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Supply Chain and Sustainability Research (SCSR), 1, 2, 38-53

The T-cell protein tyrosine phosphatase (TCPTP/PTPN2) targets a broad variety of substrates across different subcellular compartments. In spite of that, the structural basis for the regulation of TCPTP's activity remains elusive. Here, we investigated whether the activity of TCPTP is regulated by a potential allosteric site in a comparable manner to its most similar PTP family member (PTP1B/PTPN1). We determined two crystal structures of TCPTP at 1.7 and 1.9 Å resolutions that include helix α7 at the TCPTP C-terminus. Helix α7 has been functionally characterized in PTP1B and was identified as its allosteric switch. However, its function is unknown in TCPTP. Here, we demonstrate that truncation or deletion of helix α7 reduced the catalytic efficiency of TCPTP by ∼4-fold. Collectively, our data supports an allosteric role of helix α7 in regulation of TCPTP's activity, similar to its function in PTP1B, and highlights that the coordination of helix α7 with the core catalytic domain is essential for the efficient catalytic function of TCPTP.

Dengue fever is a global mosquito-borne viral infectious disease that has, in recent years, rapidly spread to almost all regions of the world. Lack of vaccination and directed treatment makes detection at the infection's early stages extremely important for disease prevention and clinical care. In this paper, we developed a rapid and highly sensitive dengue detection tool using a novel platform of diagnosis, called spin-enhanced lateral flow immunoassay (SELFIA) with a fluorescent nanodiamond (FND) as a reporter. Taking advantage of the unique magneto-optical properties of negatively charged nitrogen-vacancy centers in the FND, the SELFIA platform utilizes alternating electromagnetic fields to modulate signals from FND's fluorescence to provide sensitive and specific results. With sandwich SELFIA, we could efficiently detect all four dengue non-structural protein (NS1) serotypes (DV1, DV2, DV3, and DV4). The lowest detection concentration of the dengue NS1 antigens varied from 0.1 to 1.3 ng/mL, which is among the lowest limits of detection to date. The FND-based SELFIA technique is up to 500 and 5000 times more sensitive than carbon black and conventional gold nanoparticles, respectively. By using different anti-NS1 antibodies, we could differentiate the NS1 antigen serotypes contained in the tested samples via three simultaneous assays. Proposed SELFIA allows for both qualitative and quantitative differentiation between different NS1 protein serotypes, which will assist in the development of a highly sensitive and specific detection platform for dengue screening that has the potential to detect the disease at its early stages, especially in high-risk and limited-resource areas.

Specific antibody interactions with short peptides have made epitope tagging systems a vital tool employed in virtually all fields of biological research. Here, we present a novel epitope tagging system comprised of a monoclonal antibody named GD-26, which recognises the TD peptide (GTGATPADD) derived from Haloarcula marismortui bacteriorhodopsin I (HmBRI) D94N mutant. The crystal structure of the antigen-binding fragment (Fab) of GD-26 complexed with the TD peptide was determined to a resolution of 1.45 A. The TD peptide was found to adopt a 310 helix conformation within the binding cleft, providing a characteristic peptide structure for recognition by GD-26 Fab. Based on the structure information, polar and non-polar forces collectively contribute to the strong binding. Attempts to engineer the TD peptide show that the proline residue is crucial for the formation of the 310 helix in order to fit into the binding cleft. Isothermal calorimetry (ITC) reported a dissociation constant KD of 12 ± 2.8 nM, indicating a strong interaction between the TD peptide and GD-26 Fab. High specificity of GD-26 IgG to the TD peptide was demonstrated by Western blotting, enzyme-linked immunosorbent assays (ELISA) and immunofluorescence as only TD-tagged proteins were detected, suggesting the effectiveness of the GD-26/TD peptide tagging system. In addition to already-existing epitope tags such as the FLAG tag and the ALFA tag adopting either extended or α-helix conformations, the unique 310 helix conformation of the TD peptide together with the corresponding monoclonal antibody GD-26 offers a novel tagging option for research.

Linker design is crucial to the success of antibody-drug conjugates (ADCs). In this work, we developed a modular linker format for attaching molecular cargos to antibodies based on strand pairing between complementary oligonucleotides. We prepared antibody-oligonucleotide conjugates (AOCs) by attaching 18-mer oligonucleotides to an anti-HER2 antibody through thiol-maleimide chemistry, a method generally applicable to any immunoglobulin with interchain disulfide bridges. The hybridization of drug-bearing complementary oligonucleotides to our AOCs was rapid, stoichiometric, and sequence-specific. AOCs loaded with cytotoxic payloads were able to selectively target HER2-overexpressing cell lines such as SK-BR-3 and N87, with in vitro potencies similar to that of the marketed ADC Kadcyla (T-DM1). Our results demonstrated the potential of utilizing AOCs as a highly versatile and modular platform, where a panel of well-characterized AOCs bearing DNA, RNA, or various nucleic acid analogs, such as peptide nucleic acids, could be easily paired with any cargo of choice for a wide range of diagnostic or therapeutic applications.

Background Polyethylene glycol (PEG) is widely used in industry and medicine. Anti-PEG antibodies have been developed for characterizing PEGylated drugs and other applications. However, the underlying mechanism for specific PEG binding has not been elucidated. Methods The Fab of two cognate anti-PEG antibodies 3.3 and 2B5 were each crystallized in complex with PEG, and their structures were determined by X-ray diffraction. The PEG-Fab interactions in these two crystals were analyzed and compared with those in a PEG-containing crystal of an unrelated anti-hemagglutinin 32D6-Fab. The PEG-binding stoichiometry was examined by using analytical ultracentrifuge (AUC). Results A common PEG-binding mode to 3.3 and 2B5 is seen with an S-shaped core PEG fragment bound to two dyad-related Fab molecules. A nearby satellite binding site may accommodate parts of a longer PEG molecule. The core PEG fragment mainly interacts with the heavy-chain residues D31, W33, L102, Y103 and Y104, making extensive contacts with the aromatic side chains. At the center of each half-circle of the S-shaped PEG, a water molecule makes alternating hydrogen bonds to the ether oxygen atoms, in a similar configuration to that of a crown ether-bound lysine. Each satellite fragment is clamped between two arginine residues, R52 from the heavy chain and R29 from the light chain, and also interacts with several aromatic side chains. In contrast, the non-specifically bound PEG fragments in the 32D6-Fab crystal are located in the elbow region or at lattice contacts. The AUC data suggest that 3.3-Fab exists as a monomer in PEG-free solution but forms a dimer in the presence of PEG-550-MME, which is about the size of the S-shaped core PEG fragment. Conclusions The differing amino acids in 3.3 and 2B5 are not involved in PEG binding but engaged in dimer formation. In particular, the light-chain residue K53 of 2B5-Fab makes significant contacts with the other Fab in a dimer, whereas the corresponding N53 of 3.3-Fab does not. This difference in the protein-protein interaction between two Fab molecules in a dimer may explain the temperature dependence of 2B5 in PEG binding, as well as its inhibition by crown ether.

SARS-CoV-2 viruses, responsible for the COVID-19 pandemic, continues to evolve into new mutations, which poses a significant threat to public health. Current testing methods have some limitations, such as long turnaround times, high costs, and professional laboratory requirements. In this report, the novel Spin-Enhanced Lateral Flow Immunoassay (SELFIA) platform and fluorescent nanodiamond (FND) reporter were utilized for the rapid detection of SARS-CoV-2 nucleocapsid and spike antigens from different variants, including wild-type (Wuhan-1), Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (B.1.1.529). The SARS-CoV-2 antibodies were conjugated with FND via nonspecific binding, enabling the detection of SARS-CoV-2 antigens via both direct and competitive SELFIA format. Direct SELFIA was performed by directly adding the SARS-CoV-2 antibodies-conjugated FND on the antigens-immobilized nitrocellulose (NC) membrane. Conversely, the SARS-CoV-2 antigen-containing sample was first incubated with the antibodies-conjugated FND, and then dropped on the antigen-immobilized NC membrane to carry out the competitive SELFIA. The results suggested that S44F anti-S IgG antibody can be efficiently used for the detection of wild-type, Alpha, Delta, and Omicron variants spike antigens. Findings were comparable in direct SELFIA, competitive SELFIA, and ELISA. A detection limit of 1.94, 0.77, 1.14, 1.91, and 1.68 ng/mL can be achieved for SARS-CoV-2 N protein, wild-type, Alpha, Delta, and Omicron S proteins, respectively, via competitive SELFIA assay. These results suggest that a direct SELFIA assay can be used for antibody/antigen pair screening in diagnosis development, while the competitive SELFIA assay can serve as an accurate quantitative diagnostic tool. The simplicity and rapidity of the SELFIA platform were demonstrated, which can be leveraged in the detection of other infectious diseases in the near future.

An incoherent optical system with wavefront coding extends the depth of field (DOF) by employing a cubic phase plate (CPP). We designed a digital microscope with a CPP in the aperture stop and on the surface of the lens, which extended the DOF. In addition, we proposed a method in which the CPP can be shifted and assigned to the surface of the lens by adjusting the third-order coefficient of the xy polynomial surface, so that the CPP on the surface of the lens can replace a single CPP in the aperture stop, which collided with the optical elements and mechanism in some cases, to reduce the difficulty in assembling. The microscope with flexibility and without loss of the illumination level can considerably improve the efficiency of microscopic applications.

The development of reliable and robust diagnostic tests is one of the most efficient methods to limit the spread of coronavirus disease 2019 (COVID-19), which is caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). However, most laboratory diagnostics for COVID-19, such as enzyme-linked immunosorbent assay (ELISA) and reverse transcriptase-polymerase chain reaction (RT-PCR), are expensive, time-consuming, and require highly trained professional operators. On the other hand, the lateral flow immunoassay (LFIA) is a simpler, cheaper device that can be operated by unskilled personnel easily. Unfortunately, the current technique has some limitations, mainly inaccuracy in detection. This review article aims to highlight recent advances in novel lateral flow technologies for detecting SARS-CoV-2 as well as innovative approaches to achieve highly sensitive and specific point-of-care testing. Lastly, we discuss future perspectives on how smartphones and Artificial Intelligence (AI) can be integrated to revolutionize disease detection as well as disease control and surveillance.

Based on secondary data collected during 2012-2016, this paper investigates how the increasing popularity of mobile Internet has impacted the time spent on wired Internet and traditional media. The research also examines the differences among generational cohorts and the trend of longitudinal changes. Relatively speaking, the younger the generation is, the more time is spent online, both wireless and wired. The generational differences in traditional media are limited to newspapers and television viewing. The time spent on wired and mobile Internet has increased rapidly over the past five years, but has not significantly reduced the time spent on traditional media except for newspaper. Results also point to a more complementary relationship than displacement between Internet use and traditional media use.

Laccases that are tolerant to organic solvents are powerful bio-catalysts with broad applications in biotechnology. Most of these uses must be accomplished at high concentration of organic solvents, during which proteins undergo unfolding, thereby losing enzyme activity. Here we show that organic-solvent pre-incubation provides effective and reversible 1.5- to 4.0-fold enhancement of enzyme activity of fungal laccases. Several organic solvents, including acetone, methanol, ethanol, DMSO, and DMF had an enhancement effect among all laccases studied. The enhancement was not substrate-specific and could be observed by using both phenolic and non-phenolic substrates. Laccase preincubated with organic solvents was sensitive to high temperature but remained stable at 25 °C, for an advantage for long-term storage. The acetone-pre-incubated 3-D structure of DLac, a high-efficiency fungal laccase, was determined and confirmed that the DLac protein structure remains intact and stable at a high concentration of organic solvent. Moreover, the turnover rates of fungal laccases were improved after organic-solvent pre-incubation, with DLac showing the highest enhancement among the fungal laccases examined. Our investigation sheds light on improving fungal laccase usage under extreme conditions and extends opportunities for bioremediation, decolorization, and organic synthesis.

A stratiform hyperbolic metamaterial comprises multiple units of symmetrical metal-dielectric film, stacked to have a precisely equivalent refractive index, admittance, and iso-frequency curve. A metamaterial that is composed of stacks of symmetrical films as a waveguide to couple a diffracted wave into a horizontally propagating plasmonic wave is designed herein. By tuning the parameters of the constituent thin films within a hyperbolic metamaterial, both the loss of the plasmonic wave and admittance matching are minimized and optimized, respectively.

Vibrio cholerae is the causative agent of the diarrheal disease cholera, for which biofilm communities are considered to be environmental reservoirs. In endemic regions, and after algal blooms, which may result from phosphate enrichment following agricultural runoff, the bacterium is released from biofilms resulting in seasonal disease outbreaks. However, the molecular mechanism by which V. cholerae senses its environment and switches lifestyles from the biofilm‐bound state to the planktonic state is largely unknown. Here, we report that the major biofilm scaffolding protein RbmA undergoes autocatalytic proteolysis via a phosphate‐dependent induced proximity activation mechanism. Furthermore, we show that RbmA mutants that are defective in autoproteolysis cause V. cholerae biofilms to grow larger and mechanically stronger, correlating well with the observation that RbmA stability directly affects microbial community homeostasis and rheological properties. In conclusion, our biophysical study characterizes a novel phosphate‐dependent breakdown pathway of RbmA, while microbiological data suggest a new, sensory role of this biofilm scaffolding element.

We report a highly efficient polariton organic light-emitting diode (POLED) based on an intracavity pumping architecture, where an absorbing J-aggregate dye film is used to generate polariton modes and a red fluorescent OLED is used for radiative pumping of emission from the lower polariton (LP) branch. To realize the device with large-area uniformity and adjustable coupling strength, we develop a spin-coating method to achieve high-quality J-aggregate thin films with controlled thickness and absorption. From systematic studies of the devices with different J-aggregate film thicknesses and OLED injection layers, we show that the J-aggregate film and the pump OLED play separate roles in determining the coupling strength and electroluminescence efficiency, and can be simultaneously optimized under a cavity design with a good LP-OLED emission overlap for effective radiative pumping. By increasing the absorption with thick J-aggregate film and improving the electron injection of pump OLED with Li2CO3 interlayer, we demonstrate the POLED with a large Rabi splitting energy of 192 meV and a maximum external quantum efficiency of 1.2%, a record efficiency of POLEDs reported so far. This POLED architecture can be generally applied for exploration of various organic materials to realize novel polariton devices and electrically pumped lasers.

In this paper, we propose a broadband omnidirectional near-perfect absorber that transforms light energy into heat. In contrast to previous research on structural metamaterials, this study focuses on light absorption in the epsilon-near-zero (ENZ) layers without any structural patterns. Chromium (Cr) thin films were applied as ENZ layers. Using the admittance method, we found the proper thicknesses of S i O 2 layers to match the incident medium and achieve perfect absorption. Also, the absorber is angular insensitive up to 60°. The temperature of the absorber increases from room temperature to 42°C, which is 4°C higher than the uncoated substrate at 38°C, after exposure to sunlight for 20 min.

Two systems of antibody-drug conjugates (ADCs), noncleavable H32-DM1 and cleavable H32-VCMMAE, were developed by using different linkers and drugs attached to the anti-HER2 antibody H32, which is capable of cell internalization. Activated functional groups, including an N-hydroxysuccinimidyl (NHS) ester and a maleimide, were utilized to make the ADCs. Mass spectrometry, hydrophobic interaction chromatography, polyacrylamide gel electrophoresis, and in vitro cell assays were performed to analyze and optimize the ADCs. Several H32-VCMMAE ADCs were established with higher DARs and greater synthetic yields without compromising potency. The anticancer efficacy of H32-DM1 was 2- to 8-fold greater than that of Kadcyla®. The efficacy of H32-VCMMAE was in turn better than that of H32-DM1. The anticancer efficacy of these ADCs against N87, SK-BR-3 and BT474 cells was in the following order: H32-VCMMAE series > H32-DM1 series > Kadcyla®. The optimal DAR for H32-VCMMAE was found to be 6.6, with desirable attributes including good cell penetration, a releasable payload in cancer cells, and high potency. Our results demonstrated the potential of H32-VCMMAE as a good ADC candidate.

Interleukin-1β (IL-1β) is a potent pleiotropic cytokine playing a central role in protecting cells from microbial pathogen infection or endogenous stress. After it binds to IL-1RI and recruits IL-1 receptor accessory protein (IL-1RAcP), signaling culminates in activation of NF-κB. Many pathophysiological diseases have been attributed to the derailment of IL-1β regulation. Several blocking reagents have been developed based on two mechanisms: blocking the binding of IL-1β to IL-1RI or inhibiting the recruitment of IL-1RAcP to the IL-1β initial complex. In order to simultaneously fulfill these two actions, a human anti-IL-1β neutralizing antibody IgG26 was screened from human genetic phage-display library and furthered structure-optimized to final version, IgG26AW. IgG26AW has a sub-nanomolar binding affinity for human IL-1β. We validated IgG26AW-neutralizing antibodies specific for IL-1β in vivo to prevent human IL-1β-driving IL-6 elevation in C56BL/6 mice. Mice underwent treatments with IgG26AW in A549 and MDA-MB-231 xenograft mouse cancer models have also been observed with tumor shrank and inhibition of tumor metastasis. The region where IgG26 binds to IL-1β also overlaps with the position where IL-1RI and IL-1RAcP bind, as revealed by the 26-Fab/IL-1β complex structure. Meanwhile, SPR experiments showed that IL-1β bound by IgG26AW prevented the further binding of IL-1RI and IL-1RAcP, which confirmed our inference from the result of protein structure. Therefore, the inhibitory mechanism of IgG26AW is to block the assembly of the IL-1β/IL-1RI/IL-1RAcP ternary complex which further inhibits downstream signaling. Based on its high affinity, high neutralizing potency, and novel binding epitope simultaneously occupying both IL-1RI and IL-1RAcP residues that bind to IL-1β, IgG26AW may be a new candidate for treatments of inflammation-related diseases or for complementary treatments of cancers in which the role of IL-1β is critical to pathogenesis.

Wavefront coding is an accepted technique to extend the depth of field in incoherent optical systems. We present the design of a reflecting telescope with wavefront coding by employing a cubic phase plate (CPP). We propose a method to reduce the CPP size by changing its position from the aperture stop to a secondary mirror without varying the point-spread function, which is insensitive to defocusing. This change in position reduces the diameter by almost three orders and increases the third-order coefficients of the x y polynomial surface by two orders, thus easing manufacturing.

Supplementary Materials

Additional file 1: Table S1. Dissociation constants KD of PEG and antibodies 3.3 and 2B5. Table S2. Sequence comparison in the Fv regions of 3.3 and 2B5. Figure S1. Comparison of the 32D6, 3.3 and 2B5 Fab structures. The superimposed Fab structures are colored in orange, blue and green, respectively. Figure S2. Extension of PEG molecule. Figure S3. Full-length IgG/PEG models. Figure S4. Two other examples of non-specific PEG-Fab complex structures.

supplemental 1

Prodigiosin is an intensely red pigment comprising three pyrroles. The biosynthetic pathway includes a two-step proline oxidation catalyzed by phosphatidylinositol N-acetylglucosaminyltransferase subunit A (PigA), with flavin adenine dinucleotide (FAD) as its cofactor. The enzyme is crystallized in the apo form and in complex with FAD and proline. As an acyl coenzyme A dehydrogenase (ACAD) family member, the protein folds into a β-sheet flanked by two α-helical domains. PigA forms a tetramer, which is consistent with analytical ultracentrifugation results. FAD binds to PigA in a similar way to that in the other enzymes of the ACAD family. The variable conformations of loop β4-β5 and helix αG correlate well with the structural flexibility required for substrate entrance to the Re side of FAD. Modeling with PigG, the acyl carrier protein, suggests a reasonable mode of interaction with PigA. The structure helps to explain the proline oxidation mechanism, in which Glu244 plays a central role by abstracting the substrate protons. It also reveals a plausible pocket for oxygen binding to the Si side of FAD.

A high-efficiency laccase, DLac, was isolated from Cerrena sp. RSD1. The kinetic studies indicate that DLac is a diffusion-limited enzyme. The crystal structure of DLac was determined to atomic resolution, and its overall structure shares high homology to monomeric laccases, but displays unique substrate-binding loops from those in other laccases. The substrate-binding residues with small side chain and the short substrate-binding loop IV broaden the substrate-binding cavity and may facilitate large substrate diffusion. Unlike highly glycosylated fungal laccases, the less-glycosylated DLac contains one highly conserved glycosylation site at N432 and an unique glycosylation site at N468. The N-glycans stabilize the substrate-binding loops and the protein structure, and the first N-acetylglucosamine is crucial for the catalytic efficiency. Additionally, a fivefold increase in protein yield is achieved via the submerged culture method for industrial applications. Database The atomic coordinates of the structure of DLac from Cerrena sp. RSD1 and structural factors have been deposited in the RCSB Protein Data Bank (PDB ID: 5Z1X).

We propose a see-through display with a wavefront coding (WFC) technique using a cubic phase plate to extend the depth of field (DOF) of the projected virtual image. The image projected by the WFC see-through display allows the eyes to see an object in the range of accommodation and a clear projected image simultaneously without re-focusing. The DOF of the clear projected image by the system can be extended from 250 mm to an optical infinity of 10 m.

Indium nitride (InN) films were deposited on Al 2 O 3 substrates with a zinc oxide (ZnO) interlayer using by radio-frequency metalorganic molecular beam epitaxy (RF-MOMBE). We evaluated the impact of the flow rate of trimethylindium (In(CH 3 ) 3 , TMIn) on the structure, surface morphology, and optical and electrical properties of the films using X-ray diffraction, scanning electron microscopy (SEM), transmission electron microscopy (TEM), UV–Vis spectroscopy, and Hall measurements. The XRD results indicated that all InN films were formed from single-phase wurtzite crystals with the preferred orientations along the c -axis. The SEM images indicated that the rough surfaces of the InN films grown with TMIn flow rates less than 0.55 sccm. The TEM images showed that InN and ZnO had hexagonal structures (wurtzite) that were epitaxially grown by RF-MOMBE on the substrates. The electron concentrations ranged from 7.3 × 10 19 to 2.56 × 10 20 cm −3 of the InN films were measured.

A superior mechanical properties of bilayer thin film with anti-fogging performance for polyethylene terephthalate (PET) substrate was developed. The bottom layer, acting as a mechanical support, is a hybrid organic-inorganic thin film with interpenetrating network. Atop this layer, the superhydrophilic nanoparticles were fabricated and deposited by spray-coating to yield a layer exhibiting the superhydrophilic and anti-fogging effect. Contact angles of water were measured to examine the hydrophilicity of the hybrid organic-inorganic superhydrophilic thin film. Besides, UV/VIS spectrophotometer, atomic force microscopy (AFM) and scanning electron microscope (SEM) were carried out to characterize the optical properties and film structure of the thin film. For the actual application, variety of industrial tests such as pencil test (ASTM D 3363 standard), adhesion test (ISO 2409 standard) and steam test, were employed to evaluate the prepared hybrid organic-inorganic superhydrophilic thin film. Especially, the addition of the bottom layer results in an improvement of the adhesion between the superhydrophilic nanoparticles and PET substrate. The experimental results exhibited that the mechanical, optical, superhydrophilic and anti-fogging properties were effectively improved after applying the hybrid organic-inorganic superhydrophilic thin film on PET substrate.

A novel edge sealing with solution coated gas barrier was successfully developed for the foldable AMOLED to improve reliability and reduce manufacturing cost. The foldable AMOLED with edge sealing passed reliability tests including 240 hours storage at 85°C /85% R.H. and outward folding at 3mm radius / 100k times. Besides, a mechanical debonding technology with low debonding stress was proposed and 18 inch OLEDs were successfully debonded.