Convection-driven microfabricated hydrogels for rapid biosensing.

A microscale biosensing platform using rehydration-mediated swelling of bio-functionalized hydrogel structures and rapid target analyte capture is described. Induced convective flow mitigates diffusion limited incubation times, enabling model assays to be completed in under three minutes. Assay design parameters have been evaluated, revealing fabrication criteria required to tune detection sensitivity.

An in vitro acoustic analysis and comparison of popular stethoscopes.

PURPOSE: To compare the performance of various commercially available stethoscopes using standard acoustic engineering criteria, under recording studio conditions. MATERIALS AND METHODS: Eighteen stethoscopes (11 acoustic, 7 electronic) were analyzed using standard acoustic analysis techniques under professional recording studio conditions. An organic phantom that accurately simulated chest cavity acoustics was developed. Test sounds were played via a microphone embedded within it and auscultated at its surface by the stethoscopes. Recordings were made through each stethoscope's binaurals and/or downloaded (electronic models). Recordings were analyzed using standard studio techniques and software, including assessing ambient noise (AMB) rejection. Frequency ranges were divided into those corresponding to various standard biological sounds (cardiac, respiratory, and gastrointestinal). RESULTS: Loudness and AMB rejection: Overall, electronic stethoscopes, when set to a maximum volume, exhibited greater values of perceived loudness compared to acoustic stethoscopes. Significant variation was seen in AMB rejection capability. Frequency detection: Marked variation was also seen, with some stethoscopes performing better for different ranges (eg, cardiac) vs others (eg, gastrointestinal). CONCLUSION: The acoustic properties of stethoscopes varied considerably in loudness, AMB rejection, and frequency response. Stethoscope choice should take into account clinical conditions to be auscultated and the noise level of the environment.

NMR study of the effects of some bleomycin C-termini on the structure of a DNA hairpin with the 5'-GC-3' binding site.

The antibiotics known as bleomycins constitute a family of natural products clinically employed for the treatment of a wide spectrum of cancers. The drug acts as an antitumor agent by virtue of the ability of a metal complex of the antibiotic to cleave DNA. Bleomycins are differentiated by their C-terminal regions. Previous structural studies involving metal-bleomycin-DNA triads have allowed the identification of the bithiazole-(C-terminus substituent) segment in this molecule as the one that most closely interacts with DNA. Three different modes of binding of metallo-bleomycins to DNA (partial or total intercalation of the bithiazole unit between DNA bases, or binding to the minor groove) have been proposed in the literature. The therapeutic use of bleomycin is frequently associated with the development of pulmonary fibrosis. The severity of this side effect has been attributed to the C-terminus of the antibiotic by some researchers. The degree of pulmonary toxicity of bleomycin-A2 and -A5, were found to be higher than those of bleomycin-B2 and peplomycin. Since the introduction of Blenoxane to clinical medicine in 1972, attempts have been made at modifying the basic bleomycin structure at the C-terminus to improve its therapeutic index. However, the pharmacological and toxicological importance of particular C-termini on bleomycin remains unclear. The present study was designed to determine the effect of Zn(II)bleomycin-A2, -A5, -B2, and Zn(II)peplomycin on the structure of a DNA hairpin containing the 5'-GC-3' binding site. We provide evidence that different Zn(II)bleomycins affect the structure of the tested DNA segment in different fashions.

The development of surface-enhanced Raman scattering as a detection modality for portable in vitro diagnostics: progress and challenges.

This perspective provides an overview of the diverse surface-enhanced Raman scattering (SERS)-based sensor platforms that have been developed for in vitro diagnostic applications. To provide focus, protein and nucleic acid detection assays based on the principle of extrinsic SERS sensing are emphasized, as well as their potential for translation to fully integrated point-of-care (POC) test platforms. The development of intrinsic SERS sensors, which are predicated on the direct detection of analytes by laser excitation, entails unique opportunities and challenges deserving of their own attention. As the robust sensing of disease pathogens and cancers in both clinical facilities and limited resource settings is the targeted objective of many next-generation biosensors, the majority of the research progress summarized here centers on SERS sensors developed for the rapid, sensitive and selective detection of disease-causing pathogens and biomarkers. In our effort to communicate a realistic assessment of the progress that has been made and the challenges that lie ahead, we avoid an overtly optimistic appraisal of the current status of SERS diagnostics that does not tacitly acknowledge the difficulties inherent in aligning SERS-based technologies alongside ELISA and PCR technologies as a complementary method for bioanalyte detection possessing unique advantages.

Surface-enhanced Raman scattering (SERS) detection of multiple viral antigens using magnetic capture of SERS-active nanoparticles.

A highly sensitive immunoassay based on surface-enhanced Raman scattering (SERS) spectroscopy has been developed for multiplex detection of surface envelope and capsid antigens of the viral zoonotic pathogens West Nile virus (WNV) and Rift Valley fever virus (RVFV). Detection was mediated by antibody recognition using Raman reporter-coated Au nanoparticles (GNPs) and paramagnetic nanoparticles (PMPs) conjugated with polyclonal antibodies specific for each antigen target, followed by 785nm laser excitation of magnetically concentrated GNP/antigen/PMP complexes. The discrimination of WNV and RVFV antigen detection in mixed Raman spectra was achieved by SERS enhancement of Raman spectra specific for the Raman reporter dyes Infrared 792 (IR-792) and Nile Blue (NB), respectively. Assay reactions containing dilutions of both target antigens yielded a reduction in the intensification of IR-792 and NB signature spectrum peaks and provided a conservative limit of detection of ∼5fg/ml for assays conducted in phosphate buffered saline buffer (PBS) and ∼25pg/ml for assays containing PBS spiked with fetal bovine serum. Based on the inherent simplicity of the assay, magnetic capture-based SERS assays afford promise as a biosensor platform that provides high-level multiplex detection sensitivity and can be adapted for portable diagnostic applications in limited resource settings.

Surface-enhanced Raman scattering detection of DNAs derived from virus genomes using Au-coated paramagnetic nanoparticles.

A magnetic capture-based, surface-enhanced Raman scattering (SERS) assay for DNA detection has been developed which utilizes Au-coated paramagnetic nanoparticles (Au@PMPs) as both a SERS substrate and effective bioseparation reagent for the selective removal of target DNAs from solution. Hybridization reactions contained two target DNAs, sequence complementary reporter probes conjugated with spectrally distinct Raman dyes distinct for each target, and Au@PMPs conjugated with sequence complementary capture probes. In this case, target DNAs were derived from the RNA genomes of the Rift Valley Fever virus (RVFV) or West Nile virus (WNV). The hybridization reactions were incubated for a short period and then concentrated within the focus beam of an interrogating laser by magnetic pull-down. The attendant SERS response of each individually captured DNA provided a limit of detection sensitivity in the range 20-100 nM. X-ray diffraction and UV-vis analysis validated both the desired surface plasmon resonance properties and bimetallic composition of synthesized Au@PMPs, and UV-vis spectroscopy confirmed conjugation of the Raman dye compounds malachite green (MG) and erythrosin B (EB) with the RVFV and WNV reporter probes, respectively. Finally, hybridization reactions assembled for multiplexed detection of both targets yielded mixed MG/EB spectra and clearly differentiated peaks which facilitate the quantitative detection of each DNA target. On the basis of the simple design of a single-particle DNA detection assay, the opportunity is provided to develop magnetic capture-based SERS assays that are easily assembled and adapted for high-level multiplex detection using low-cost Raman instrumentation.

Surface-enhanced Raman scattering detection of DNA derived from the west nile virus genome using magnetic capture of Raman-active gold nanoparticles.

A model paramagnetic nanoparticle (MNP) assay is demonstrated for surface-enhanced Raman scattering (SERS) detection of DNA oligonucleotides derived from the West Nile virus (WNV) genome. Detection is based on the capture of WNV target sequences by hybridization with complementary oligonucleotide probes covalently linked to fabricated MNPs and Raman reporter tag-conjugated gold nanoparticles (GNPs) and the subsequent removal of GNP-WNV target sequence-MNP hybridization complexes from solution by an externally applied magnetic source. Laser excitation of the pelleted material provided a signature SERS spectrum which is diagnostic for the reporter, 5,5'-dithiobis(succinimidy-2-nitrobenzoate) (DSNB), and restricted to hybridization reactions containing WNV target sequences. Hybridizations containing dilutions of the target oligonucleotide were characterized by a reduction in the intensification of the spectral peaks accorded to the SERS signaling of DSNB, and the limit of detection for target sequence in buffer was 10 pM. Due to the short hybridization times required to conduct the assay and ease with which reproducible Raman spectra can be acquired, the assay is amenable to adaptation within a portable, user-friendly Raman detection platform for nucleic acids.

A versatile SERS-based immunoassay for immunoglobulin detection using antigen-coated gold nanoparticles and malachite green-conjugated protein A/G.

A surface enhanced Raman scattering (SERS) immunoassay for antibody detection in serum is described in the present work. The developed assay is conducted in solution and utilizes Au nanoparticles coated with the envelope (E) protein of West Nile Virus (WNV) as the SERS-active substrate and malachite green (MG)-conjugated protein A/G (MG-pA/G) as a bi-functional Raman tag/antibody binding reporter. Upon incubation of these reagents with serum collected from rabbits inoculated with E antigen, laser interrogation of the sandwiched immunocomplex revealed a SERS signaling response diagnostic for MG. The intensification of signature spectral peaks is shown to be proportionate to the concentration of added serum and the limit of antibody detection is 2 ng/ml of serum. To assess assay performance relative to more a traditional immunoassay, indirect enzyme-linked immunosorbent assays conducted using the same concentrations of reagents were found to be >400-fold less sensitive. Quartz crystal microbalance with dissipation (QCM-D) monitoring of immunocomplex film deposition on solid Au surfaces also confirmed the formation of antigen-antibody-protein A/G trilayers and provided quantitative measurements of film thickness which likely position MG within the sensing distance of laser-elicited, enhanced electromagnetic fields. The sensitivity and inherent versatility of the assay, which is provided by the binding of pA/G to a broad spectrum of immunoglobulins in different mammalian species, suggest that it could be developed as an alternative immunoassay format to the ELISA.

SERS detection of indirect viral DNA capture using colloidal gold and methylene blue as a Raman label.

An indirect capture model assay using colloidal Au nanoparticles is demonstrated for surface enhanced Raman scattering (SERS) spectroscopy detection of DNA. The sequence targeted for capture was derived from the West Nile Virus (WNV) RNA genome and selected on the basis of exhibiting minimal secondary structure formation. Upon incubation with colloidal Au, hybridization complexes containing the WNV target sequence, a complementary capture oligonucleotide conjugated to a strong tethering group and a complementary reporter oligonucleotide conjugated to methylene blue (MB), a Raman label, anchors the resultant ternary complex to Au nanoparticles and positions MB within the required sensing distance for SERS enhancement. The subsequent elicitation of surface enhanced plasmon resonance by laser excitation provides a spectral peak signature profile that is capture-specific and characteristic of the Raman spectrum for MB. Detection sensitivity is in the submicromolar range and was shown to be highest for thiol, and less so for amino, modifications at the 5' terminus of the capture oligonucleotide. Finally, using Quartz Crystal Microbalance-Dissipation as a tool for modeling ternary complex binding to Au surfaces, quantitative measurements of surface mass coverage on Au plated sensor crystals established a positive correlation between levels of ternary complex adsorption and their correspondent levels of SERS signal intensification. Adapted to a compact Raman spectrometer, which is designed for analyte detection in capillary tubes, this assay provides a rapid, mobile and cost effective alternative to expensive spectroscopic instrumentation, which is often restricted to analytical laboratories.

Earliest changes in the left ventricular transcriptome postmyocardial infarction.

We report a genome-wide survey of early responses of the mouse heart transcriptome to acute myocardial infarction (AMI). For three regions of the left ventricle (LV), namely, ischemic/infarcted tissue (IF), the surviving LV free wall (FW), and the interventricular septum (IVS), 36,899 transcripts were assayed at six time points from 15 min to 48 h post-AMI in both AMI and sham surgery mice. For each transcript, temporal expression patterns were systematically compared between AMI and sham groups, which identified 515 AMI-responsive genes in IF tissue, 35 in the FW, 7 in the IVS, with three genes induced in all three regions. Using the literature, we assigned functional annotations to all 519 nonredundant AMI-induced genes and present two testable models for central signaling pathways induced early post-AMI. First, the early induction of 15 genes involved in assembly and activation of the activator protein-1 (AP-1) family of transcription factors implicates AP-1 as a dominant regulator of earliest post-ischemic molecular events. Second, dramatic increases in transcripts for arginase 1 (ARG1), the enzymes of polyamine biosynthesis, and protein inhibitor of nitric oxide synthase (NOS) activity indicate that NO production may be regulated, in part, by inhibition of NOS and coordinate depletion of the NOS substrate, L: -arginine. ARG1: was the single-most highly induced transcript in the database (121-fold in IF region) and its induction in heart has not been previously reported.

Simultaneous transgenic suppression of LePG and LeExp1 influences rheological properties of juice and concentrates from a processing tomato variety.

Processing tomato lines suppressed in the accumulation of ripening-related polygalacturonase or expansin were generated by introduction of transgenes to silence expression of the LePG and LeExp1 genes, respectively. The rheological properties of juice and juice reconstituted from paste produced from lines suppressed in one of these genes, or in both, were compared with azygous controls. When assayed by measuring Bostwick consistency, paste produced from either suppressed LePG or suppressed LeExp1 lines and diluted to 5 degrees Brix was approximately 18% more viscous than that produced from controls. Simultaneous suppression of LePG and LeExp1 produced a small additional increase in viscosity of 4%. Rheometric flow analysis at 5 or 10 degrees Brix also showed substantial increases in the consistency index due to suppression of either LePG or LeExp1 alone, and a small additional increase when both genes were suppressed in the same transgenic line. Measurements by laser diffraction and [1H]NMR showed that suppression of LePG or LeExp1 accumulation altered the size distribution of insoluble particles and modified their surface properties. The data are consistent with suppression of LePG increasing serum viscosity, and suppression of either LePG or LeExp1 altering the properties of the insoluble particles and improving some aspect of particle-particle or particle-serum interaction, or both. However, relative to that caused by suppression of either gene alone, the additional increase in viscosity caused by simultaneous suppression of LePG and LeExp1 together was slight.

Inverted repeat of a heterologous 3'-untranslated region for high-efficiency, high-throughput gene silencing.

This report describes a method for the easy generation of inverted repeat constructs for the silencing of genes of unknown sequence which is applicable to high-throughput studies. This improved procedure for high-efficiency gene silencing is specific for a target gene, but does not require inverted repeat DNA of the target gene in the construct. The method employs an inverted repeat of the 3'-untranslated region (3'-UTR) of a heterologous gene, and has been demonstrated using the 3'-UTR region of the nopaline synthase (nos) gene from Agrobacterium tumefaciens, which is often used as the 3'-UTR for transgene constructs. In a population of independent tomato primary transformants harboring a stably integrated polygalacturonase (PG) transgene driven by a constitutive promoter and linked to an inverted repeat of the nos 3'-UTR, 51 of 56 primary transformants (91% of the population) showed highly effective post-transcriptional silencing of the PG gene, with PG mRNA abundance in ripe fruit reduced by 98% or more. The method was also effective in Arabidopsis, where two different, relatively uncharacterized plant transcription factors were also targeted effectively. This method has the advantage of ease and rapidity in preparation of the constructs, since a gene of interest can be inserted into a binary vector already containing the promoter and the inverted nos domain in a single-cloning step, and does not require any knowledge of the DNA sequence. The approach is suitable for high-throughput gene silencing studies, where it is necessary to investigate the function of hundreds to thousands of uncharacterized genes.

Suppression of a ripening-related endo-1,4-beta-glucanase in transgenic pepper fruit does not prevent depolymerization of cell wall polysaccharides during ripening.

The function of the ripening-related endo-1,4-beta-D-glucanase (EGase) CaCel1 in fruit softening was investigated by suppression of CaCel1 gene expression in transgenic pepper (Capsicum annuum L.) plants using constitutive expression of a truncated sense CaCel1 transgene. In suppressed lines, immunodetectable CaCel1 protein and extractable CMCase activity were reduced to at or below the limit of detection in ripe mature red fruit, suggesting that in pepper ripening-related CMCase activity is the product of a single gene. However, the abundances of two mRNAs derived from the CaCel1 gene by differential transcription initiation were affected differently in suppressed lines. Accumulation of a 1.7 kb CaCel1 transcript was strongly suppressed, whereas the abundance of a 2.1 kb CaCel1 transcript was only partially reduced. This implies that the 1.7 kb mRNA is responsible for producing CaCel1 protein, while the 2.1 kb mRNA is translationally inactive, and as such is recalcitrant to co-suppression. Chelator-soluble polyuronides exhibited little or no depolymerization during ripening, but matrix glycans including xyloglucan were extensively depolymerized. Depolymerization of non-xyloglucan matrix glycans was the prominant cell wall change observed during pepper ripening. However, the lack of CaCel1 activity in suppressed fruit had no detectable effect on ripening-related matrix glycan depolymerization, which occurred at wild-type levels. Recombinant CaCel1 protein purified from a transgenic pepper line over-expressing functional CaCel1 was active against pepper matrix glycans in vitro, and showed greater activity against non-xyloglucan polysaccharides than against xyloglucan. Transgenic suppression of CaCel1 EGase activity has not identified the natural cell wall substrate for this enzyme, and shows that activities other than CaCel1 are responsible for the depolymerization of matrix glycans occurring during ripening in pepper.

Constitutive overexpression of a ripening-related pepper endo-1,4-beta-glucanase in transgenic tomato fruit does not increase xyloglucan depolymerization or fruit softening.

The ripening-related pepper endo-1,4-beta-D-glucanase (EGase) CaCel1 was over-expressed in transgenic tomato plants under the control of the constitutive 35S promoter to investigate the effects on plant growth and fruit softening of high levels of a potential cell wall-degrading activity. In transgenic fruit, recombinant CaCel1 protein was associated with a high-salt putative cell wall fraction, and extractable CMCase activity was increased by up to 20-fold relative to controls. However, the effects of high levels of EGase activity on fruit cell wall metabolism were relatively small. The largest consequence observed was a decrease of up to 20% in the amount of matrix glycans in a 24% KOH-soluble fraction consisting of polysaccharides tightly bound to cellulose. This decrease was confined to polysaccharides other than xyloglucan, did not affect the size distribution of remaining molecules, and was not correlated with a corresponding increase in glycans in a 4% KOH-soluble fraction loosely bound to cellulose, suggesting that the missing polymers had been degraded to fragments small enough to be lost from the extracts. The amount of matrix glycans in the 4% KOH-soluble fraction was not substantially changed, but the size distribution showed a small relative increase in the amount of polymers in a peak eluting close to a linear dextran marker of 71 kDa. This could be due either to an increase in the amount of polymers of this size, or to a loss from the extract of other polymers present in peaks of higher molecular weight. Transgenic fruit were not softer than controls but appeared the same or slightly firmer at both green and red developmental stages, and no differences in plant vegetative growth were observed. CaCel1 did not cause depolymerization of tomato fruit xyloglucan in vivo, but differences in the amount or molecular weight profile of other matrix glycans were observed. The data suggest that degradation of a proportion of matrix glycans other than xyloglucan does not result in fruit softening, and that fruit softening is not limited by the amount of EGase activity present during ripening.