An overview of ambient sound using Ocean Observatories Initiative hydrophones.

The Ocean Observatories Initiative (OOI) sensor network provides a unique opportunity to study ambient sound in the north-east Pacific Ocean. The OOI sensor network has five low frequency (Fs = 200 Hz) and six broadband (Fs = 64 kHz) hydrophones that have been recording ambient sound since 2015. In this paper, we analyze acoustic data from 2015 to 2020 to identify prominent features that are present in the OOI acoustic dataset.

Cas1/2 Endonuclease Complex Modifies Self-Targeting CRISPR/Cascade Spacers Reducing Silencing Guide Stability.

CRISPR-based interference has become common in various applications from genetic circuits to dynamic metabolic control. In , the native CRISPR Cascade system can be utilized for silencing by deletion of the nuclease along with expression of guide RNA arrays, where multiple genes can be silenced from a single transcript. We notice the loss of spacer sequences from guide arrays utilized for dynamic silencing.

Macrocycle peptides delineate locked-open inhibition mechanism for microorganism phosphoglycerate mutases.

Glycolytic interconversion of phosphoglycerate isomers is catalysed in numerous pathogenic microorganisms by a cofactor-independent mutase (iPGM) structurally distinct from the mammalian cofactor-dependent (dPGM) isozyme. The iPGM active site dynamically assembles through substrate-triggered movement of phosphatase and transferase domains creating a solvent inaccessible cavity. Here we identify alternate ligand binding regions using nematode iPGM to select and enrich lariat-like ligands from an mRNA-display macrocyclic peptide library containing >10 members.

Measurements of translation initiation from all 64 codons in E. coli.

Our understanding of translation underpins our capacity to engineer living systems. The canonical start codon (AUG) and a few near-cognates (GUG, UUG) are considered as the 'start codons' for translation initiation in Escherichia coli. Translation is typically not thought to initiate from the 61 remaining codons.

When Wavelengths Collide: Bias in Cell Abundance Measurements Due to Expressed Fluorescent Proteins.

The abundance of bacteria in liquid culture is commonly inferred by measuring optical density at 600 nm. Red fluorescent proteins (RFPs) can strongly absorb light at 600 nm. Increasing RFP expression can falsely inflate apparent cell density and lead to underestimations of mean per-cell fluorescence by up to 10%.

Total protein quantitation using the bicinchoninic acid assay and gradient elution moving boundary electrophoresis.

We investigated the ability of gradient elution moving boundary electrophoresis (GEMBE) with capacitively coupled contactless conductivity detection (C(4) D) to assay total protein concentration using the bicinchoninic acid (BCA) reaction. We chose this format because GEMBE-C(4) D behaves as a concentration dependent detection system, unlike optical methods that also rely on pathlength (due to Beer's law). This system tolerates proteins well compared with other capillary electrophoretic methods, allowing the capillary to be reused without coatings or additional hydroxide wash steps.

Gradient elution moving boundary electrophoresis with channel current detection in relatively long capillaries.

A variant of gradient elution moving boundary electrophoresis with channel current detection is described, which uses relatively long channels (1.5 cm) for separation and detection. The signal for each analyte is determined to have the shape of a parabola ending with a break in slope.

Capturing rare cells from blood using a packed bed of custom-synthesized chitosan microparticles.

We describe batch generation of uniform multifunctional chitosan microparticles for isolation of rare cells, such as circulating tumor cells (CTCs), from a sample of whole blood. The chitosan microparticles were produced in large numbers using a simple and inexpensive microtubing arrangement. The particles were functionalized through encapsulation of carbon black, to control autofluorescence, and surface attachment of streptavidin, to enable interactions with biotinylated antibodies.

Theoretical analysis of a magnetophoresis-diffusion T-sensor immunoassay.

We present the analytical investigation of a microfluidic homogeneous competitive immunoassay that incorporates antibody-conjugated superparamagnetic nanoparticles and magnetophoretic transport to enhance the limits of detection and dynamic range. The analytical model considers the advective, diffusive, and magnetophoretic transport of the antibody-coated nanoparticles relative to the labeled and sample antigens of interest in a T-sensor configuration. The magnetophoresis-diffusion immunoassay identified clear improvements to the assay response and reductions to the limit of detection for increased magnetophoretic velocities and larger nanoparticles.

A simple packed bed device for antibody labelled rare cell capture from whole blood.

We have developed a system to isolate rare cells from whole blood using commercially available components and simple microfluidics. We characterized the capture of MCF-7 cells spiked into whole human blood using this system to demonstrate that enrichment and enumeration studies give results similar to in situ surface-modified devices while reducing fabrication and operation complexity.

Image-based feedback control for real-time sorting of microspheres in a microfluidic device.

We describe a control system to automatically distribute antibody-functionalized beads to addressable assay chambers within a PDMS microfluidic device. The system used real-time image acquisition and processing to manage the valve states required to sort beads with unit precision. The image processing component of the control system correctly counted the number of beads in 99.

T7-based linear amplification of low concentration mRNA samples using beads and microfluidics for global gene expression measurements.

We have demonstrated in vitro transcription (IVT) of cDNA sequences from purified Jurkat T-cell mRNA immobilized on microfluidic packed beds down to single-cell quantities. The microfluidically amplified antisense-RNA (aRNA) was nearly identical in length and quantity compared with benchtop reactions using the same starting sample quantities. Microarrays were used to characterize the number and population of genes in each sample, allowing comparison of the microfluidic and benchtop processes.

Development of aptamer-based affinity assays using temperature gradient focusing: minimization of the limit of detection.

A method is described for an aptamer-based affinity assay using a combination of two nonconventional techniques, temperature gradient focusing (TGF) and field-amplified continuous sample injection TGF (FACSI-TGF), with fluorescence detection. Human immunodeficiency virus reverse transcriptase (HIVRT) is used as the protein target for the assay. The TGF and FACSI-TGF assays are compared to similar results obtained with conventional CE.

Counterflow rejection of adsorbing proteins for characterization of biomolecular interactions by temperature gradient focusing.

A new technique is described for the analysis of small molecules in samples containing serum proteins and for the measurement of the binding of small molecules to serum proteins. The new technique is based on temperature gradient focusing (TGF) and takes advantage of the counterflow used with TGF to exclude serum proteins from the analysis channel while small molecules are focused for detection. The technique is demonstrated for the measurement of the binding constant between a small molecule and serum albumin using both a direct measurement of the free fraction of the small molecule as well as using a competitive binding assay.

Temperature gradient focusing with field-amplified continuous sample injection for dual-stage analyte enrichment and separation.

We describe the serial combination of temperature gradient focusing (TGF) and field-amplified continuous sample injection (FACSI) for improved analyte enrichment and electrophoretic separation. TGF is a counterflow equilibrium gradient method for the simultaneous concentration and separation of analytes. When TGF is implemented with a low conductivity sample buffer and a (relatively) high conductivity separation buffer, a form of sample enrichment similar to field-amplified sample stacking (FASS) or field-amplified sample injection (FASI) is achieved in addition to the normal TGF sample enrichment.

Gradient elution moving boundary electrophoresis for high-throughput multiplexed microfluidic devices.

A novel method for performing electrophoretic separations is described-gradient elution moving boundary electrophoresis (GEMBE). The technique utilizes the electrophoretic migration of chemical species in combination with variable hydrodynamic bulk counterflow of the solution through a separation capillary or microfluidic channel. Continuous sample introduction is used, eliminating the need for a sample injection mechanism.

Scanning temperature gradient focusing.

Temperature gradient focusing (TGF) is a recently developed technique for the simultaneous concentration and electrophoretic separation of ionic analytes in microfluidic channels. One drawback to TGF as it has previously been described is the limited peak capacity; only a small number of analyte peaks (approximately 2-3) can be simultaneously focused and separated. In this paper, we report on a variation of the TGF method whereby the bulk flow rate is varied over time so that a large number of analytes can be sequentially focused, moved past a fixed detection point, and flushed to waste.

Quantitative temperature gradient focusing performed using background electrolytes at various pH values.

Temperature gradient focusing (TGF) has previously been shown to be a practical technique for simultaneous concentration and separation of a variety of samples. In this paper, we demonstrate that TGF can be conducted at a wide range of pH values. Techniques for first-order prediction of the suitability of a given BGE for focusing are discussed.

On-chip titration of an anticoagulant argatroban and determination of the clotting time within whole blood or plasma using a plug-based microfluidic system.

This paper describes extending plug-based microfluidics to handling complex biological fluids such as blood, solving the problem of injecting additional reagents into plugs, and applying this system to measuring of clotting time in small volumes of whole blood and plasma. Plugs are droplets transported through microchannels by fluorocarbon fluids. A plug-based microfluidic system was developed to titrate an anticoagulant (argatroban) into blood samples and to measure the clotting time using the activated partial thromboplastin time (APTT) test.

Characterization of the local temperature in space and time around a developing Drosophila embryo in a microfluidic device.

This paper characterizes a microfluidic platform that differentially controls the temperature of each half of a living Drosophila melanogaster fruitfly embryo in space and time (E. M. Lucchetta, J.

Diffusion based analysis in a sheath flow microchannel: the sheath flow T-sensor.

This paper describes a microfluidic channel that allows for diffusion-based analysis of adsorbing species without passivation of the channel surfaces. The sheath flow configuration was used to measure the diffusion coefficient of fluorescently labeled species from their spatial distribution within the microchannel by analyzing the derivative of the intensity profile at the interface between two distinct core fluids. Measurements for both a small molecule (rhodamine B) and an intermediate-sized protein (wheat germ agglutinin) were made, demonstrating the utility of the sheath flow T-sensor.

Suppression of non-specific adsorption using sheath flow.

The use of a confining sheath fluid within a microfluidic channel in order prevent non-specific adsorption of analytes to the walls of microchannels is demonstrated. A sheath-flow channel fabricated using laser cutting of Mylar films is developed. Numerical simulations of convective and diffusive mass transport within the channel are presented.

Passive electrophoresis in microchannels using liquid junction potentials.

The formation of the liquid junction potential (LJP) is a well-studied phenomenon that occurs in the presence of ionic concentration gradients. Although the LJP has been well characterized, its impact has generally been overlooked in microfluidic applications. The characteristics of flow in microfluidic channels cause this phenomenon to be particularly important, both as a source of deviation from anticipated results and as a tool capable of being harnessed to perform useful tasks.