Non-equilibrium folding of individual DNA molecules recaptured up to 1000 times in a solid state nanopore.

We investigate translocation of linear and circular double-stranded DNA molecules through solid state nanopores where each molecule is recaptured and re-translocated many times. Single molecules can be recaptured by switching voltage polarity for hundreds or even thousands of times. The large number of recapture events allows statistics on the translocation of individual molecules.

Spatial structure facilitates cooperation in a social dilemma: empirical evidence from a bacterial community.

Cooperative organisms are ubiquitous in nature, despite their vulnerability to exploitation by cheaters. Although numerous theoretical studies suggest that spatial structure is critical for cooperation to persist, the spatial ecology of microbial cooperation remains largely unexplored experimentally. By tracking the community dynamics of cooperating (rpoS wild-type) and cheating (rpoS mutant) Escherichia coli in well-mixed flasks and microfabricated habitats, we demonstrate that spatial structure stabilizes coexistence between wild-type and mutant and thus facilitates cooperator maintenance.

Genetic and environmental determinants of human NK cell diversity revealed by mass cytometry.

Natural killer (NK) cells play critical roles in immune defense and reproduction, yet remain the most poorly understood major lymphocyte population. Because their activation is controlled by a variety of combinatorially expressed activating and inhibitory receptors, NK cell diversity and function are closely linked. To provide an unprecedented understanding of NK cell repertoire diversity, we used mass cytometry to simultaneously analyze 37 parameters, including 28 NK cell receptors, on peripheral blood NK cells from 5 sets of monozygotic twins and 12 unrelated donors of defined human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptor (KIR) genotype.

Tailoring the hydrophobicity of graphene for its use as nanopores for DNA translocation.

Graphene nanopores are potential successors to biological and silicon-based nanopores. For sensing applications, it is however crucial to understand and block the strong nonspecific hydrophobic interactions between DNA and graphene. Here we demonstrate a novel scheme to prevent DNA-graphene interactions, based on a tailored self-assembled monolayer.

Immediate hypersensitivity reactions following monovalent 2009 pandemic influenza A (H1N1) vaccines: reports to VAERS.

Background: Hypersensitivity disorders following vaccinations are a cause for concern.

Objective: To determine the type and rate by age, gender, and vaccine received for reported hypersensitivity reactions following monovalent 2009 pandemic influenza A (H1N1) vaccines.

Design: A systematic review of reports to the Vaccine Adverse Event Reporting System (VAERS) following monovalent 2009 pandemic influenza A (H1N1) vaccines.

Randomized, placebo-controlled trial to assess the safety and immunogenicity of an adenovirus type 35-based circumsporozoite malaria vaccine in healthy adults.

Malaria results in over 650,000 deaths each year; thus, there is an urgent need for an effective vaccine. Pre-clinical studies and recently reported human trials suggest that pre-erythrocytic stage vaccines can provide protection against infection. A Phase 1, randomized, placebo-controlled, dose-escalation study was conducted with a vaccine composed of a replication-deficient adenovirus-35 backbone with P.

Genetic measurement of memory B-cell recall using antibody repertoire sequencing.

Annual influenza vaccinations aim to protect against seasonal infections, and vaccine strain compositions are updated every year. This protection is based on antibodies that are produced by either newly activated or memory B cells recalled from previous encounters with influenza vaccination or infection. The extent to which the B-cell repertoire responds to vaccination and recalls antibodies has so far not been analyzed at a genetic level--which is to say, at the level of antibody sequences.

Scanning a DNA molecule for bound proteins using hybrid magnetic and optical tweezers.

The functional state of the genome is determined by its interactions with proteins that bind, modify, and move along the DNA. To determine the positions and binding strength of proteins localized on DNA we have developed a combined magnetic and optical tweezers apparatus that allows for both sensitive and label-free detection. A DNA loop, that acts as a scanning probe, is created by looping an optically trapped DNA tether around a DNA molecule that is held with magnetic tweezers.

Characterization of influenza vaccine immunogenicity using influenza antigen microarrays.

Background: Existing methods to measure influenza vaccine immunogenicity prohibit detailed analysis of epitope determinants recognized by immunoglobulins. The development of highly multiplex proteomics platforms capable of capturing a high level of antibody binding information will enable researchers and clinicians to generate rapid and meaningful readouts of influenza-specific antibody reactivity.

Methods: We developed influenza hemagglutinin (HA) whole-protein and peptide microarrays and validated that the arrays allow detection of specific antibody reactivity across a broad dynamic range using commercially available antibodies targeted to linear and conformational HA epitopes.

Apoptosis and other immune biomarkers predict influenza vaccine responsiveness.

Despite the importance of the immune system in many diseases, there are currently no objective benchmarks of immunological health. In an effort to identifying such markers, we used influenza vaccination in 30 young (20-30 years) and 59 older subjects (60 to >89 years) as models for strong and weak immune responses, respectively, and assayed their serological responses to influenza strains as well as a wide variety of other parameters, including gene expression, antibodies to hemagglutinin peptides, serum cytokines, cell subset phenotypes and in vitro cytokine stimulation. Using machine learning, we identified nine variables that predict the antibody response with 84% accuracy.

Plasmonic nanopore for electrical profiling of optical intensity landscapes.

We present a novel method for sensitive mapping of optical intensity distributions at subdiffraction-limited resolution. This is achieved with a novel device, a plasmonic nanopore, which combines a plasmonic bowtie nanoantenna with a 10 nm-in-diameter solid-state nanopore. Variations in the local optical intensity modulate the plasmonic heating, which we measure electrically through changes in the ionic conductance of the nanopore.

Lineage structure of the human antibody repertoire in response to influenza vaccination.

The human antibody repertoire is one of the most important defenses against infectious disease, and the development of vaccines has enabled the conferral of targeted protection to specific pathogens. However, there are many challenges to measuring and analyzing the immunoglobulin sequence repertoire, including that each B cell's genome encodes a distinct antibody sequence, that the antibody repertoire changes over time, and the high similarity between antibody sequences. We have addressed these challenges by using high-throughput long read sequencing to perform immunogenomic characterization of expressed human antibody repertoires in the context of influenza vaccination.

Controllable atomic scale patterning of freestanding monolayer graphene at elevated temperature.

We show that by operating a scanning transmission electron microscope (STEM) with a 0.1 nm 300 kV electron beam, one can sculpt free-standing monolayer graphene with close-to-atomic precision at 600 °C. The same electron beam that is used for destructive sculpting can be used to image the sculpted monolayer graphene nondestructively.

Fast translocation of proteins through solid state nanopores.

Measurements on protein translocation through solid-state nanopores reveal anomalous (non-Smoluchowski) transport behavior, as evidenced by extremely low detected event rates; that is, the capture rates are orders of magnitude smaller than what is theoretically expected. Systematic experimental measurements of the event rate dependence on the diffusion constant are performed by translocating proteins ranging in size from 6 to 660 kDa. The discrepancy is observed to be significantly larger for smaller proteins, which move faster and have a lower signal-to-noise ratio.

Clinical assessment of serious adverse events in children receiving 2009 H1N1 vaccination.

Background: Monovalent 2009 H1N1 influenza vaccines were licensed and administered in the United States during the H1N1 influenza pandemic between 2009 and 2013.

Methods: Vaccine Adverse Event Reporting System received reports of adverse events following immunization (AEFI) after H1N1 vaccination. Selected reports were referred to the Centers for Disease Control and Prevention's Clinical Immunization Safety Assessment network for additional review.

Periodic modulations of optical tweezers near solid-state membranes.

Optical tweezers operated near solid-state membranes show unexplained periodic modulations in the optical trap position. An experimental study of the oscillations is presented, as well as optical simulations based on the finite-difference time-domain method, providing insight into the underlying interference phenomenon. This work provides a complete description as well as a solution to the enduring problem of modulations in optical traps near solid-state membranes.

Heterovariant cross-reactive B-cell responses induced by the 2009 pandemic influenza virus A subtype H1N1 vaccine.

Background: The generation of heterovariant immunity is a highly desirable feature of influenza vaccines. The goal of this study was to compare the heterovariant B-cell response induced by the monovalent inactivated 2009 pandemic influenza A virus subtype H1N1 (A[H1N1]pdm09) vaccine with that induced by the 2009 seasonal trivalent influenza vaccine (sTIV) containing a seasonal influenza A virus subtype H1N1 (A[H1N1]) component in young and elderly adults.

Methods: Plasmablast-derived polyclonal antibodies (PPAb) from young and elderly recipients of A(H1N1)pdm09 vaccine or sTIV were tested for binding activity to various influenza antigens.

Rapid manufacturing of low-noise membranes for nanopore sensors by trans-chip illumination lithography.

In recent years, the concept of nanopore sensing has matured from a proof-of-principle method to a widespread, versatile technique for the study of biomolecular properties and interactions. While traditional nanopore devices based on a nanopore in a single layer membrane supported on a silicon chip can be rapidly fabricated using standard microfabrication methods, chips with additional insulating layers beyond the membrane region can provide significantly lower noise levels, but at the expense of requiring more costly and time-consuming fabrication steps. Here we present a novel fabrication protocol that overcomes this issue by enabling rapid and reproducible manufacturing of low-noise membranes for nanopore experiments.

Causality assessment of adverse events reported to the Vaccine Adverse Event Reporting System (VAERS).

Unlabelled: Adverse events following immunization (AEFI) reported to the national Vaccine Adverse Event Reporting System (VAERS) represent true causally related events, as well as events that are temporally, but not necessarily causally related to vaccine.

Objective: We sought to determine if the causal relationships between the vaccine and the AEFI reported to VAERS could be assessed through expert review.

Design: A stratified random sample of 100 VAERS reports received in 2004 contained 13 fatal cases, 19 cases with non-fatal disabilities, 39 other serious non-fatal cases and 29 non-serious cases.

NAP1-assisted nucleosome assembly on DNA measured in real time by single-molecule magnetic tweezers.

While many proteins are involved in the assembly and (re)positioning of nucleosomes, the dynamics of protein-assisted nucleosome formation are not well understood. We study NAP1 (nucleosome assembly protein 1) assisted nucleosome formation at the single-molecule level using magnetic tweezers. This method allows to apply a well-defined stretching force and supercoiling density to a single DNA molecule, and to study in real time the change in linking number, stiffness and length of the DNA during nucleosome formation.

Estrogen augmentation in schizophrenia: a quantitative review of current evidence.

Background: Sex differences in the incidence, onset and course of schizophrenia have led to the hypothesis that estrogens play a protective role in the pathophysiology of this disorder. Several trials have assessed the potential of estrogens in reducing schizophrenia symptoms, showing inconsistent results. This quantitative review summarizes available evidence on the efficacy of estrogens in the treatment of schizophrenia.

Dynamics of DNA supercoils.

DNA in cells exhibits a supercoiled state in which the double helix is additionally twisted to form extended intertwined loops called plectonemes. Although supercoiling is vital to many cellular processes, its dynamics remain elusive. In this work, we directly visualize the dynamics of individual plectonemes.

Magnetic forces and DNA mechanics in multiplexed magnetic tweezers.

Magnetic tweezers (MT) are a powerful tool for the study of DNA-enzyme interactions. Both the magnet-based manipulation and the camera-based detection used in MT are well suited for multiplexed measurements. Here, we systematically address challenges related to scaling of multiplexed magnetic tweezers (MMT) towards high levels of parallelization where large numbers of molecules (say 10(3)) are addressed in the same amount of time required by a single-molecule measurement.

Biologically plausible and evidence-based risk intervals in immunization safety research.

In immunization safety research, individuals are considered at risk for the development of certain adverse events following immunization (AEFI) within a specific period of time referred to as the risk interval. These intervals should ideally be determined based on biologic plausibility considering features of the AEFI, presumed or known pathologic mechanism, and the vaccine. Misspecification of the length and timing of these intervals may result in introducing bias in epidemiologic and clinical studies of immunization safety.