Sample-to-answer on molecular diagnosis of bacterial infection using integrated lab--on--a--disc

Sepsis by bacterial infection causes high mortality in patients in intensive care unit (ICU). Rapid identification of bacterial infection is essential to ensure early appropriate administration of antibiotics to save lives of patients, yet the present benchtop molecular diagnosis is time-consuming and labor-intensive, which limits the treatment efficiency especially when the number of samples to be tested is extensive. Therefore, we hereby report a microfluidic platform lab-on-a-disc (LOAD) to provide a sample-to-answer solution. Our LOAD customized design of microfluidic channels allows automation to mimic sequential analytical steps in benchtop environment. It relies on a simple but controllable centrifugation force for the actuation of samples and reagents. Our LOAD system performs three major functions, namely DNA extraction, isothermal DNA amplification and real-time signal detection, in a predefined sequence. The disc is self-contained for conducting sample heating with chemical lysis buffer and silica microbeads are employed for DNA extraction from clinical specimens. Molecular diagnosis of specific target bacteria DNA sequences is then performed using a real-time loop-mediated isothermal amplification (RT-LAMP) with SYTO-9 as the signal reporter. Our LOAD system capable of bacterial identification of Mycobacterium tuberculosis (TB) and Acinetobacter baumanii (Ab) with the detection limits 103cfu/mL TB in sputum and 102cfu/mL Ab in blood within 2h after sample loading. The reported LOAD based on an integrated approach should address the growing needs for rapid point-of-care medical diagnosis in ICU.

A non-PCR SPR platform using RNase H to detect MicroRNA 29a-3p from throat swabs of human subjects with influenza A virus H1N1 infection

As in all RNA viruses, influenza viruses change and mutate constantly because their RNA polymerase has no proofreading ability. This poses a serious threat to public health nowadays. In addition, traditional pathogen-based detection methods may not be able to report an infection from an unknown type or a subtype of virus if its nucleotide sequence is not known. Because of these factors, targeting host microRNA signatures may be an alternative to classify infections and distinguish types of pathogens as microRNAs are produced in humans shortly after infection. Although this approach is in its infant stage, there is an urgent need to develop a rapid reporter assay for microRNA for disease control and prevention. As a proof of concept, we report herein for the first time a non-PCR MARS (MicroRNA-RNase-SPR) assay to detect the microRNA miR-29a-3p from human subjects infected with influenza virus H1N1 by surface plasmon resonance (SPR). In our MARS assay, RNase H is employed to specifically hydrolyze the RNA probes immobilized on the gold surface where they hybridize with its cognate target cDNAs miR-29a-3p, where it was formed from reverse transcription with mature miR-29a-3p specific stem-looped primers. After the digestion of the RNA probe by RNase H, the intact cDNA was released from the RNA-DNA hybrid and bound to a new RNA probe for another enzymatic reaction cycle to amplify signals. With assay optimization, the detection limit of our MARS assay for miR-29a-3p was found to be 1 nM, and this new assay could be completed within 1 hour without thermal cycling. This non-PCR assay with high selectivity for mature microRNA provides a new platform for rapid disease diagnosis, quarantine and disease control.

Quantitative comparison of structure and dynamics of elastin following three isolation schemes by 13C solid state NMR and MALDI mass spectrometry

Methods for isolating elastin from fat, collagen, and muscle, commonly used in the design of artificial elastin based biomaterials, rely on exposing tissue to harsh pH levels and temperatures that usually denature many proteins. At present, a quantitative measurement of the modifications to elastin following isolation from other extracellular matrix constituents has not been reported. Using magic angle spinning (13)C NMR spectroscopy and relaxation methodologies, we have measured the modification in structure and dynamics following three known purification protocols. Our experimental data reveal that the (13)C spectra of the hydrated samples appear remarkably similar across the various purification methods. Subtle differences in the half maximum widths were observed in the backbone carbonyl suggesting possible structural heterogeneity across the different methods of purification. Additionally, small differences in the relative signal intensities were observed between purified samples. Lyophilizing the samples results in a reduction of backbone motion and reveals additional differences across the purification methods studied. These differences were most notable in the alanine motifs indicating possible changes in cross-linking or structural rigidity. The measured correlation times of glycine and proline moieties are observed to also vary considerably across the different purification methods, which may be related to peptide bond cleavage. Lastly, the relative concentration of desmosine cross-links in the samples quantified by MALDI mass spectrometry is reported.

An aptamer-based bio-barcode assay with isothermal recombinase polymerase amplification for cytochrome-c detection and anti-cancer drug screening

Based on a recently reported ultra-sensitive bio-barcode (BBC) assay, we have developed an aptamer-based bio-barcode (ABC) alternative to detect a cell death marker cytochrome-c (Cyto-c) and its subsequent application to screen anti-cancer drugs. Aptamer is a short single-stranded DNA selected from a synthetic DNA library by virtue of its high binding affinity and specificity to its target based on its unique 3D structure from the nucleotide sequence after folding. In the BBC assay, an antigen (Ag) in analytes is captured by a micro-magnetic particle (MMP) coated with capturing antibodies (Abs). Gold nanoparticles (NPs) with another recognition Ab against the same target and hundreds of identical DNA molecules of known sequence are subsequently added to allow the formation of sandwich structures ([MMP-Ab1]-Ag-[Ab2-NP-DNA]). After isolating the sandwiches by a magnetic field, the DNAs hybridized to their complementary DNAs covalently bound on the NPs are released from the sandwiches after heating. Acting as an Ag identification tag, these bio-barcode DNAs with known DNA sequence are then amplified by polymerase chain reaction (PCR) and detected by fluorescence. In our ABC assay, we employed a Cyto-c-specific aptamer to substitute both the recognition Ab and barcode DNAs on the NPs in the BBC assay; and a novel isothermal recombinase polymerase amplification for the time-consuming PCR. The detection limit of our ABC assay for the Cyto-c was found to be 10 ng/mL and this new assay can be completed within 3h. Several potential anti-cancer drugs have been tested in vitro for their efficacy to kill liver cancer with or without multi-drug resistance.

An integrated lab-on-a-disc for automated cell-based allergen screening bioassays

We have utilized various valving scheme to leverage purely rotation-regulated flow control to enable comprehensive cell-based bioassays (CBBs) on centrifuge-based lab-on-a-disc (LOAD). A LOAD has been developed to examine allergic degranulation from live basophils for allergens screening for the first time, which can also be adjusted to suit a wide range of CBBs. In this system, controlled allergic reaction together with mediator separation from basophils using siphon valving and centrifugal sedimentation are realized inside microstructured network. The entire degranulation analysis process including on-demand release of samples, reaction and degranulation, allergic mediator separation and detection is executed in an automatic sequence within a single run. To validate our cell-based approach, detection of degranulation mediated by known secretagagues, ionomycin or chemotatic peptide formyl-methionine-leucine-pheylalanine (fMLP), is first demonstrated. Further experiments using real allergens house dust mite protein (Der p1) and its corresponding human serum IgE also show positive results. The overall efficiency of the assay is 80.6%, which is comparable to other conventional methods. With 4 identical units on a disc running in a parallel format, the device offers the possibility of single-step, multiplexed allergens screening. The device is capable of reporting a result within 30 min. It has many desirable merits including fast and multiplexed analysis, low cost, single-step operation, minimal sample volume, less discomfort and most importantly increased safety as patients are no longer susceptible to possible anaphylactic shock reactions induced by the common skin-prick-test. The flexibility of the flow control within the device makes it suitable to a wide range of CBBs.

Phase sensitive SPR sensor for wide dynamic range detection

Phase detection has been utilized to enhance the sensitivity of surface plasmon resonance (SPR) sensors for a long time. However, an inherent drawback for phase sensitive SPR sensors are their limited dynamic range, which has greatly hindered wide applications of such sensors. In this Letter, a design combining phase detection and angular interrogation has been proposed to provide an SPR sensor with both high sensitivity and wide dynamic range. As a result, a resolution of 2.2×10^-7 RIU with a dynamic range of over 0.06 RIU has been achieved simultaneously. An added advantage of this design is the flexibility for sensitivity and dynamic range adjustment.

Aptamer-based bio-barcode assay for the detection of cytochrome-c released from apoptotic cells

The recently developed bio-barcode (BBC) assay using polymerase chain reaction (PCR) to generate signals has been shown to be an extraordinarily sensitive method to detect protein targets. The BBC assay involves a magnetic microparticle (with antibody to capture the target of interest) and gold nanoparticle (with recognition antibody and thiolated single-stranded barcode DNAs) to form a sandwich around the target. The concentration of target is determined by the amount of barcode DNA released from the nanoparticles. Here we describe a modification using aptamers to substitute the gold nanoparticles for the BBC assay. In this study, we isolated a 76-mer monoclonal aptamer against cytochrome-c (cyto-c) and this single-stranded DNA in defined 3D structure for cyto-c was used in the BBC assay for both recognition and readout reporting. After magnetic separation, the aptamer was amplified by PCR and this aptamer-based barcode (ABC) assay was sensitive enough to detect the cyto-c in culture medium released from the apoptotic cells after drug treatment at the picomolar level. When compared to the conventional cyto-c detection by Western blot analysis, our ABC assay is sensitive, and time for the detection and quantification with ready-made probes was only 3 h.

Computational investigation of nanohole array based SPR sensing using phase shift

We present a new high spatial resolution sensor for monitoring refractive index variations caused by binding of organic and biological molecules to the metallic surface containing arrays of nanoholes. Signal transduction is provided through detecting the optical phase change in the extraordinary optical transmission (EOT) effected by surface plasmon resonance (SPR). These 2D nanoholes are well suited for the sensor chip format in which high dense integration is readily achievable. While the sensor operates at normal illumination, practical implementation of the sensor is much easier in comparison to the traditional Kretschmann arrangement for SPR sensing. Various design parameters of the device have been studied by simulation. Our results indicate that the scheme has a shot-noise limited sensitivity threshold of 4.37 x 10(-9) refractive index units (RIU) and a dynamic range of 0.17 RIU, which compare favorably with typical SPR sensors, particularly in terms of achieving high resolution and wide dynamic range sensor attributes. The phase change is also quite linear over the entire refractive index detection range.

Improving the sensitivity limit of surface plasmon resonance biosensors by detecting mixed interference signals

We demonstrate that the sensitivity limit of intensity-based surface plasmon resonance (SPR) biosensors can be enhanced when we combine the effects of the phase and amplitude contributions instead of detecting the amplitude variation only. Experimental results indicate that an enhancement factor of as much as 20 times is achievable, yet with no compromise in measurement dynamic range. While existing SPR biosensor systems are predominantly based on the angular scheme, which relies on detecting intensity variations associated with amplitude changes only, the proposed scheme may serve as a direct system upgrade approach for these systems. The new measurement scheme may therefore lead to a strong impact in the design of SPR biosensors.

Two-dimensional biosensor arrays based on surface plasmon resonance phase imaging

We present a biosensor design based on capturing the two-dimensional (2D) phase image of surface plasmon resonance (SPR). This 2D SPR imaging technique may enable parallel label-free detection of multiple analytes and is compatible with the microarray chip platform. This system uses our previously reported differential phase measurement approach, in which 2D phase maps obtained from the signal (P) and reference (S) polarizations are compared pixel by pixel. This technique greatly improves detection resolution as the subtraction step can eliminate measurement fluctuations caused by external disturbances as they essentially appear in both channels. Unlike conventional angular SPR systems, in which illumination from a range of angles must be used, phase measurement requires illumination from only one angle, thus making it well suited for 2D measurement. Also, phase-stepping introduced from a moving mirror provides the necessary modulation for accurate detection of the phase. In light of the rapidly increasing need for fast real-time detection, quantification, and identification of a range of proteins for various biomedical applications, our 2D SPR phase imaging technique should hold a promising future in the medical device market.

Application of two-dimensional spectral surface plasmon resonance to imaging of pressure distribution in elastohydrodynamic lubricant films

What we believe to be a novel two-dimensional spectral surface plasmon resonance imaging technique determining pressure distribution in elastohydrodynamic lubricant films is presented. This technique makes use of the spectral characteristics associated with the surface plasmon resonance (SPR) effect, and it provides more spectral information in refractive index mapping than conventional contrast SPR imaging. Two-dimensional imaging is demonstrated and applied to a highly pressurized liquid lubricant trapped inside an elastohydrodynamic lubrication (EHL) dimple. The hydrostatic pressure inside the EHL dimple causes a localized change of the refractive index of the lubrication oil. This also results in a shift in the spectral SPR absorption dip. By monitoring the color changes within the SPR image and calibrating with lubricants of known refractive index profiles, we can obtain a direct measurement of the refractive index distribution within the EHL dimple. PB 2400 lubricant dimples were studied in our experiments. The proposed SPR imaging approach is irrespective of the absolute lubricant film thickness h, therefore overcoming the major limitations of a conventional optical interference technique. With further development of the two-dimensional refractive index mapping technique, widespread applications in various fields are possible, including high-throughput sensors and the detection of bioaffinity interactions.

Real-time optical biosensor based on differential phase measurement of surface plasmon resonance

We report a real-time differential phase measurement technique which can be implemented in optical surface plasmon resonance biosensors. The important feature of our design is that sensitivity has been greatly improved by measuring the differential phase change between the s and p-polarizations. Real-time measurement capability is achieved by using a phase extracting routine which continuously monitors the waveforms captured by two photo-detectors. Measurement capability of our setup is demonstrated through real-time monitoring of bovine serum albumin (BSA)/anti-BSA binding reaction. The estimated sensitivity of our current setup is 7.4 ng/ml.

Highly sensitive differential phase-sensitive surface plasmon resonance biosensor based on the Mach-Zehnder configuration

A high-sensitivity surface plasmon resonance (SPR) biosensor based on the Mach-Zehnder interferometer design is presented. The novel feature of the new design is the use of a Wollaston prism through which the phase quantities of the p and s polarizations are interrogated simultaneously. Since SPR affects only the p polarization, the signal due to the s polarization can be used as the reference. Consequently, the differential phase between the two polarizations allows us to eliminate all common-path phase noise while keeping the phase change caused by the SPR effect. Experimental results obtained from glycerin-water mixtures indicate that the sensitivity limit of our scheme is 5.5 x 10(-8) refractive-index units per 0.01 degrees phase change. To our knowledge, this is a significant improvement over previously obtained results when gold was used as the sensor surface. Such an improvement in the sensitivity limit should allow SPR biosensors to become a possible replacement for conventional biosensing techniques based on fluorescence. Monitoring of the bovine serum albumin (BSA) binding reaction with BSA antibodies is also demonstrated.

[Serotonin uptake inhibitors provide rapid relief from premenstrual dysphoria. New findings shed light on how serotonin modulates sex hormone-related behavior]

Premenstrual dysphoria (PMD) is a severe form of premenstrual syndrome, afflicting 5-10% of all women. The cardinal symptom--surfacing between ovulation and menstruation, and disappearing within a few days after the onset of the bleeding--is irritability. Serotonin reuptake inhibitors (SRIs), but not non-serotonergic antidepressants, reduce the symptoms of PMD very effectively. Since the, onset of action of SRIs is rapid when used for PMD, medication may be restricted to the luteal phase. The finding that SRIs are effective for PMD lends support for the hypothesis that a major role for brain serotonin is to modulate sex steroid-driven behavior.

Prenatal cytokine exposure results in obesity and gender-specific programming

Prenatal events appear to program hormonal homeostasis, contributing to the development of somatic disorders at an adult age. The aim of this study was to examine whether maternal exposure to cytokines or to dexamethasone (Dxm) would be followed by hormonal consequences in the offspring at adult age. Pregnant rats were injected on days 8, 10, and 12 of gestation with either human interleukin-6 (IL-6) or tumor necrosis factor-alpha (TNF-alpha) or with Dxm. Control dams were injected with vehicle. All exposed offspring developed increased body weight (P < 0.05--0.001), apparently due to an increase of 30--40% in adipose tissue weight (P < 0.05--0.01). Corticosterone response to stress was increased in the IL-6 group (P < 0.05-0.01). Dxm-treated male rats exhibited blunted Dexamethasone suppression test results. In male rats, insulin sensitivity was decreased after IL-6 exposure (P < 0.01), whereas basal insulin was elevated in the TNF-alpha group (P < 0.01). In female rats, plasma testosterone levels were higher in all exposed groups compared with controls (P < 0.01--0.001), with the exception of Dxm-exposed offspring. Males in the TNF-alpha group showed decreased locomotor activity (P < 0.05), and females in the IL-6 group showed increased locomotor activity (P < 0.05). These results indicate that prenatal exposure to cytokines or Dxm leads to increased fat depots in both genders. In females, cytokine exposure was followed by a state of hyperandrogenicity. The results suggest that prenatal exposure to cytokines or Dxm can induce gender-specific programming of neuroendocrine regulation with consequences in adult life.

The serotonin reuptake inhibitor fluoxetine reduces sex steroid-related aggression in female rats: an animal model of premenstrual irritability?

The aggressive behavior displayed by some (but not all) female Wistar rats when an unfamiliar rat is being introduced into their home cage (the resident intruder paradigm) was found to be higher in non-receptive phases (metestrus, diestrus) than in the receptive phases (proestrus, estrus) of the estrus cycle, and effectively reduced by ovariectomy. When removal of the ovaries was followed by administration of estradiol and progesterone, in a regimen mimicking the normal cyclical release of these hormones, aggressive behavior was elicited, two days after estrus, in animals that had displayed aggressive behavior before ovariectomy, but not in those that had not. Short-term administration of a serotonin reuptake inhibitor (fluoxetine hydrochloride; 10 mg/kg, i.p.; 4-5 days) reduced both the aggressive behavior displayed during the diestrus phase by normally cycling rats, and the aggressive behavior elicited by administration of estradiol plus progesterone after ovariectomy. It is suggested that the aggressive behavior displayed by the female Wistar rat in the resident intruder paradigm may serve as an animal model of premenstrual dysphoria.

Highly stable differential phase optical interferometer using rotating Ronchi gratings

We describe a dual-beam differential phase interferometer that performs direct phase measurement by using a rotating Ronchi grating filter. Two laser beams derived from a single source are focused onto the sample surface. The reflected light will retrace the same path and intersect at the back focus of the objective lens. Interference between the reflected rays will therefore produce intensity fringes with their spatial location governed primarily by the differential optical phase of the probes. When the fringes are projected onto a rotating grating filter with identical periodicity, the transmitted optical signal becomes an oscillating signal from which the optical phase can be measured by standard phase-sensitive techniques. This approach has the advantages of simple system configuration, effective isolation from environmental disturbance, and low-frequency operation, which permit the use of high impedance electronics with shot-noise-limited performance at low laser power.

Effectiveness of the Sonicare sonic toothbrush on reduction of plaque, gingivitis, probing pocket depth and subgingival bacteria in adolescent orthodontic patients

The Sonicare sonic toothbrush and a traditional manual toothbrush were compared for efficacy in improving periodontal health in young orthodontic patients with existing gingival inflammation. A 4-week, single-blind clinical trial was employed. Twenty-four subjects, ages 11-17 years, who were fully bonded and banded with fixed orthodontic appliances were selected. Subjects were randomly assigned to use either the manual or the Sonicare toothbrush, instructed in its use, and asked to brush each morning and evening for 2 minutes. Plaque index, gingival index, percentage of sites which bled on probing, pocket depth, and total gram-negative bacteria in a subgingival plaque sample were assessed at baseline and 4 weeks around the banded teeth. The results demonstrate that the Sonicare brush was significantly more effective than the manual brush in all clinical parameters. Sonicare was statistically superior to the manual brush in supragingival plaque reduction (57% vs. 10%, respectively; p < 0.001). Gingival Index scores fell by 29 percent in the Sonicare group, but only 3 percent in the manual group. Reduction of bleeding on probing was significantly greater in the Sonicare group than in the manual group (p < 0.001). The Sonicare group decreased from 78% bleeding sites at baseline to 24.5% after 1 month. In the manual group there was only a slight reduction in bleeding on probing (70% of sites at baseline and 64.6% sites after 1 month). Mean pocket depths were significantly reduced compared to baseline values in both the Sonicare and the manual groups (p < 0.001). Pocket depth reduction in the Sonicare group was, however, significantly greater than in the manual group (28% vs. 6%, respectively: p < 0.001). Total gram-negative bacteria in subgingival plaque samples from banded test teeth of a subset of patients were reduced in the Sonicare group (p < or = 0.05), but increased in the manual group. These results clearly demonstrate that the Sonicare sonic toothbrush is superior to a manual toothbrush in improving periodontal health in adolescent orthodontic patients with existing gingivitis.

Effect of caloric restriction during pregnancy on maternal and fetal body composition in the obese Sprague-Dawley rat

The effects of 15, 30 or 50% caloric restriction during pregnancy on maternal and fetal compartments was determined in obese Sprague-Dawley rats. Pregnant and nonpregnant animals were assigned on a weight basis to one of the dietary treatments. All nutrients, except calories, were fed at levels to meet dietary requirements. Animals were killed on day 20 of treatment and fetuses were taken by Caesarian section. Pregnant animals achieved positive weight gain during 20 days of gestation at all levels of caloric restriction. Nonpregnant animals lost body weight when calories were restricted by 30 and 50%. Number of fetuses, fetal body nitrogen, and pup weight were not statistically different (P less than 0.05) among groups. Animals fed the 30 and 50% calorie-restricted diets showed a significant (P less than 0.05) decrease in total-body fat. Percent carcass protein tended to increase as dietary caloric restriction increased. The fetal compartment was apparently not affected by maternal caloric restriction up to 50% during pregnancy provided that all other nutrients were supplied in adequate amounts. Maternal stores were adversely affected at levels of 30 and 50% caloric restriction.