Roby P. Bhattacharyya

The Structure and Function of Proline Recognition Domains

One particularly abundant group of modular recognition domains consists of those that bind proline-rich motifs. Such modules, including the SH3, WW, and EVH1 domains, play a critical role in the assembly and regulation of many intracellular signaling complexes. These domains use strikingly similar molecular mechanisms of proline recognition. We discuss some of the potential biological advantages conferred by proline recognition, which may explain its widespread use in signaling. This STKE Review describes one class of protein interaction domains: the proline-binding domains. Conserved protein domains are critical to the assembly and regulation of many intracellular signaling complexes and pathways. Proline-binding domains serve two main functions: to serve as assembly points in signaling complexes and to serve a regulatory role in controlling protein activity. With seven figures and one table, this review provides detailed structural information about three main proline-binding motifs (the SH3, WW, and EVH1 domains), as well as brief descriptions of other proline-binding domains. The review has 91 references, seven figures, one table, and five interactive images.

Nucleic acid detection with CRISPR-Cas13a/C2c2

Sensitive and specific CRISPR diagnostics Methods are needed that can easily detect nucleic acids that signal the presence of pathogens, even at very low levels. Gootenberg et al. combined the allele-specific sensing ability of CRISPR-Cas13a with recombinase polymerase amplification methods to detect specific RNA and DNA sequences. The method successfully detected attomolar levels of Zika virus, as well as the presence of pathogenic bacteria. It could also be used to perform human genotyping from cell-free DNA. Science, this issue p. 438 An ortholog of CRISPR-Cas13a/C2c2 can be used as a highly sensitive detector of specific RNA and DNA sequences. Rapid, inexpensive, and sensitive nucleic acid detection may aid point-of-care pathogen detection, genotyping, and disease monitoring. The RNA-guided, RNA-targeting clustered regularly interspaced short palindromic repeats (CRISPR) effector Cas13a (previously known as C2c2) exhibits a “collateral effect” of promiscuous ribonuclease activity upon target recognition. We combine the collateral effect of Cas13a with isothermal amplification to establish a CRISPR-based diagnostic (CRISPR-Dx), providing rapid DNA or RNA detection with attomolar sensitivity and single-base mismatch specificity. We use this Cas13a-based molecular detection platform, termed Specific High-Sensitivity Enzymatic Reporter UnLOCKing (SHERLOCK), to detect specific strains of Zika and Dengue virus, distinguish pathogenic bacteria, genotype human DNA, and identify mutations in cell-free tumor DNA. Furthermore, SHERLOCK reaction reagents can be lyophilized for cold-chain independence and long-term storage and be readily reconstituted on paper for field applications.

Simultaneous generation of many RNA-seq libraries in a single reaction

Although RNA-seq is a powerful tool, the considerable time and cost associated with library construction has limited its utilization for various applications. RNAtag-Seq, an approach to generate multiple RNA-seq libraries in a single reaction, lowers time and cost per sample, and it produces data on prokaryotic and eukaryotic samples that are comparable to those generated by traditional strand-specific RNA-seq approaches.

A 52-year-old Cuban immigrant with weight loss, dyspnea, and fever. Splenic tuberculosis.

Clinical Infectious Diseases 2011;52(3):368 The Author 2011. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions @oup.com. 1058-4838/2011/00-0001

Case 30-2017

37.00 DOI: 10.1093/cid/ciq162 Figure 1. Computed tomographic scan of the abdomen showing a spleen diffusely infiltrated by small, hypodense lesions. Figure 2. Gross pathology of resected spleen showing anatomic correlates of radiographic lesions shown in Figure 1.

Case 4-2016

A 65-year-old woman with autoimmune hepatitis presented for an evaluation for liver transplantation. Fever, hypotension, and worsening liver and renal failure developed. A blood culture revealed corkscrew-shaped gram-negative rods. A diagnosis was made.

Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits.

A 58-year-old woman presented during the summer with fever, neck swelling, and an ulcerated lesion on the forehead. Imaging of the neck showed enlarged, centrally hypodense lymph nodes with infiltration of the surrounding fat. Tests were performed, and a diagnosis was made.