formally authenticated, but confirmation of expected gene expression patterns were performed for RNA-seq and eCLIP experiments. Cell lines were routinely tested for mycoplasma contamination (MycoAlert, Lonza).

Genomes encompass all the information necessary to specify the development and function of an organism. In addition to genes, genomes also contain a myriad of functional elements that control various steps in gene expression. A major class of these elements function only when transcribed into RNA as they serve as the binding sites for RNA binding proteins (RBPs) which act to control post-transcriptional processes including splicing, cleavage and polyadenylation, RNA editing, RNA localization, translation, and RNA stability. Despite the importance of these functional RNA elements encoded in the genome, they have been much less studied than genes and DNA elements. Here, we describe the mapping and characterization of RNA elements recognized by a large collection of human RBPs in K562 and HepG2 cells. These data expand the catalog of functional elements encoded in the human genome by addition of a large set of elements that function at the RNA level through interaction with RBPs.Van Nostrand et al.

SUMMARY During microbial infection, responding CD8+ T lymphocytes differentiate into heterogeneous subsets that together provide immediate and durable protection. To elucidate the dynamic transcriptional changes that underlie this process, we applied a single-cell RNA sequencing approach and analyzed individual CD8+ T lymphocytes sequentially throughout the course of a viral infection in vivo. Our analyses revealed a striking transcriptional divergence among cells that had undergone their first division and identified previously unknown molecular determinants controlling CD8+ T lymphocyte fate specification. These findings suggest a model of terminal effector cell differentiation initiated by an early burst of transcriptional activity and subsequently refined by epigenetic silencing of transcripts associated with memory lymphocytes, highlighting the power and necessity of single-cell approaches.

As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing and/or sequencing capacity, which can also introduce biases1–3. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing4,5. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We developed and deployed improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detected emerging variants of concern up to 14 days earlier in wastewater samples, and identified multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.