Life Science Applications Research Articles

Open-Gate Junction Field Effect Transistor (OG-JFET) for Life Science Applications: Design, Implementation, and Characterization

This article introduces a new foundry-based ion-sensitive field-effect transistor named open-gate junction field-effect transistor (OG-JFET), which is intended to be used for chemical and biological sensing applications. OG-JFET can be realized by removing the n-type gate in a p-type JFET to open the space for electrolyte gating. The new configuration enables applying a bias voltage via back-gate that results in more efficient channel current control. Accordingly, a <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$1.6 ~{\mu }\text{m}$ </tex-math></inline-formula> thick p-type conductive layer has been epitaxially grown on a <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$450 ~{\mu }\text{m}$ </tex-math></inline-formula> thick n-type silicon layer based on a standard foundry process. The design promotes a large sensing area including seven p-type conduction channels with dimensions of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$1000\,\, {\mu }\text{m}\,\,{\times }\,\,100\,\, {\mu }\text{m}$ </tex-math></inline-formula> (W <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${\times }$ </tex-math></inline-formula> L) and depth of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$1.6 ~{\mu }\text{m}$ </tex-math></inline-formula> . All the necessary transfer characteristics required for biosensing/ion-sensing of OG-JFET have been derived. Furthermore, we have conducted a COMSOL Multiphysics simulation on OG-JFET to verify the operation of the sensor, which helps to comprehend the functionality of the sensor in different biasing conditions. The COMSOL semiconductor simulation results showed good consistency with experimental results that make the simulations a reliable reference for optimization and customizing the chip for specific applications. OG-JFET showed a sensitivity of 55.29 mV/pH, a hysteresis of 16 mV, and drift of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$3 ~{\mu }\text{A}$ </tex-math></inline-formula> /hours which are in the order of standard ISFET sensors in the literature. The simulation and experimental results in this paper, for the first time, put forward the OG-JFET as a new foundry-process-based, mass-producible ion-sensitive FET sensor for chemical and biological applications.

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples.

Recent advances in mass spectrometry have resulted in deep proteomicanalysis along with the generation ofrobust andreproducible datasets. However, despite the considerable technical advancements, sample preparation from biospecimens such as patient blood, CSF, and tissue still poses considerable challenges. For identifying biomarkers, tissue proteomics often provides an attractive sample source to translate the research findings from the bench to the clinic. It can reveal potential candidate biomarkers for early diagnosis of cancer and neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, etc. Tissue proteomics also yields a wealth of systemic information based on the abundance of proteins and helps to address interesting biological questions. Quantitative proteomics analysis can be grouped into two broad categories: a label-based and a label-free approach. In the label-based approach, proteins or peptides are labeled using stable isotopes such as SILAC (stable isotope labeling with amino acids in cell culture) or by chemical tags such as ICAT (isotope-coded affinity tags), TMT (tandem mass tag) or iTRAQ (isobaric tag for relative and absolute quantitation). Label-based approaches have the advantage of more accurate quantitation of proteins and using isobaric labels, multiple samples can be analyzed in a single experiment. The label-free approach provides a cost-effective alternative to label-based approaches. Hundreds of patient samples belonging to a particular cohort can be analyzed and compared with other cohorts based on clinical features. Here, we have described an optimized quantitative proteomics workflow for tissue samples using label-free and label-based proteome profiling methods, which is crucial for applications in life sciences, especially biomarker discovery-based projects.

Electronic Sensing Platform (ESP) Based on Open-Gate Junction Field-Effect Transistor (OG-JFET) for Life Science Applications: Design, Modeling and Experimental Results.

This paper presents a new field-effect sensor called open-gate junction gate field-effect transistor (OG-JFET) for biosensing applications. The OG-JFET consists of a p-type channel on top of an n-type layer in which the p-type serves as the sensing conductive layer between two ohmic contacted sources and drain electrodes. The structure is novel as it is based on a junction field-effect transistor with a subtle difference in that the top gate (n-type contact) has been removed to open the space for introducing the biomaterial and solution. The channel can be controlled through a back gate, enabling the sensor’s operation without a bulky electrode inside the solution. In this research, in order to demonstrate the sensor’s functionality for chemical and biosensing, we tested OG-JFET with varying pH solutions, cell adhesion (human oral neutrophils), human exhalation, and DNA molecules. Moreover, the sensor was simulated with COMSOL Multiphysics to gain insight into the sensor operation and its ion-sensitive capability. The complete simulation procedures and the physics of pH modeling is presented here, being numerically solved in COMSOL Multiphysics software. The outcome of the current study puts forward OG-JFET as a new platform for biosensing applications.

An open-source automated PEG precipitation assay to measure the relative solubility of proteins with low material requirement

The solubility of proteins correlates with a variety of their properties, including function, production yield, pharmacokinetics, and formulation at high concentrations. High solubility is therefore a key requirement for the development of protein-based reagents for applications in life sciences, biotechnology, diagnostics, and therapeutics. Accurate solubility measurements, however, remain challenging and resource intensive, which limits their throughput and hence their applicability at the early stages of development pipelines, when long-lists of candidates are typically available in minute amounts. Here, we present an automated method based on the titration of a crowding agent (polyethylene glycol, PEG) to quantitatively assess relative solubility of proteins using about 200 µg of purified material. Our results demonstrate that this method is accurate and economical in material requirement and costs of reagents, which makes it suitable for high-throughput screening. This approach is freely-shared and based on a low cost, open-source liquid-handling robot. We anticipate that this method will facilitate the assessment of the developability of proteins and make it substantially more accessible.

PRMT7: A Pivotal Arginine Methyltransferase in Stem Cells and Development.

Protein arginine methylation is a posttranslational modification catalyzed by protein arginine methyltransferases (PRMTs), which play critical roles in many biological processes. To date, nine PRMT family members, namely, PRMT1, 2, 3, 4, 5, 6, 7, 8, and 9, have been identified in mammals. Among them, PRMT7 is a type III PRMT that can only catalyze the formation of monomethylarginine and plays pivotal roles in several kinds of stem cells. It has been reported that PRMT7 is closely associated with embryonic stem cells, induced pluripotent stem cells, muscle stem cells, and human cancer stem cells. PRMT7 deficiency or mutation led to severe developmental delay in mice and humans, which is possibly due to its crucial functions in stem cells. Here, we surveyed and summarized the studies on PRMT7 in stem cells and development in mice and humans and herein provide a discussion of the underlying molecular mechanisms. Furthermore, we also discuss the roles of PRMT7 in cancer, adipogenesis, male reproduction, cellular stress, and cellular senescence, as well as the future perspectives of PRMT7-related studies. Overall, PRMT7 mediates the proliferation and differentiation of stem cells. Deficiency or mutation of PRMT7 causes developmental delay, including defects in skeletal muscle, bone, adipose tissues, neuron, and male reproduction. A better understanding of the roles of PRMT7 in stem cells and development as well as the underlying mechanisms will provide information for the development of strategies for in-depth research of PRMT7 and stem cells as well as their applications in life sciences and medicine.

Recent Progress in the Development of a-Se/CMOS Sensors for X-ray Detection

Amorphous selenium (a-Se) is a glass-former capable of deposition at high rates by thermal evaporation over a large area. It was chosen as a direct conversion material due to its appealing properties for imaging in both low and high X-ray energy ranges (&lt;30 keV and &lt;30 keV, respectively). It has a bandgap of 2.2 eV and can achieve high photodetection efficiency at short wavelengths less than 400 nm which makes it appealing for indirect conversion detectors. The integration of a-Se with readout integrated circuits started with thin-film transistors for digital flat panel X-ray detectors. With increasing applications in life science, biomedical imaging, X-ray imaging, high energy physics, and industrial imaging that require high spatial resolution, the integration of a-Se and CMOS is one direct way to improve the high-contrast visualization and high-frequency response. Over the past decade, significant improvements in a-Se/CMOS technologies have been achieved with improvements to modulation transfer function and detective quantum efficiency. We summarize recent advances in integrating and photon-counting detectors based on a-Se coupled with CMOS readout and discuss some of the shortcomings in the detector structure, such as low charge conversion efficiency at low electric field and high dark current at high electric field. Different pixel architectures and their performance will be highlighted.

Controlling Topography and Crystallinity of Melt Electrowritten Poly(ɛ-Caprolactone) Fibers.

Melt electrowriting (MEW) is an aspiring 3D printing technology with an unprecedented resolution among fiber-based printing technologies. It offers the ability to direct-write predefined designs utilizing a jet of molten polymer to fabricate constructs composed of fibers with diameters of only a few micrometers. These dimensions enable unique construct properties. Poly(ɛ-caprolactone) (PCL), a semicrystalline polymer mainly used for biomedical and life science applications, is the most prominent material for MEW and exhibits excellent printing properties. Despite the wealth of melt electrowritten constructs that have been fabricated by MEW, a detailed investigation, especially regarding fiber analysis on a macro- and microlevel is still lacking. Hence, this study systematically examines the influence of process parameters such as spinneret diameter, feeding pressure, and collector velocity on the diameter and particularly the topography of PCL fibers and sheds light on how these parameters affect the mechanical properties and crystallinity. A correlation between the mechanical properties, crystallite size, and roughness of the deposited fiber, depending on the collector velocity and applied feeding pressure, is revealed. These findings are used to print constructs composed of fibers with different microtopography without affecting the fiber diameter and thus the macroscopic assembly of the printed constructs.

Emerging artificial intelligence in piezoelectric and triboelectric nanogenerators

Piezoelectric nanogenerators (PENG) and triboelectric nanogenerators (TENG) have opened an exciting venue to sustainably harvest electrical energy from the environments, which have led to multifunctional applications in different fields. More recently, a paradigm shift has directed to the emerging artificial intelligence (AI) in PENG and TENG, aiming to address the challenges of the nanogenerators in analysis, design, fabrication, and application. AI-PENG and AI-TENG are envisioned to enhance and optimize the mechanical-to-electrical performance of the nanogenerators to a favorable behavior. However, an overview on the topic of AI-PENG and AI-TENG has not yet been exploited in the literature. In this review article, we showcase the recent progress of PENG and TENG and discuss the future trends of AI-enhanced nanogenerators with desirable electrical performance, i.e., using AI-enabled design models as a viable tool to design, predict, and optimize the structures and materials of PENG and TENG. This topical review explains why the nanogenerators are extensively considered as one of the promising energy solutions and are especially suitable for certain applications in engineering and life science, how to surpass the limitations of PENG and TENG by AI-based structural design and material discovery, and what technological avenues that AI-PENG and AI-TENG may provide for green energy in future innovations. • Piezoelectric nanogenerators (PENG). • Triboelectric nanogenerators (TENG). • Artificial intelligence (AI).

Methods and platforms for analysis of nucleic acids from single-cell based on microfluidics.

Single-cell nucleic acid analysis aims at discovering the genetic differences between individual cells which is well known as the cellular heterogeneity. This technology facilitates cancer diagnosis, stem cell research, immune system analysis, and other life science applications. The conventional platforms for single-cell nucleic acid analysis more rely on manual operation or bulky devices. Recently, the emerging microfluidic technology has provided a perfect platform for single-cell nucleic acid analysis with the characteristic of accurate and automatic single-cell manipulation. In this review, we briefly summarized the procedure of single-cell nucleic acid analysis including single-cell isolation, single-cell lysis, nucleic acid amplification, and genetic analysis. And then, three representative microfluidic platforms for single-cell nucleic acid analysis are concluded as valve-, microwell-, and droplet-based platforms. Furthermore, we described the state-of-the-art integrated single-cell nucleic acid analysis systems based on the three platforms. Finally, the future development and challenges of microfluidics-based single-cell nucleic acid analysis are discussed as well.

Integrated phase-sensitive photonic sensors: a system design tutorial

Photonic integration has seen tremendous progress over the previous decade, and several integration platforms have reached industrial maturity. This evolution has prepared the ground for miniaturized photonic sensors that lend themselves to efficient analysis of gaseous and liquid media, exploiting large interactions lengths of guided light with surrounding analytes, possibly mediated by chemically functionalized waveguide surfaces. Among the various sensor concepts, phase-sensitive approaches are particularly attractive: offering a flexible choice of the operation wavelength, these schemes are amenable to large-scale integration on mature technology platforms such as silicon photonics or silicon nitride ( S i 3 N 4 ) that have been developed in the context of tele- and data-communication applications. This paves the path toward miniaturized and robust sensor systems that offer outstanding scalability and that are perfectly suited for high-volume applications in life sciences, industrial process analytics, or consumer products. However, as the maturity of the underlying photonic integrated circuits (PICs) increases, system-level aspects of mass-deployable sensors gain importance. These aspects include, e.g., robust system concepts that can be operated outside controlled laboratory environments as well as readout schemes that can be implemented based on low-cost light sources, without the need for benchtop-type tunable lasers as typically used in scientific demonstrations. It is, thus, the goal of this tutorial to provide a holistic system model that allows us to better understand and to quantitatively benchmark the viability and performance of different phase-sensitive photonic sensor concepts under the stringent limitations of mass-deployable miniaturized systems. Specifically, we explain and formulate a generally applicable theoretical framework that allows for a quantitatively reliable end-to-end analysis of the overall signal chain. Building upon this framework, we identify and explain the most important technical parameters of the system, comprising the photonic sensor circuit, the light source, and the detector, as well as the readout and control scheme. We quantify and compare the achievable performance and the limitations that are associated with specific sensor structures based on Mach–Zehnder interferometers (MZIs) or high-Q optical ring resonators (RRs), and we condense our findings by formulating design guidelines both for sensor concepts. As a particularly attractive example, we discuss an MZI-based sensor implementation, relying on a vertical-cavity surface-emitting laser (VCSEL) as a power-efficient low-cost light source in combination with a simple and robust readout and control scheme. In contrast to RR-based sensor implementations, MZIs can be resilient to laser frequency noise, at the cost of a slightly lower sensitivity and a moderately increased footprint. To facilitate the application of our model, we provide a MATLAB-based application that visualizes the underlying physical principles and that can be readily used to estimate the achievable performance of a specific sensor system. The system-level design considerations are complemented by an overview of additional aspects that are important for successful sensor system implementation such as the design of the underlying waveguides, photonic system assembly concepts, and schemes for analyte handling.

Compact Quantum-Dot Microbeads with Sub-Nanometer Emission Linewidth.

Fluorescent microbeads are widely used for applications in life sciences and medical diagnosis. The spectral contrast and sharpness of photoluminescence are critical in the utilities of microbeads for imaging and multiplexing. Here, we demonstrate microbeads capable of generating single-peak laser emission with a sub-nanometer linewidth. The microbeads are made of quantum dots that are tightly packed and crosslinked via ligand exchange for high optical gain and refractive index as well as material stability. Bright single-mode lasing with no photobleaching is achieved with particle diameters as small as 1.5 μm in the air. Sub-nm lasing emission is maintained even inside high-index surroundings, such as organic solvents and biological tissues. Feasibility of intracellular tagging and multi-color imaging in vivo is demonstrated.

Organic Hyperbolic Material Assisted Illumination Nanoscopy.

Resolution capability of the linear structured illumination microscopy (SIM) plays a key role in its applications in physics, medicine, biology, and life science. Many advanced methodologies have been developed to extend the resolution of structured illumination by using subdiffraction‐limited optical excitation patterns. However, obtaining SIM images with a resolution beyond 40 nm at visible frequency remains as an insurmountable obstacle due to the intrinsic limitation of spatial frequency bandwidth of the involved materials and the complexity of the illumination system. Here, a low‐loss natural organic hyperbolic material (OHM) that can support record high spatial‐frequency modes beyond 50k 0, i.e., effective refractive index larger than 50, at visible frequencies is reported. OHM‐based speckle structured illumination microscopy demonstrates imaging resolution at 30 nm scales with enhanced fluorophore photostability, biocompatibility, easy to use and low cost. This study will open up a new route in super‐resolution microscopy by utilizing OHM films for various applications including bioimaging and sensing.

Protein‐Polymer Bioconjugates Prepared by Post‐Polymerization Modification of Alternating Copolymers

AbstractProtein‐polymer bioconjugates have shown great promise in biomedical and life science applications including drug delivery and diagnosis. The current bioconjugation strategies suffer from lack of efficiency and versatility. In this article, poly(styrene‐alt‐maleic anhydride) copolymers were first prepared by RAFT polymerization and characterized by different analytical techniques. Then, the poly(styrene‐alt‐maleic anhydride) precursors were functionalized with primary amine such as azidopropylamine and amino poly(ethylene glycol). The reaction of amino compounds with maleic anhydride was found to be a highly efficient, a versatile, and a facile chemical ligation reaction for the synthesis of macromolecules with quantitative yield under mild conditions. The main benefit is the incorporation of a wide range of functionality by easily changing the primary amine compound. For the amphiphilic graft copolymers based on poly(ethylene glycol), aggregation behavior in water was investigated. In a second part, azido‐functionalized polystyrene copolymers were used to prepare a new protein‐polymer bioconjugate by copper‐free click chemistry reaction.

3D‐Printed Acoustofluidic Devices for Raman Spectroscopy of Cells

Acoustofluidics technology can be used to trap live cells (and also micro/nanoparticles) in microenvironments suitable for cell assays. Herein, a cheap and easy‐to‐fabricate device is proposed that works with Raman spectroscopy for biosensing applications. The device comprises a 3D‐printed microchamber working as a half‐wavelength acoustic resonator. By tuning the resonance frequency with a low voltage (≈4 V), cells or particles are aggregated and levitated in seconds by the action of the acoustic radiation force. Based on finite element simulations, the radiation force field produced inside the device is described. In the cellular enrichment (aggregation) process, a metastable honeycomb lattice is formed mostly due to the cell‐to‐cell attraction caused by the secondary acoustic radiation force. Orderly and metastable levitating aggregates provide an excellent arrangement for Raman spectroscopy to investigate cells individually. Polystyrene particles are used for the device characterization and Raman acquisition process. Biosensing applications are showcased with live murine macrophages J774.A1, which are used in infection assay of leishmaniasis disease. The unique features of the device, e.g., simple fabrication process with cheap materials, simple operation, fast time response, and formation of metastable cellular aggregates; hold a noteworthy potential for applications in life sciences and biotechnology involving cell assays.

Nanograting-Enhanced Optical Fibers for Visible and Infrared Light Collection at Large Input Angles

The efficient incoupling of light into particular fibers at large angles is essential for a multitude of applications; however, this is difficult to achieve with commonly used fibers due to low numerical aperture. Here, we demonstrate that commonly used optical fibers functionalized with arrays of metallic nanodots show substantially improved large-angle light-collection performances at multiple wavelengths. In particular, we show that at visible wavelengths, higher diffraction orders contribute significantly to the light-coupling efficiency, independent of the incident polarization, with a dominant excitation of the fundamental mode. The experimental observation is confirmed by an analytical model, which directly suggests further improvement in incoupling efficiency through the use of powerful nanostructures such as metasurface or dielectric gratings. Therefore, our concept paves the way for high-performance fiber-based optical devices and is particularly relevant within the context of endoscopic-type applications in life science and light collection within quantum technology.

Approaches for containerized scientific workflows in cloud environments with applications in life science

Containers are gaining popularity in life science research as they provide a solution for encompassing dependencies of provisioned tools, simplify software installations for end users and offer a form of isolation between processes. Scientific workflows are ideal for chaining containers into data analysis pipelines to aid in creating reproducible analyses. In this article, we review a number of approaches to using containers as implemented in the workflow tools Nextflow, Galaxy, Pachyderm, Argo, Kubeflow, Luigi and SciPipe, when deployed in cloud environments. A particular focus is placed on the workflow tool’s interaction with the Kubernetes container orchestration framework.

Tailorable Membrane-Penetrating Nanoplatform for Highly Efficient Organelle-Specific Localization.

Given the breadth of currently arising opportunities and concerns associated with nanoparticles for biomedical imaging, various types of nanoparticles have been widely exploited, especially for cellular/subcellular level probing. However, most currently reported nanoparticles either have inefficient delivery into cells or lack specificity for intracellular destinations. The absence of well-defined nanoplatforms remains a critical challenge hindering practical nano-based bio-imaging. Herein, the authors elaborate on a tailorable membrane-penetrating nanoplatform as a carrier with encapsulated actives and decorated surfaces to tackle the above-mentioned issues. The tunable contents in such a versatile nanoplatform offer huge flexibility to reach the expected properties and functions. Aggregation-induced emission luminogen (AIEgen) is applied to achieve sought-after photophysical properties, specific targeting moieties are installed to give high affinity towards different desired organelles, and critical grafting of cell-penetrating cyclic disulfides (CPCDs) to promote cellular uptake efficiency without sacrificing the specificity. Hereafter, to validate its practicability, the tailored nano products are successfully applied to track the dynamic correlation between mitochondria and lysosomes during autophagy. The authors believe that the strategy and described materials can facilitate the development of functional nanomaterials for various life science applications.

Opto-refrigerative tweezers.

Optical tweezers offer revolutionary opportunities for both fundamental and applied research in materials science, biology, and medical engineering. However, the requirement of a strongly focused and high-intensity laser beam results in potential photon-induced and thermal damages to target objects, including nanoparticles, cells, and biomolecules. Here, we report a new type of light-based tweezers, termed opto-refrigerative tweezers, which exploit solid-state optical refrigeration and thermophoresis to trap particles and molecules at the laser-generated cold region. While laser refrigeration can avoid photothermal heating, the use of a weakly focused laser beam can further reduce the photodamages to the target object. This novel and noninvasive optical tweezing technique will bring new possibilities in the optical control of nanomaterials and biomolecules for essential applications in nanotechnology, photonics, and life science.

Dual Emission: Classes, Mechanisms, and Conditions.

There has been much interest in dual-emission materials in the past few years for materials and life science applications; however, a systematic overview of the underlying processes is so-far missing. We resolve this issue herein by classifying dual-emission (DE) phenomena as relying on one emitter with two emitting states (DE1), two independent emitters (DE2), or two correlated emitters (DE3). Relevant DE mechanisms for materials science are then briefly described together with the electronic and/or geometrical conditions under which they occur. For further reading, references are given that offer detailed insight into the complex mechanistic aspects of the various DE processes or provide overviews on materials families or their applications. By avoiding ambiguities and misinterpretations, this systematic, insightful Review might inspire future targeted designs of DE materials.

(Invited) Bioelectronics with Nanocarbons

We focus on developing a new class of nanoscale materials for the investigation of biological entities at multiple length scales, from the molecular level to complex cellular networks. Our highly flexible bottom-up nanomaterials synthesis capabilities allow us to form unique hybrid-nanomaterials. Recently, we have demonstrated highly controlled synthesis of 3D out-of-plane single- to few-layer fuzzy graphene (3DFG) on a Si nanowire (SiNW) mesh template. By varying graphene growth conditions, we control the size, density, and electrical properties of the NW templated 3DFG (NT-3DFG). This flexible synthesis inspires formation of complex hybrid-nanomaterials with tailored optical and electrical properties to be used in biosensing, and energy-related research. The exceptional synthetic control and flexible assembly of nanomaterials provide powerful tools for fundamental studies and applications in life science and open up the potential to seamlessly merge either nanomaterials-based platforms or unique nanosensor geometries and topologies with cells, fusing nonliving and living systems together.