Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

Large-scale surveys of single-cell gene expression have the potential to reveal rare cell populations and lineage relationships, but require efficient methods for cell capture and mRNA sequencing^1–4. Although cellular barcoding strategies allow parallel sequencing of single cells at ultra-low depths⁵, the limitations of shallow sequencing have not been directly investigated. By capturing 301 single cells from 11 populations using microfluidics and analyzing single-cell transcriptomes across downsampled sequencing depths, we demonstrate that shallow single-cell mRNA sequencing (~50,000 reads per cell) is sufficient for unbiased cell-type classification and biomarker identification. In developing cortex we identify diverse cell types including multiple progenitor and neuronal subtypes, and we identify EGR1 and FOS as previously unreported candidate targets of Notch signaling in human but not mouse radial glia. Our strategy establishes an efficient method for unbiased analysis and comparison of cell populations from heterogeneous tissue by microfluidic single-cell capture and low-coverage sequencing of many cells.

Structure of Mycobacterium tuberculosis RuvA, a protein involved in recombination

The process of recombinational repair is crucial for maintaining genomic integrity and generating biological diversity. In association with RuvB and RuvC, RuvA plays a central role in processing and resolving Holliday junctions, which are a critical intermediate in homologous recombination. Here, the cloning, purification and structure determination of the RuvA protein from Mycobacterium tuberculosis (MtRuvA) are reported. Analysis of the structure and comparison with other known RuvA proteins reveal an octameric state with conserved subunit-subunit interaction surfaces, indicating the requirement of octamer formation for biological activity. A detailed analysis of plasticity in the RuvA molecules has led to insights into the invariant and variable regions, thus providing a framework for understanding regional flexibility in various aspects of RuvA function.

Laboratory scale structural genomics

At Lawrence Livermore National Laboratory, the development of the TB structural genomics consortium crystallization facility has paralleled several local proteomics research efforts that have grown out of gene expression microarray and comparative genomics studies. Collective experience gathered from TB consortium labs and other centers involved in the NIH-NIGMS protein structure initiative allows us to explore the possibilities and challenges of pursuing structural genomics on an academic laboratory scale. We discuss our procedures and protocols for genomic targeting approaches, primer design, cloning, small scale expression screening, scale-up and purification, through to automated crystallization screening and data collection. The procedures are carried out by a small group using a combination of traditional approaches, innovative molecular biochemistry approaches, software automation, and a modest investment in robotic equipment.

The TB structural genomics consortium crystallization facility: towards automation from protein to electron density

The crystallization facility of the TB (Tuberculosis) structural genomics consortium, one of nine NIH sponsored p50 structural genomic centres, provides TB consortium members with automated crystallization, data collection and basic molecular replacement (MR) structure solution up to bias minimized electron density maps. Crystallization setup of up to ten proteins per day follows the CRYSTOOL combinatorial screen protocol using a modular and affordable robotic design with an open architecture. Components include screen preparation, plate setup, automated image acquisition and analysis, and optimisation design. A new 96 well crystallization plate has been designed for optimal robotic handling while maintaining ease of manual crystal harvesting. Robotic crystal mounting, screening, and data collection are conducted in-house and at the Advanced Light Source (ALS) in Berkeley. A simple automated protocol based on MR and homology based structure prediction automatically solves modestly difficult problems. Multiple search models are evaluated in parallel MR and the best multi-segment rigid body refined MR solution is subjected to simulated annealing torsion angle molecular dynamics using CNS, bringing even marginal MR solutions within the convergence radius of the subsequent highly effective bias removal and map reconstruction protocol, Shake&wARP, used to generate electron density for initial rebuilding. Real space correlation plots allow rapid assessment of local structure quality. Modular design of robotics and automated scripts using publicly available programs for structure solution allow for efficient high throughput crystallography - at a reasonable cost.

[Unilateral cavernous angioma of the thalamus disclosed by transitional disorders in the upward gaze]

We describe a case of a cavernous angioma of the right thalamus, identified by MRI, showing transient vertical diplopia in the upward gaze, present only in protracted recumbency. We consider possible pathogenetic mechanisms in an attempt to explain this peculiar disturbances. In addition we emphasize that MRI is the most sensitive procedure for detection of the cavernous angioma.

Subacute parkinsonism from a single lacunar infarct in the basal ganglia

The authors describe the case of a patient showing a lateralized and subacute parkinsonism with CT-evidence of a single lacunar infarct in the contralateral basal ganglia. The vascular origin of this type of subacute parkinsonism is emphasized.

Risk factors in lacunar strokes. A retrospective study of 52 patients

A retrospective analysis was carried out on 52 patients with CT-identified lacunar infarcts in order to identify possible risk factors. It was found that arterial hypertension, cardiac emboli and/or emboli from epiaortic vessels play a significant role in the genesis of lacunar infarcts. No preferential relationship was found between "small" lacunes and arterial hypertension or between "large" lacunes and embolic disease.

A case of cheiralgia paresthetica secondary to diabetes mellitus

The anatomy and etiology of cheiralgia paresthetica are discussed in the light of a case of this syndrome in a diabetic. The variability of the area affected can be ascribed to anatomical variants in the innervation of the hand ("ulnar intervention" in the radical sensory distribution). In patients in whom mechanical causes have been excluded diabetes mellitus should be considered as a possible cause.