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News 244 Publications 8 Members

Molecular probe technology detects bacteria without culture PDF available through Get Fulltext Research

Hyman, Richard W St Onge, Robert P Kim, Hyunsung Tamaresis, John S Miranda, Molly Aparicio, Ana Maria Fukushima, Marilyn Pourmand, Nader Giudice, Linda C Davis, Ronald W ...

Published in BMC Microbiology

BackgroundOur ultimate goal is to detect the entire human microbiome, in health and in disease, in a single reaction tube, and employing only commercially available reagents. To that end, we adapted molecular inversion probes to detect bacteria using solely a massively multiplex molecular technology. This molecular probe technology does not require...

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes PDF available through Get Fulltext Research

St John, John A Braun, Edward L Isberg, Sally R Miles, Lee G Chong, Amanda Y Gongora, Jaime Dalzell, Pauline Moran, Christopher Bed'Hom, Bertrand Abzhanov, Arkhat ...

Published in Genome Biology

The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.

NanoStriDE: normalization and differential expression analysis of NanoString nCounter data PDF available through Get Fulltext Research

Brumbaugh, Christopher D Kim, Hyunsung J Giovacchini, Mario Pourmand, Nader

Published in BMC Bioinformatics

BackgroundThe nCounter analysis system (NanoString Technologies, Seattle, WA) is a technology that enables the digital quantification of multiplexed target RNA molecules using color-coded molecular barcodes and single-molecule imaging. This system gives discrete counts of RNA transcripts and is capable of providing a high level of precision and sen...

Whole-transcriptome RNAseq analysis from minute amount of total RNA. PDF available through Get Fulltext Research

Tariq, Muhammad A Kim, Hyunsung J Jejelowo, Olufisayo Pourmand, Nader

Published in Nucleic acids research

RNA sequencing approaches to transcriptome analysis require a large amount of input total RNA to yield sufficient mRNA using either poly-A selection or depletion of rRNA. This feature makes it difficult to miniaturize transcriptome analysis for greater efficiency. To address this challenge, we devised and validated a simple procedure for the prepar...

Acceleration of emergence of bacterial antibiotic resistance in connected microenvironments.

Zhang, Qiucen Lambert, Guillaume Liao, David Kim, Hyunsung Robin, Kristelle Tung, Chih-kuan Pourmand, Nader Austin, Robert H

Published in Science (New York, N.Y.)

The emergence of bacterial antibiotic resistance is a growing problem, yet the variables that influence the rate of emergence of resistance are not well understood. In a microfluidic device designed to mimic naturally occurring bacterial niches, resistance of Escherichia coli to the antibiotic ciprofloxacin developed within 10 hours. Resistance eme...

Voltage-controlled metal binding on polyelectrolyte-functionalized nanopores.

Actis, Paolo Vilozny, Boaz Seger, R Adam Li, Xiang Jejelowo, Olufisayo Rinaudo, Marguerite Pourmand, Nader

Published in Langmuir : the ACS journal of surfaces and colloids

Most of the research in the field of nanopore-based platforms is focused on monitoring ion currents and forces as individual molecules translocate through the nanopore. Molecular gating, however, can occur when target analytes interact with receptors appended to the nanopore surface. Here we show that a solid state nanopore functionalized with poly...

Dynamic control of nanoprecipitation in a nanopipette. PDF available through Get Fulltext Research

Vilozny, Boaz Actis, Paolo Seger, R Adam Pourmand, Nader

Published in ACS nano

Studying the earliest stages of precipitation at the nanoscale is technically challenging but quite valuable as such phenomena reflect important processes such as crystallization and biomineralization. Using a quartz nanopipette as a nanoreactor, we induced precipitation of an insoluble salt to generate oscillating current blockades. The reversible...

The effect of acute dose charge particle radiation on expression of DNA repair genes in mice

Tariq, Muhammad Akram Soedipe, Ayodotun Ramesh, Govindarajan Wu, Honglu Zhang, Ye Shishodia, Shishir Pourmand, Nader Jejelowo, Olufisayo

Published in Molecular and Cellular Biochemistry

The space radiation environment consists of trapped particle radiation, solar particle radiation, and galactic cosmic radiation (GCR), in which protons are the most abundant particle type. During missions to the moon or to Mars, the constant exposure to GCR and occasional exposure to particles emitted from solar particle events (SPE) are major heal...

Structure of a core fragment of glycoprotein H from pseudorabies virus in complex with antibody.

Backovic, Marija DuBois, Rebecca M Cockburn, Joseph J Sharff, Andrew J Vaney, Marie-Christine Granzow, Harald Klupp, Barbara G Bricogne, Gerard Mettenleiter, Thomas C Rey, Felix A ...

Published in Proceedings of the National Academy of Sciences of the United States of America

Compared with many well-studied enveloped viruses, herpesviruses use a more sophisticated molecular machinery to induce fusion of viral and cellular membranes during cell invasion. This essential function is carried out by glycoprotein B (gB), a class III viral fusion protein, together with the heterodimer of glycoproteins H and L (gH/gL). In pseud...

Replication of individual DNA molecules under electronic control using a protein nanopore.

Olasagasti, Felix Lieberman, Kate R Benner, Seico Cherf, Gerald M Dahl, Joseph M Deamer, David W Akeson, Mark

Published in Nature nanotechnology

Nanopores can be used to analyse DNA by monitoring ion currents as individual strands are captured and driven through the pore in single file by an applied voltage. Here, we show that serial replication of individual DNA templates can be achieved by DNA polymerases held at the α-haemolysin nanopore orifice. Replication is blocked in the bulk phase,...

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