Electronic Mapping of a Bacterial Genome with Dual Solid-State Nanopores and Active Single-Molecule Control.

We present an electronic mapping of a bacterial genome using solid-state nanopore technology. A dual-nanopore architecture and active control logic are used to produce single-molecule data that enables estimation of distances between physical tags installed at sequence motifs within double-stranded DNA. Previously developed "DNA flossing" control logic generates multiple scans of each captured DNA. We extended this logic in two ways: first, to automate "zooming out" on each molecule to progressively increase the number of tags scanned during flossing, and second, to automate recapture of a molecule that exited flossing to enable interrogation of the same and/or different regions of the molecule. Custom analysis methods were developed to produce consensus alignments from each multiscan event. The combined multiscanning and multicapture method was applied to the challenge of mapping from a heterogeneous mixture of single-molecule fragments that make up the Escherichia coli (E. coli) chromosome. Coverage of 3.1× across 2355 resolvable sites of the E. coli genome was achieved after 5.6 h of recording time. The recapture method showed a 38% increase in the merged-event alignment length compared to single-scan alignments. The observed intertag resolution was 150 bp in engineered DNA molecules and 166 bp natively within fragments of E. coli DNA, with detection of 133 intersite intervals shorter than 200 bp in the E. coli reference map. We present results on estimating distances in repetitive regions of the E. coli genome. With an appropriately designed array, higher throughput implementations could enable human-sized genome and epigenome mapping applications.

Tensin regulates pharyngeal pumping in Caenorhabditis elegans.

Tensin is a focal adhesion molecule that is known to regulate cell adhesion, migration, and proliferation. Although there are four tensin homologs (TNS1, TNS2, TNS3, and CTEN/TNS4) in mammals, only one tensin gene is found in Caenorhabditis elegans. Sequence analysis suggests that Caenorhabditis elegans tensin is slightly closer aligned with human TNS1 than with other human tensins. To establish the role of TNS1 in Caenorhabditis elegans, we have generated TNS1 knockout (KO) worms by CRISPR-Cas9 and homologous recombination directed repair approaches. Lack of TNS1 does not appear to affect the development or gross morphology of the worms. Nonetheless, defecation cycles are significantly longer in TNS1 KO worms. In addition, their pharyngeal pumping rate is markedly faster, which is likely due to a shorter pump duration in the KO worms. These findings indicate that TNS1 is not required for the development and survival of Caenorhabditis elegans but point to a critical role in modulating defecation and pharyngeal pumping rates.

Phosphorylation of Arabidopsis eIF4E and eIFiso4E by SnRK1 inhibits translation.

Regulation of protein synthesis is critical for maintaining cellular homeostasis. In mammalian systems, translational regulatory networks have been elucidated in considerable detail. In plants, however, regulation occurs through different mechanisms that remain largely elusive. In this study, we present evidence that the Arabidopsis thaliana energy sensing kinase SnRK1, a homologue of mammalian AMP-activated kinase and yeast sucrose non-fermenting 1 (SNF1), inhibits translation by phosphorylating the cap binding proteins eIF4E and eIFiso4E. We establish that eIF4E and eIFiso4E contain two deeply conserved SnRK1 consensus target sites and that both interact with SnRK1 in vivo. We then demonstrate that SnRK1 phosphorylation inhibits the ability of Arabidopsis eIF4E and eIFiso4E to complement a yeast strain lacking endogenous eIF4E, and that inhibition correlates with repression of polysome formation. Finally, we show that SnRK1 over-expression in Nicotiana benthamiana plants reduces polysome formation, and that this effect can be counteracted by transient expression of eIF4E or mutant eIF4E containing non-phosphorylatable SnRK1 target residues, but not by a phosphomimic eIF4E. Together, these studies elucidate a novel and direct pathway for translational control in plant cells. In light of previous findings that SnRK1 conditions an innate antiviral defense and is inhibited by geminivirus pathogenicity factors, we speculate that phosphorylation of cap binding proteins may be a component of the resistance mechanism.

Conferring resistance to geminiviruses with the CRISPR-Cas prokaryotic immune system.

To reduce crop losses due to geminivirus infection, we targeted the bean yellow dwarf virus (BeYDV) genome for destruction with the CRISPR-Cas (clustered, regularly interspaced short palindromic repeats-CRISPR-associated proteins) system. Transient assays using BeYDV-based replicons revealed that CRISPR-Cas reagents introduced mutations within the viral genome and reduced virus copy number. Transgenic plants expressing CRISPR-Cas reagents and challenged with BeYDV had reduced virus load and symptoms, thereby demonstrating a novel strategy for engineering resistance to geminiviruses.

ATP-dependent nucleosome unwrapping catalyzed by human RAD51.

Double-strand breaks (DSB) occur in chromatin following replication fork collapse and chemical or physical damage [Symington and Gautier (Double-strand break end resection and repair pathway choice. Annu. Rev. Genet. 2011;45:247-271.)] and may be repaired by homologous recombination (HR) and non-homologous end-joining. Nucleosomes are the fundamental units of chromatin and must be remodeled during DSB repair by HR [Andrews and Luger (Nucleosome structure(s) and stability: variations on a theme. Annu. Rev. Biophys. 2011;40:99-117.)]. Physical initiation of HR requires RAD51, which forms a nucleoprotein filament (NPF) that catalyzes homologous pairing and strand exchange (recombinase) between DNAs that ultimately bridges the DSB gap [San Filippo, Sung and Klein. (Mechanism of eukaryotic HR. Annu. Rev. Biochem. 2008;77:229-257.)]. RAD51 forms an NPF on single-stranded DNA and double-stranded DNA (dsDNA). Although the single-stranded DNA NPF is essential for recombinase initiation, the role of the dsDNA NPF is less clear. Here, we demonstrate that the human RAD51 (HsRAD51) dsDNA NPF disassembles nucleosomes by unwrapping the DNA from the core histones. HsRAD51 that has been constitutively or biochemically activated for recombinase functions displays significantly reduced nucleosome disassembly activity. These results suggest that HsRAD51 can perform ATP hydrolysis-dependent nucleosome disassembly in addition to its recombinase functions.

Preparation of fully synthetic histone H3 reveals that acetyl-lysine 56 facilitates protein binding within nucleosomes.

Posttranslational modification (PTM) of histones plays a central role in genome regulation. Engineering histones with defined PTMs on one residue or on multiple residues is crucial for understanding their function within nucleosomes and chromatin. We introduce a sequential native chemical ligation strategy that is suitable for the preparation of fully synthetic histone proteins, allowing for site-specific incorporation of varied PTMs throughout the sequence. We demonstrate this method with the generation of histone H3 acetylated at lysine 56 [H3(K56ac)]. H3(K56ac) is essential for transcription, replication, and repair. We examined the influence of H3(K56ac) on the targeting of a model DNA binding factor (LexA) to a site ∼30 bp within the nucleosome. We find that H3(K56ac) increases LexA binding to its DNA target site by 3-fold at physiological ionic strength. We then demonstrate that H3(K56ac) facilitates LexA binding by increasing DNA unwrapping, not by nucleosome repositioning. Furthermore, we find that H3(K56Q) quantitatively imitates H3(K56ac) function. Together, these studies introduce powerful tools for the analysis of histone PTM functions.

Delays and efficiency in the bronchoscopy suite: perception meets reality.

Procedural delays or late start times in the bronchoscopy suite can impact operational efficiencies and potentially patient care. To date, little data have been published examining the potential causes of such delays or ways to prevent them in the bronchoscopy unit. In a quality assessment project at a major medical center, we surveyed members of the bronchoscopy team to determine perceptions of the existence of delays in the bronchoscopy suite and possible causes. For comparison, we prospectively observed procedures in the bronchoscopy suite and retrospectively reviewed the records of past procedures to identify delays in the delivery of care. A total of 31 procedures were prospectively observed, with delays (defined a priori as procedures beginning 15 minutes after the scheduled start time) occurring 80% of the time. Two hundred thirty-four procedures were retrospectively reviewed, with delays occurring 71% of the time. In both data sets, the largest portion of time the patient spent in the bronchoscopy suite was during the preprocedure period. Delays often occur in the bronchoscopy suite, with preprocedure activities identified as an area for potential improvement.

Community-acquired methicillin-resistant Staphylococcus aureus epidural abscess with bacteremia and multiple lung abscesses: case report.

A systemic infection due to community-acquired methicillin-resistant Staphylococcus aureus occurred in a hospital-naive 17-year-old girl with no history of soft-tissue infection. Although the initial signs and symptoms were indolent, systemic manifestations occurred, including extensive lung parenchymal damage and acute respiratory distress syndrome. The patient required long-term mechanical ventilation and was given linezolid for 8 weeks. Blood cultures eventually became negative for the staphylococci, and the patient was discharged to a rehabilitation facility. A probable source of the infection was the patient's self-cutting and self-piercing.

Optimizing bronchodilator therapy in emphysema.

The treatment objectives for chronic obstructive pulmonary disease (COPD) include relieving symptoms such as dyspnea and cough, slowing the accelerated decline in lung function, decreasing exacerbations, and improving quality of life. All major guidelines for COPD management recommend beginning treatment with bronchodilators. There are several classes of bronchodilators, including beta-agonists, anticholinergics, and phosphodiesterase inhibitors, each with a specific mechanism of action. The overall approach to managing stable COPD involves a stepwise increase in treatment. Because of the progressive nature of emphysema, such an approach often involves combining bronchodilators from different pharmacologic classes. This review focuses on the pharmacologic properties of various bronchodilators and on recent studies that have examined combination therapy as a means to optimize treatment.

Imaging of pleural masses: which to choose?

The differential diagnosis of pleural masses is limited. Asbestos-related disease and invasive bronchogenic carcinoma make up the majority of cases. The diagnostic yield of biopsies is low, and invasive procedures are often required to achieve diagnosis. A variety of imaging techniques are available to help differentiate between benign and malignant disease to help discern which patients to biopsy. While computed tomography has a relatively good sensitivity and specificity, magnetic resonance imaging (MRI) and positron emission tomography (PET) both appear to have higher accuracy. MRI has the added benefit of being an excellent aid in determining surgical resectability of tumors. MRI and PET are limited, however, by their cost and availability in certain regions.

Role of early detection and pharmacotherapy in chronic obstructive pulmonary disease.

Chronic obstructive pulmonary disease (COPD) is defined as airflow limitation that is not fully reversible, usually progressive and associated with an abnormal inflammatory response to noxious particles or gases. By the time COPD has progressed to the point of clinical symptoms, over half of lung function may have been lost. This review will first describe studies that have examined the feasibility and yield of early detection of COPD using spirometry as a gold standard. Next, we will review existing studies that have examined the effects of pharmacotherapy on early (mild-to-moderate) COPD, specifically focusing on studies that have attempted to alter the natural history of disease. Finally, we will briefly discuss studies that have tested the effects of various pharmacologic interventions on biomarkers felt to be relevant to disease pathogenesis. Discovery of effective pharmacotherapy that can prevent disease progression in early-stage COPD has enormous public-health implications, given the current global burden of disease and the proportion of individuals at risk - aging current and former smokers.