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Objective Bone augmentation delays implant placement and increases risks due to additional surgeries. Implant systems compatible with reduced alveolar bone volume are required. To design, manufacture, and test a non‐cylindrical dental implant system using piezotomes and custom‐designed matching titanium mini‐implants to address the needs of patients with missing teeth and narrow jawbone. Materials and methods Tapered mini‐implants with a rectangular cross‐section (4.6 mm × 2.1 mm) were machined with dimensions that could accommodate narrow alveolar ridges. The performance of the implants were tested in both static and fatigue cycle 30° compression tests. Tapered, rectangular cutting tools that matched the overall trapezoidal morphology of the implant were also designed. These novel tools were engineered to be compatible with commercially available piezoelectric osteotomes. Tools were optimized using finite element analysis and were manufactured accordingly and were used by a periodontal surgery team in a pork rib bone model to monitor utility of the device and ease of use. Results The rectangular design of the implant allows for a full occlusal load due to the larger implant flexural rigidity compared to a similar diameter mini‐implant with a standard cylindrical design. During 30° compression fatigue tests, the implant tested at 340 N did not fail after 5M cycles as shown in Kaplan‐Meier survival curves. Finite element analysis allowed for functional optimization of the roughing and finishing tools. In the pork rib model, these tools successfully cut trapezoidal holes that matched the dimensions of the implant. Conclusions The implant system here demonstrates the feasibility of a mini‐implant system that has superior flexural rigidity and potentially circumvents the need for patient bone augmentation.

Significance: Diffuse optical imaging (DOI) provides in vivo quantification of tissue chromophores such as oxy- and deoxyhemoglobin (HbO2 and HHb, respectively). These parameters have been shown to be useful for predicting neoadjuvant treatment response in breast cancer patients. However, most DOI devices designed for the breast are nonportable, making frequent longitudinal monitoring during treatment a challenge. Furthermore, hemodynamics related to the respiratory cycle are currently unexplored in the breast and may have prognostic value. Aim: To design, fabricate, and validate a high optode-density wearable continuous wave diffuse optical probe for the monitoring of breathing hemodynamics in breast tissue. Approach: The probe has a rigid-flex design with 16 dual-wavelength sources and 16 detectors. Performance was characterized on tissue-simulating phantoms, and validation was performed through flow phantom and cuff occlusion measurements. The breasts of N = 4 healthy volunteers were measured while performing a breathing protocol. Results: The probe has 512 unique source-detector (S-D) pairs that span S-D separations of 10 to 54 mm. It exhibited good performance characteristics: ma drift of 0.34%/h, ma precision of 0.063%, and mean SNR > 24 dB up to 41 mm S-D separation. Absorption contrast was detected in flow phantoms at depths exceeding 28 mm. A cuff occlusion measurement confirmed the ability of the probe to track expected hemodynamics in vivo. Breast measurements on healthy volunteers during paced breathing revealed median signal-to-motion artifact ratios ranging from 8.1 to 8.7 dB. Median DHbO2 and DHHb amplitudes ranged from 0.39 to 0.67 mM and 0.08 to 0.12 mM, respectively. Median oxygen saturations at the respiratory rate ranged from 82% to 87%. Conclusions: A wearable diffuse optical probe has been designed and fabricated for the measurement of breast tissue hemodynamics. This device is capable of quantifying breathing-related hemodynamics in healthy breast tissue.

Additive manufacturing is poised to enable the next biomedical revolution, where customized, patient-specific tools, therapies, pharmaceuticals, and even replacement organs are taking strides in the biomedical research and development space. Polymeric materials are capable of making inroads in a wide variety of biomedical applications, and in recent years a growing number are being used with additive manufacturing techniques. This review highlights some of the emerging classes of polymers used in additive manufacturing and examples of their use in biomedical applications, with a focus on the delineation of ‘hard’ polymers versus ‘soft’ polymers and the specific applications where they are utilized.

Supplemental Digital Content is Available in the Text., Purpose: Loss of corneal endothelial cells (CECs) bears disastrous consequences for the patient, including corneal clouding and blindness. Corneal transplantation is currently the only therapy for severe corneal disorders. However, the worldwide shortages of corneal donor material generate a strong demand for personalized stem cell–based alternative therapies. Because human mesenchymal stem cells are known to be sensitive to their mechanical environments, we investigated the mechanotransductive potential of Descemet membrane–like microtopography (DLT) to differentiate human mesenchymal stem cells into CEC-like cells. Methods: Master molds with inverted DLT were produced by 2-photon lithography (2-PL). To measure the mechanotransductive potential of DLT, mesenchymal stem cells were cultivated on silicone or collagen imprints with DLT. Changes in morphology were imaged, and changes in gene expression of CEC typical genes such as zonula occludens (ZO-1), sodium/potassium (Na/K)-ATPase, paired-like homeodomain 2 (PITX2), and collagen 8 (COL-8) were measured with real-time polymerase chain reaction. At least immunofluorescence analysis has been conducted to confirm gene data on the protein level. Results: Adhesion of MSCs to DLT molded in silicone and particularly in collagen initiates polygonal morphology and monolayer formation and enhances not only transcription of CEC typical genes such as ZO-1, Na/K-ATPase, PITX2, and COL-8 but also expression of the corresponding proteins. Conclusions: Artificial reproduction of Descemet membrane with respect to topography and similar stiffness offers a potential innovative way to bioengineer a functional CEC monolayer from autologous stem cells.

Stem cells play a dominant role in biological research and have a significant potential, as test systems for drug screening, disease modeling and therapeutic applications. The automated production of different stem cell types such as iPS and MSC has been realized in recent years by a few research groups. Yet, it requires different approaches in parallelization compared to conventional automated production because of the nature of the living cells on the one hand, and the production system with various interconnected devices on the other hand. Within this work, we present an approach for parallel processing on an automated cell culture platform.

One of the main challenges in the diagnosis of infectious diseases is the need for rapid and accurate detection of the causative pathogen in any setting. Rapid diagnosis is key to avoiding the spread of the disease, to allow proper clinical decisions to be made in terms of patient treatment, and to mitigate the rise of drug-resistant pathogens. In the last decade, significant interest has been devoted to the development of point-of-care reverse transcription polymerase chain reaction (PCR) platforms for the detection of RNA-based viral pathogens. We present the development of a microfluidic, real-time, fluorescence-based, continuous-flow reverse transcription PCR system. The system incorporates a disposable microfluidic chip designed to be produced industrially with cost-effective roll-to-roll embossing methods. The chip has a long microfluidic channel that directs the PCR solution through areas heated to different temperatures. The solution first travels through a reverse transcription zone where RNA is converted to complementary DNA, which is later amplified and detected in real time as it travels through the thermal cycling area. As a proof of concept, the system was tested for Ebola virus detection. Two different master mixes were tested, and the limit of detection of the system was determined, as was the maximum speed at which amplification occurred. Our results and the versatility of our system suggest its promise for the detection of other RNA-based viruses such as Zika virus or chikungunya virus, which constitute global health threats worldwide. Graphical abstract Photograph of the RT-PCR thermoplastic chip.

The increased world-wide availability of point-of-care (POC) tests utilizing fingerstick blood has led to testing scenarios in which multiple separate fingersticks are performed during a single patient encounter, generating cumulative discomfort and reducing testing efficiency. We have developed a device capable of a) collection of up to 100 μL of fingerstick blood from a single fingerstick by capillary action, and b) dispensing this blood in variable increments set by the user. We tested the prototype device both in a controlled laboratory setting and in a fingerstick study involving naive device users, and found it to have accuracy and precision similar to a conventional pipettor. The users also found the device to be easy to use, and recommended minor ergonomic improvements. Our device would allow performance of multiple POC tests from a single fingerstick blood sample, thus providing a novel functionality that may be of use in many testing settings worldwide.

Due to its relatively low level of antigenicity and high durability, titanium has successfully been used as the major material for biological implants. However, because the typical interface between titanium and tissue precludes adequate transmission of load into the surrounding bone, over time, load-bearing implants tend to loosen and revision surgeries are required. Osseointegration of titanium implants requires presentation of both biological and mechanical cues that promote attachment of and trigger mineral deposition by osteoblasts. While many factors contribute to differentiation, the relative importance of the various cues is unclear. To substantially improve osseointegration of titanium implants, we generated a gelatin methacryloyl (GelMA) scaffold, using an extrusion-based 3D bioprinter, which can be directly printed on and grafted to the titanium implant surface. We demonstrate that this scaffold is able to trigger mineral deposition of both MG63 osteoblasts and primary normal human osteoblasts in the absence of any exogenous osteogenic factors. Films of the same formulation failed to promote mineral deposition suggesting that the three dimensional scaffold was able to tip the balance in favor of differentiation despite other potentially unfavorable differentiation cues of the material. We further show that these GelMA lattices can be directly grafted to titanium alloy and are secure in vitro over a period of seven weeks. When grafted within a groove system, the GelMA hydrogel is protected from shearing forces in a marrow implantation model. This prepares the way for osteogenic coatings to be directly manufactured on the implant surface and packaged for surgery.

Viable cells from healthy tissues are a rich resource in high demand for many next-generation therapeutics and regenerative medicine applications. Cell extraction from the dense connective matrix of most tissues is a labor-intensive task and high variability makes cGMP compliance difficult. To reduce costs and ensure greater reproducibility, automated tissue dissociators compatible with robotic liquid handling systems are required. Here we demonstrate the utility of our automated tissue dissociator that is compatible with standard microtiter well plates for high-throughput processing. We show that viable cell yields match or exceed manual methods while reducing processing time by at least 85%.

To accurately diagnose microbial infections in blood, it is essential to recover as many microorganisms from a sample as possible. Unfortunately, recovery of such microorganisms depends significantly on their adhesion to the surfaces of diagnostic devices. Consequently, we sought to minimize the adhesion of methicillin-sensitive Staphylococcus aureus (MSSA) to the surface of polypropylene- and acrylic-based bacteria concentration devices. These devices were treated with 11 different coatings having various charges and hydrophobicities. Some coatings promoted bacterial adhesion under centrifugation, whereas others were more likely to prevent it. Experiments were run using a simple buffer system and lysed blood, both inoculated with MSSA. Under both conditions, Hydromer's 7-TS-13 and Aqua 65JL were most effective in reducing bacterial adhesion.

We present a new continuous-wave wearable diffuse optical probe aimed at investigating the hemodynamic response of locally advanced breast cancer patients during neoadjuvant chemotherapy infusions. The system consists of a flexible printed circuit board that supports an array of six dual wavelength surface-mount LED and photodiode pairs. The probe is encased in a soft silicone housing that conforms to natural breast shape. Probe performance was evaluated using tissue-simulating phantoms and in vivo normal volunteer measurements. High SNR (71 dB), low source-detector crosstalk (−60 dB), high measurement precision (0.17%), and good thermal stability (0.22% Vrms/°C) were achieved in phantom studies. A cuff occlusion experiment was performed on the forearm of a healthy volunteer to demonstrate the ability to track rapid hemodynamic changes. Proof-of-principle normal volunteer measurements were taken to demonstrate the ability to collect continuous in vivo breast measurements. This wearable probe is a first of its kind tool to explore prognostic hemodynamic changes during chemotherapy in breast cancer patients.

Traditional methods for identifying pathogens in bacteremic patients are slow (24–48+ h). This can lead to physicians making treatment decisions based on an incomplete diagnosis and potentially increasing the patient’s mortality risk. To decrease time to diagnosis, we have developed a novel technology that can recover viable bacteria directly from whole blood and identify them in less than 7 h. Our technology combines a sample preparation process with surface-enhanced Raman spectroscopy (SERS). The sample preparation process enriches viable microorganisms from 10 mL of whole blood into a 200 μL aliquot. After a short incubation period, SERS is used to identify the microorganisms. We further demonstrated that SERS can be used as a broad detection method, as it identified a model set of 17 clinical blood culture isolates and microbial reference strains with 100% identification agreement. By applying the integrated technology of sample preparation and SERS to spiked whole blood samples, we were able to correctly identify both Staphylococcus aureus and Escherichia coli 97% of the time with 97% specificity and 88% sensitivity.

The dominant molecular species contributing to the surface-enhanced Raman spectroscopy (SERS) spectra of bacteria excited at 785 nm are the metabolites of purine degradation: adenine, hypoxanthine, xanthine, guanine, uric acid, and adenosine monophosphate. These molecules result from the starvation response of the bacterial cells in pure water washes following enrichment from nutrient-rich environments. Vibrational shifts due to isotopic labeling, bacterial SERS spectral fitting, SERS and mass spectrometry analysis of bacterial supernatant, SERS spectra of defined bacterial mutants, and the enzymatic substrate dependence of SERS spectra are used to identify these molecular components. The absence or presence of different degradation/salvage enzymes in the known purine metabolism pathways of these organisms plays a central role in determining the bacterial specificity of these purine-base SERS signatures. These results provide the biochemical basis for the development of SERS as a rapid bacterial diagnostic and illustrate how SERS can be applied more generally for metabolic profiling as a probe of cellular activity. Graphical Abstract Bacterial typing by metabolites released under stress.

The 5-year survival rate for ovarian cancer is only 45% largely due to lack of effective screening methods. Current methods include palpation, transvaginal ultrasound, and the CA-125 blood test. Finding disease reliably and at an early stage increase survival to 92%. We have designed and built a 0.7 mm endoscope for the early detection of ovarian cancer. Inserted transvaginally through the working channel of a hysteroscope, the falloposcope creates a minimally invasive procedure for the screening of high risk women. To improve the ease-of-use and safety of falloposcope deployment, we are working to create an everting balloon. Currently, the falloposcope would require a skilled user to operate due to the challenging anatomy of the fallopian tubes – a small opening from the uterus (< 1 mm), tortuous path, and delicate lumenal features. A balloon delivery system would gently open the fallopian tube and guide the falloposcope down the center of lumen. We show balloon design and discuss integration with the falloposcope prototype. We test possible mechanical damage to the tissue due to scraping, puncture, or overstretching. Successful introduction of the everting balloon to simplify falloposcope delivery could expand screening beyond specialized centers to smaller clinical locations.

We present a new continuous-wave (CW) wearable diffuse optical device aimed at investigating the hemodynamic response of locally advanced breast cancer patients during a patient’s first neoadjuvant chemotherapy infusion. The system consists of a flexible substrate that supports an array of surface-mount LED and photodiode pairs (i.e. optodes). Probe performance was evaluated using solid tissue-simulating phantoms. Measurements revealed high SNR (65dB), low source-detector crosstalk (-59 dB), high measurement precision (0.17%), and good thermal stability (0.2% V rms /°C). A cuff occlusion experiment was performed on the forearm of a healthy volunteer to demonstrate the ability to track rapid hemodynamic changes.

In this paper, we present a portable and low cost point-of-care (POC) PCR system for quantitative detection of pathogens. Our system is based on continuous flow PCR which maintains fixed temperatures zones and pushes the PCR solution between two heated areas allowing for faster heat transfer and as a result, a faster PCR. The PCR system is built around a 46.0 mm × 30.9 mm × 0.4 mm disposable thermoplastic chip. In order to make the single-use chip economically viable, it was manufactured by hot embossing and was designed to be compatible with roll-to-roll embossing for large scale production. The prototype instrumentation surrounding the chip includes two heaters, thermal sensors, and an optical system. The optical system allows for pathogen detection via real time fluorescence measurements. FAM probes were used as fluorescent reporters of the amplicons generated during the PCR. To demonstrate the function of the chip, two infectious bacteria targets were selected: Chlamydia trachomatis and Escherichia coli O157:H7. For both bacteria, the limit of detection of the system was determined, PCR efficiencies were calculated, and different flow velocities were tested. We have demonstrated successful detection for these two bacterial pathogens highlighting the versatility and broad utility of our portable, low-cost, and rapid PCR diagnostic device.

A strong natural selection for microbial antibiotic resistance has resulted from the extensive use and misuse of antibiotics. Though multiple factors are responsible for this crisis, the most significant factor – widespread prescription of broad-spectrum antibiotics – is largely driven by the fact that the standard process for determining antibiotic susceptibility includes a 1–2-day culture period, resulting in 48–72 hours from patient sample to final determination. Clearly, disruptive approaches, rather than small incremental gains, are needed to address this issue. The field of microfluidics promises several advantages over existing macro-scale methods, including: faster assays, increased multiplexing, smaller volumes, increased portability for potential point-of-care use, higher sensitivity, and rapid detection methods. This Perspective will cover the advances made in the field of microfluidic, phenotypic antibiotic susceptibility testing (AST) over the past two years. Sections are organized based on the functionality of the chip – from simple microscopy platforms, to gradient generators, to antibody-based capture devices. Microfluidic AST methods that monitor growth as well as those that are not based on growth are presented. Finally, we will give our perspective on the major hurdles still facing the field, including the need for rapid sample preparation and affordable detection technologies.

We present a lab-on-a-chip and associated instrument for heterogeneous enzyme-linked immunosorbent assay (ELISA)-based detection of proteins from liquid samples. The system performs all necessary ELISA steps (starting from antigen incubation) in a quarter of the time required for corresponding plate-based protocols. We have previously described the instrument, which automates fluidic control via remote valve switching and detects fluorescence from reacted substrate, for use in a molecular diagnostics application. The ELISA chip reported here utilizes a high surface area bead bed to enhance capture efficiency and increase the dynamic range of the assay as compared to a standard plate-based ELISA. Its functionality is demonstrated using human IL-10 as a model antigen, but theoretically any sandwich ELISA could be ported onto this “open source platform.” We show that our automated on-chip assays have greater sensitivities than the corresponding standard manual plate-based ELISAs, and that single samples can be assayed in a fraction of the time.

We have developed a three-dimensional (3D) bioprinting system capable of multimaterial and multiscale deposition to enable the next generation of “bottom-up” tissue engineering. This area of research resides at the interface of engineering and life sciences. As such, it entails the design and implementation of diverse elements: a novel hydrogel-based bioink, a 3D bioprinter, automation software, and mammalian cell culture. Our bioprinter has three components uniquely combined into a comprehensive tool: syringe pumps connected to a selector valve that allow precise application of up to five different materials with varying viscosities and chemistries, a high velocity/high-precision x–y–z stage to accommodate the most rapid speeds allowable by the printed materials, and temperature control of the bioink reservoirs, lines, and printing environment. Our custom-designed bioprinter is able to print multiple materials (or multiple cell types in the same material) concurrently with various feature sizes (100 μm–1 mm wide; 100 μm–1 cm high). One of these materials is a biocompatible, printable bioink that has been used to test for cell survival within the hydrogel following printing. Hand-printed (HP) controls show that our bioprinter does not adversely affect the viability of the printed cells. Here, we report the design and build of the 3D bioprinter, the optimization of the bioink, and the stability and viability of our printed constructs.

Appropriate care for bacteremic patients is dictated by the amount of time needed for an accurate diagnosis. However, the concentration of microbes in the blood is extremely low in these patients (1-100 CFU/mL), traditionally requiring growth (blood culture) or amplification (e.g., PCR) for detection. Current culture-based methods can take a minimum of two days, while faster methods like PCR require a sample free of inhibitors (i.e., blood components). Though commercial kits exist for the removal of blood from these samples, they typically capture only DNA, thereby necessitating the use of blood culture for antimicrobial testing. Here, we report a novel, scaled-up sample preparation protocol carried out in a new microbial concentration device. The process can efficiently lyse 10 mL of bacteremic blood while maintaining the microorganisms' viability, giving a 30-mu L final output volume. A suite of six microorganisms (Staphylococcus aureus, Streptococcus pneumoniae, Escherichia coli, Haemophilus influenzae, Pseudomonas aeruginosa, and Candida albicans) at a range of clinically relevant concentrations was tested. All of the microorganisms had recoveries greater than 55% at the highest tested concentration of 100 CFU/mL, with three of them having over 70% recovery. At the lowest tested concentration of 3 CFU/mL, two microorganisms had recoveries of ca. 40-50% while the other four gave recoveries greater than 70%. Using a Taqman assay for methicillin-sensitive S. aureus (MSSA) to prove the feasibility of downstream analysis, we show that our microbial pellets are clean enough for PCR amplification. PCR testing of 56 spiked-positive and negative samples gave a specificity of 0.97 and a sensitivity of 0.96, showing that our sample preparation protocol holds great promise for the rapid diagnosis of bacteremia directly from a primary sample.

Thyroid nodules are a frequent clinical finding and the most common endocrine malignancy is thyroid cancer. The standard of care in the management of a patient with a thyroid nodule is to perform a preoperative fine needle aspiration (FNA) biopsy of the suspect nodule under ultrasound imaging guidance. In a significant percentage of the cases, cytological assessment of the biopsy material yields indeterminate results, the consequence of which is diagnostic thyroidectomy. Unfortunately, 75–80% of diagnostic thyroidectomies following indeterminate cytology result in benign designation by post-surgery histopathology, indicating potentially unnecessary surgeries. Clearly, the potential exists for the improvement in patient care and the reduction of overall procedure costs if an improved preoperative diagnostic technique was developed. Elastic scattering spectroscopy (ESS) is an optical biopsy technique that is mediated by optical fiber probes and has been shown to be effective in differentiating benign from malignant thyroid tissue in ex vivo surgical tissue samples. The goal of the current research was to integrate the ESS fiber optic probes into a device that can also collect cells for cytological assessment and, thus, enable concurrent spectroscopic interrogation and biopsy of a suspect nodule with a single needle penetration. The primary challenges to designing the device included miniaturizing the standard ESS fiber optic probe to fit within an FNA needle and maintaining the needle’s aspiration functionality. We demonstrate the value of the fabricated prototype devices by assessing their preliminary performance in an on-going clinical study with >120 patients. The devices have proven to be clinically friendly, collecting both aspirated cells and optical data from the same location in thyroid nodules and with minimal disruption of clinical procedure. In the future, such integrated devices could be used to complement FNA-based cytological results and have the potential to both reduce the number of diagnostic thyroidectomies on benign nodules and improve the surgical approach for patients with thyroid malignancies, thereby, decreasing healthcare costs and improving patient outcomes.

Background Compared with traditional open surgery, minimally invasive surgery may improve recovery and patient satisfaction while maintaining surgical principles. Laparoscopic, single incision, natural orifice, and robotic approaches hold their own appeal. However, they lack the ability to manipulate organs as easily as the human hand. Advances in minimally invasive surgical techniques require new tools with increased functionality of the end effectors. Multifunctional tools with greater dexterity than those currently available are highly desired. Methods To address this need, we designed, fabricated, and tested the first prototype of a laparoscopic tool that provides the dexterity of a hand. The ""hand"" has two jointed fingers and a jointed thumb attached to a laparoscopic sheath that can be collapsed to fit through a 12-mm trocar or small orifice. The handle provides control for three independent degrees of freedom: finger motion (bending/spreading), fingertip bending, and thumb bending. The tool can be used for pinching, grasping, and spreading motions. Furthermore, the thumb is ""double jointed"" so that the tool can be converted to a rake configuration to allow lifting motions. The initial prototype has been tested in a cadaver lab to demonstrate its utility. Results Our ""lap-hand"" was used to complete standard surgical tasks in a simulation device in a time comparable to open and laparoscopic approaches, including ""bowel"" manipulation and peg movement. Cadaver testing confirmed the ability to grasp, elevate, and move liver, stomach, colon, and small bowel in a fashion expected by the hand. No adverse events were noted, and no bowel injury or perforation resulted from over-grasping. Conclusions We have designed, built, and tested a first prototype of an artificial hand for minimally invasive surgery. Use of such tools could both reduce the number of hand-incisions required and potentially transition more patients to undergo their abdominal procedures laparoscopically.

We have developed a rapid microfluidic method for antibiotic susceptibility testing in a stress-based environment. Fluid is passed at high speeds over bacteria immobilized on the bottom of a microfluidic channel. In the presence of stress and antibiotic, susceptible strains of bacteria die rapidly. However, resistant bacteria survive these stressful conditions. The hypothesis behind this method is new: stress activation of biochemical pathways, which are targets of antibiotics, can accelerate antibiotic susceptibility testing. As compared to standard antibiotic susceptibility testing methods, the rate-limiting step - bacterial growth - is omitted during antibiotic application. The technical implementation of the method is in a combination of standard techniques and innovative approaches. The standard parts of the method include bacterial culture protocols, defining microfluidic channels in polydimethylsiloxane (PDMS), cell viability monitoring with fluorescence, and batch image processing for bacteria counting. Innovative parts of the method are in the use of culture media flow for mechanical stress application, use of enzymes to damage but not kill the bacteria, and use of microarray substrates for bacterial attachment. The developed platform can be used in antibiotic and nonantibiotic related drug development and testing. As compared to the standard bacterial suspension experiments, the effect of the drug can be turned on and off repeatedly over controlled time periods. Repetitive observation of the same bacterial population is possible over the course of the same experiment.

Many new and exciting portable HIV viral load testing technologies are emerging for use in global medicine. While the potential to provide fast, isothermal, and quantitative molecular diagnostic information to clinicians in the field will soon be a reality, many of these technologies lack a robust front end for sample clean up and nucleic acid preparation. Such a technology would enable many different downstream molecular assays. Here, we present a portable system for centrifuge-free room temperature nucleic acid extraction from small volumes of whole blood (70 mL), using only thermally stable reagents compatible with storage and transport in low resource settings. Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) analysis of simulated samples demonstrate a lower limit of detection of 1000 copies per mL, with the ability to detect differences in viral load across four orders of magnitude. The system can also be used to store extracted RNA on detachable cartridges for up to one week at ambient temperature, and can be operated using only hand generated air pressure.

A fully automated "factory" was developed that uses tobacco plants to produce large quantities of vaccines and other therapeutic biologics within weeks. This first-of-a-kind factory takes advantage of a plant viral vector technology to produce specific proteins within the leaves of rapidly growing plant biomass. The factory's custom-designed robotic machines plant seeds, nurture the growing plants, introduce a viral vector that directs the plant to produce a target protein, and harvest the biomass once the target protein has accumulated in the plants-all in compliance with Food and Drug Administration (FDA) guidelines (e. g., current Good Manufacturing Practices). The factory was designed to be time, cost, and space efficient. The plants are grown in custom multiplant trays. Robots ride up and down a track, servicing the plants and delivering the trays from the lighted, irrigated growth modules to each processing station as needed. Using preprogrammed robots and processing equipment eliminates the need for human contact, preventing potential contamination of the process and economizing the operation. To quickly produce large quantities of protein-based medicines, we transformed a laboratory-based biological process and scaled it into an industrial process. This enables quick, safe, and cost-effective vaccine production that would be required in case of a pandemic.

Sample preparation for DNA and RNA assays is a prime candidate for laboratory automation. A novel, parallel processing device that performs the three separate liquid-handling functions necessary for such sample preparation-dispensing, pipetting, and pressurizing-is presented. The device comprises an array of fine nozzles connected by fluidic channels to automatically and precisely distribute flow between one source and an array of points. The design principles, as well as the experimental and computational methods used to develop the device, are described. Test results, including accuracy, uniformity, volume range, and timing, are presented. The functionality of the device is demonstrated by performing a solid-phase extraction of DNA with two types of microcolumns.

The emergence and spread of bacterial resistance to ever increasing classes of antibiotics intensifies the need for fast phenotype-based clinical tests for determining antibiotic susceptibility. Standard susceptibility testing relies on the passive observation of bacterial growth inhibition in the presence of antibiotics. In this paper, we present a novel microfluidic platform for antibiotic susceptibility testing based on stress-activation of biosynthetic pathways that are the primary targets of antibiotics. We chose Staphylococcus aureus (S. aureus) as a model system due to its clinical importance, and we selected bacterial cell wall biosynthesis as the primary target of both stress and antibiotic. Enzymatic and mechanical stresses were used to damage the bacterial cell wall, and a beta-lactam antibiotic interfered with the repair process, resulting in rapid cell death of strains that harbor no resistance mechanism. In contrast, resistant bacteria remained viable under the assay conditions. Bacteria, covalently-bound to the bottom of the microfluidic channel, were subjected to mechanical shear stress created by flowing culture media through the microfluidic channel and to enzymatic stress with sub-inhibitory concentrations of the bactericidal agent lysostaphin. Bacterial cell death was monitored via fluorescence using the Sytox Green dead cell stain, and rates of killing were measured for the bacterial samples in the presence and absence of oxacillin. Using model susceptible (Sanger 476) and resistant (MW2) S. aureus strains, a metric was established to separate susceptible and resistant staphylococci based on normalized fluorescence values after 60 min of exposure to stress and antibiotic. Because this ground-breaking approach is not based on standard methodology, it circumvents the need for minimum inhibitory concentration (MIC) measurements and long wait times. We demonstrate the successful development of a rapid microfluidic-based and stress-activated antibiotic susceptibility test by correctly designating the phenotypes of 16 additional clinically relevant S. aureus strains in a blinded study. In addition to future clinical utility, this method has great potential for studying the effects of various stresses on bacteria and their antibiotic susceptibility.

Tissue homogenization is a common sample preparation procedure in the analysis of clinical samples, but to date there has been no good way to incorporate it into high throughput assays. The classic mortar and pestle is still in common use in laboratories for homogenizing small samples in low quantities. Blenders and high pressure valve processors are used when large quantities of tissue must be homogenized. There are two technologies in the market that process multiple samples simultaneously: bead beating and sonication. Both have been implemented on a standard microplate form factor, but have their drawbacks. Bead beating requires the careful addition and subsequent removal and sanitizing of the beads, which can be a costly and time-intensive process. Sonication works well only with very small samples and does not always give consistent results. This paper describes the development of a new instrument that is capable of quickly homogenizing an array of unique tissue sa mples directly in a microplate. The instrument requires no special training to achieve uniform, repeatable results, and is thus adaptable to semi- and fully automated equipment. Additionally, the system is easy to clean and sterilize, has adjustable speed and force to control shear and unwanted heating, and is useful for sample sizes ranging the entire breadth needed for clinical samples (microliters to milliliters).

The life science and healthcare communities have been redefining the importance of ribonucleic acid (RNA) through the study of small molecule RNA (in RNAi/siRNA technologies), micro RNA (in cancer research and stem cell research), and mRNA (gene expression analysis for biologic drug targets). Research in this field increasingly requires efficient and high-throughput isolation techniques for RNA. Currently, several commercial kits are available for isolating RNA from cells. Although the quality and quantity of RNA yielded from these kits is sufficiently good for many purposes, limitations exist in terms of extraction efficiency from small cell populations and the ability to automate the extraction process. Traditionally, automating a process decreases the cost and personnel time while simultaneously increasing the throughput and reproducibility. As the RNA field matures, new methods for automating its extraction, especially from low cell numbers and in high throughput, are needed to achieve these improvements. The technology presented in this article is a step toward this goal. The method is based on a solid-phase extraction technology using a porous polymer monolith (PPM). A novel cell lysis approach and a larger binding surface throughout the PPM extraction column ensure a high yield from small starting samples, increasing sensitivity and reducing indirect costs in cell culture and sample storage. The method ensures a fast and simple procedure for RNA isolation from eukaryotic cells, with a high yield both in terms of quality and quantity. The technique is amenable to automation and streamlined workflow integration, with possible miniaturization of the sample handling process making it suitable for high-throughput applications.

We studied the unzipping kinetics of single molecules of double-stranded DNA by pulling one of their two strands through a narrow protein pore. PCR analysis yielded the first direct proof of DNA unzipping in such a system. The time to unzip each molecule was inferred from the ionic current signature of DNA traversal. The distribution of times to unzip under various experimental conditions fit a simple kinetic model. Using this model, we estimated the enthalpy barriers to unzipping and the effective charge of a nucleotide in the pore, which was considerably smaller than previously assumed., Comment: 10 pages, 5 figures, Accepted: Physics Review Letters

In this paper, we present a fully integrated lab-on-a-chip and associated instrument for the detection of bacteria from liquid samples. The system conducts bacterial lysis, nucleic acid isolation and concentration, polymerase chain reaction (PCR), and end-point fluorescent detection. To enable truly low-cost manufacture of the single-use disposable chip, we designed the plastic chip in a planar format without any active components to be amenable to injection molding and utilized a novel porous polymer monolith (PPM) embedded with silica that has been shown to lyse bacteria and isolate the nucleic acids from clinical samples (M. D. Kulinski, M. Mahalanabis, S. Gillers, J. Y. Zhang, S. Singh and C. M. Klapperich, Biomed. Microdevices, 2009, 11, 671-678).(1) The chip is made of Zeonex (R), a thermoplastic with a high melting temperature to allow PCR, good UV transmissibility for UV-curing of the PPM, and low auto-fluorescence for fluorescence detection of the amplicon. We have built a prototype instrument to automate control of the fluids, temperature cycling, and optical detection with the capability of accommodating various chip designs. To enable fluid control without including valves or pumps on the chip, we utilized a remote valve switching technique. To allow fluid flow rate changes on the valveless chip, we incorporated speed changing fluid reservoirs. The PCR thermal cycling was achieved with a ceramic heater and air cooling, while end-point fluorescence detection was accomplished with an optical spectrometer; all integrated in the instrument. The chip seamlessly and automatically is mated to the instrument through an interface block that presses against the chip. The interface block aligns and ensures good contact of the chip to the temperature controlled region and the optics. The integrated functionality of the chip was demonstrated using Bacillus subtilis as a model bacterial target. A Taqman assay was employed on-chip to detect the isolated bacterial DNA.