De novo fabrication of custom-sequence plasmids for the synthesis of long DNA constructs with extrahelical features.

DNA constructs for single-molecule experiments often require specific sequences and/or extrahelical/noncanonical structures to study DNA-processing mechanisms. The precise introduction of such structures requires extensive control of the sequence of the initial DNA substrate. A commonly used substrate in the synthesis of DNA constructs is plasmid DNA. Nevertheless, the controlled introduction of specific sequences and extrahelical/noncanonical structures into plasmids often requires several rounds of cloning on pre-existing plasmids whose sequence one cannot fully control. Here, we describe a simple and efficient way to synthesize 10.1-kb plasmids de novo using synthetic gBlocks that provides full control of the sequence. Using these plasmids, we developed a 1.5-day protocol to assemble 10.1-kb linear DNA constructs with end and internal modifications. As a proof of principle, we synthesize two different DNA constructs with biotinylated ends and one or two internal 3' single-stranded DNA flaps, characterize them using single-molecule force and fluorescence spectroscopy, and functionally validate them by showing that the eukaryotic replicative helicase Cdc45/Mcm2-7/GINS (CMG) binds the 3' single-stranded DNA flap and translocates in the expected direction. We anticipate that our approach can be used to synthesize custom-sequence DNA constructs for a variety of force and fluorescence single-molecule spectroscopy experiments to interrogate DNA replication, DNA repair, and transcription.

Inverse design of metasurface based off-axis image relay.

The rapid advancement of portable electronics has created enormous demand for compact optical imaging systems. Such systems often require folded optical systems with beam steering and shaping components to reduce sizes and minimize image aberration at the same time. In this study, we present a solution that utilizes an inverse-designed dielectric metasurface for arbitrary-angle image-relay with aberration correction. The metasurface phase response is optimized by a series of artificial neural networks to compensate for the severe aberrations in the deflected images and meet the requirements for device fabrication at the same time. We compare our results to the solutions found by the global optimization tool in Zemax OpticStudio and show that the proposed method can predict better point-spread functions and images with less distortion. Finally, we designed a metasurface to achieve the optimized phase profile.

Giant optical second- and third-order nonlinearities at a telecom wavelength.

A material platform that excels in both optical second- and third-order nonlinearities at a telecom wavelength is theoretically and experimentally demonstrated. In this TiN-based coupled metallic quantum well structure, electronic subbands are engineered to support doubly resonant inter-subband transitions for an exceptionally high second-order nonlinearity and provide single-photon transitions for a remarkable third-order nonlinearity within the 1400-1600 nm bandwidth. The second-order susceptibility χ(2) reaches 2840 pm/V at 1440 nm, while the Kerr coefficient n2 arrives at 2.8 × 10-10 cm2/W at 1460 nm. The achievement of simultaneous strong second- and third-order nonlinearities in one material at a telecom wavelength creates opportunities for multi-functional advanced applications in the field of nonlinear optics.

Iterative Machine Learning for Classification and Discovery of Single-Molecule Unfolding Trajectories from Force Spectroscopy Data.

We report the application of machine learning techniques to expedite classification and analysis of protein unfolding trajectories from force spectroscopy data. Using kernel methods, logistic regression, and triplet loss, we developed a workflow called Forced Unfolding and Supervised Iterative Online (FUSION) learning where a user classifies a small number of repeatable unfolding patterns encoded as images, and a machine is tasked with identifying similar images to classify the remaining data. We tested the workflow using two case studies on a multidomain XMod-Dockerin/Cohesin complex, validating the approach first using synthetic data generated with a Monte Carlo algorithm and then deploying the method on experimental atomic force spectroscopy data. FUSION efficiently separated traces that passed quality filters from unusable ones, classified curves with high accuracy, and identified unfolding pathways that were undetected by the user. This study demonstrates the potential of machine learning to accelerate data analysis and generate new insights in protein biophysics.

Untrained, physics-informed neural networks for structured illumination microscopy.

Structured illumination microscopy (SIM) is a popular super-resolution imaging technique that can achieve resolution improvements of 2× and greater depending on the illumination patterns used. Traditionally, images are reconstructed using the linear SIM reconstruction algorithm. However, this algorithm has hand-tuned parameters which can often lead to artifacts, and it cannot be used with more complex illumination patterns. Recently, deep neural networks have been used for SIM reconstruction, yet they require training sets that are difficult to capture experimentally. We demonstrate that we can combine a deep neural network with the forward model of the structured illumination process to reconstruct sub-diffraction images without training data. The resulting physics-informed neural network (PINN) can be optimized on a single set of diffraction-limited sub-images and thus does not require any training set. We show, with simulated and experimental data, that this PINN can be applied to a wide variety of SIM illumination methods by simply changing the known illumination patterns used in the loss function and can achieve resolution improvements that match theoretical expectations.

Mapping Mechanostable Pulling Geometries of a Therapeutic Anticalin/CTLA-4 Protein Complex.

We used single-molecule AFM force spectroscopy (AFM-SMFS) in combination with click chemistry to mechanically dissociate anticalin, a non-antibody protein binding scaffold, from its target (CTLA-4), by pulling from eight different anchor residues. We found that pulling on the anticalin from residue 60 or 87 resulted in significantly higher rupture forces and a decrease in koff by 2-3 orders of magnitude over a force range of 50-200 pN. Five of the six internal anchor points gave rise to complexes significantly more stable than N- or C-terminal anchor points, rupturing at up to 250 pN at loading rates of 0.1-10 nN s-1. Anisotropic network modeling and molecular dynamics simulations helped to explain the geometric dependency of mechanostability. These results demonstrate that optimization of attachment residue position on therapeutic binding scaffolds can provide large improvements in binding strength, allowing for mechanical affinity maturation under shear stress without mutation of binding interface residues.

Ultrathin Layered Hyperbolic Metamaterial-Assisted Illumination Nanoscopy.

Metamaterial-assisted illumination nanoscopy (MAIN) has been proven to be a promising approach for super-resolution microscopy with up to a 7-fold improvement in imaging resolution. Further resolution enhancement is possible in principle, however, has not yet been demonstrated due to the lack of high-quality ultrathin layered hyperbolic metamaterials (HMMs) used in the MAIN. Here, we fabricate a low-loss composite HMM consisting of high-quality bilayers of Al-doped Ag and MgO with a nominal thickness of 2.5 nm, and then use it to demonstrate an ultrathin layered hyperbolic metamaterial-assisted illumination nanoscopy (ULH-MAIN) with a 14-fold imaging resolution improvement. This improvement of resolution is achieved in fluorescent beads super-resolution experiments and verified with scanning electron microscopy. The ULH-MAIN presents a simple super-resolution imaging approach that offers distinct benefits such as low illumination power, low cost, and a broad spectrum of selectable probes, making it ideal for dynamic imaging of life science samples.

[Chemical constituents in different parts of Ixeris sonchifolia based on UPLC-LTQ-Orbitrap-MS~n].

The chemical constituents in stem leaf, root, and flower of Ixeris sonchifolia were identified by the ultra performance li-quid chromatography coupled with linear ion trap quadrupole-orbitrap mass spectrometry(UPLC-LTQ-Orbitrap-MS~n). The separation was performed on an Acquity UPLC BEH C_(18) column(2.1 mm×100 mm, 1.7 µm) with a mobile phase of water(containing 0.1% formic acid, A)-acetonitrile(B) with gradient elution. With electrospray ionization source, the data of 70% methanol extract from stem leaf, root and flower of I. sonchifolia were collected by high-resolution full-scan Fourier transform spectroscopy, data dependent acquisition, precursor ion scan, and selected ion monitoring in the negative and positive ion modes. The compounds were identified based on accurate molecular weight, retention time, fragment ions, comparison with reference standard, Clog P and references. A total of 131 compounds were identified from the 70% methanol extract of I. sonchifolia, including nucleosides, flavonoids, organic acids, terpenoids, and phenylpropanoids, and 119, 110, and 126 compounds were identified from the stem leaf, root and flower of I. sonchifolia, respectively. In addition, isorhamnetin, isorhamnetin-7-O-sambubioside and caffeylshikimic acid were discovered from I. sonchifolia for the first time. This study comprehensively analyzed and compared the chemical constituents in different parts of I. sonchifolia, which facilitated the discovery of effective substances and the development and application of medicinal material resources of I. sonchifolia.

Direct Comparison of Lysine versus Site-Specific Protein Surface Immobilization in Single-Molecule Mechanical Assays.

Single-molecule force spectroscopy (SMFS) is powerful for studying folding states and mechanical properties of proteins, however, it requires protein immobilization onto force-transducing probes such as cantilevers or microbeads. A common immobilization method relies on coupling lysine residues to carboxylated surfaces using 1-ethyl-3-(3-dimethyl-aminopropyl) carbodiimide and N-hydroxysuccinimide (EDC/NHS). Because proteins typically contain many lysine groups, this strategy results in a heterogeneous distribution of tether positions. Genetically encoded peptide tags (e.g., ybbR) provide alternative chemistries for achieving site-specific immobilization, but thus far a direct comparison of site-specific vs. lysine-based immobilization strategies to assess effects on the observed mechanical properties was lacking. Here, we compared lysine- vs. ybbR-based protein immobilization in SMFS assays using several model polyprotein systems. Our results show that lysine-based immobilization results in significant signal deterioration for monomeric streptavidin-biotin interactions, and loss of the ability to correctly classify unfolding pathways in a multipathway Cohesin-Dockerin system. We developed a mixed immobilization approach where a site-specifically tethered ligand was used to probe surface-bound proteins immobilized through lysine groups, and found partial recovery of specific signals. The mixed immobilization approach represents a viable alternative for mechanical assays on in vivo-derived samples or other proteins of interest where genetically encoded tags are not feasible.

Fourier Optical Spin Splitting Microscopy.

In this Letter, we propose a new quantitative phase imaging methodology named Fourier optical spin splitting microscopy (FOSSM). FOSSM relies on a metasurface located at the Fourier plane of a polarized microscope to separate the object image into two replicas of opposite circularly polarized states. The bias retardation between the two replicas is tuned by translating the metasurface or rotating the analyzer. Combined with a polarized camera, FOSSM can easily achieve single-shot quantitative phase gradient imaging, which greatly reduces the complexity of current phase microscope setups, paving the way for the next generation high-speed real-time multifunctional microscopy.

The lateral femoral notch sign and coronal lateral collateral ligament sign in magnetic resonance imaging failed to predict dynamic anterior tibial laxity.

PURPOSE: To investigate the relationship between the lateral femoral notch sign as well as the coronal lateral collateral ligament (LCL) sign and anterior tibial translation using the GNRB arthrometer in patients with anterior cruciate ligament (ACL) injuries. METHODS: Forty-six patients with ACL injuries were retrospectively included from May 2020 to February 2022; four patients were excluded due to incomplete data. Magnetic resonance imaging (MRI) were reviewed for the lateral femoral notch sign and the coronal LCL sign. The GNRB arthrometer was used to evaluate the dynamic anterior tibial translation of the knee, and the side-to-side differences (SSDs) in tibial translation between the injured knee and healthy knee were calculated at different force levels. Two types of slopes for displacement-force curves were acquired. RESULTS: Six patients (14.3%) had the positive lateral femoral notch sign (notch depth > 2.0 mm), and 14 patients (33.3%) had the positive coronal LCL sign. The SSD of the anterior tibial translations under different loads as well as the slopes of displacement-force curves were the same in the positive and negative notch sign groups (p all > 0.05) and between the positive and negative coronal LCL sign groups (p all > 0.05). Meanwhile, the measured notch depth and notch length were also not significantly correlated with the anterior tibial translation SSD in the GNRB. CONCLUSION: The presence of the lateral femoral notch sign and the coronal LCL sign did not indicate greater dynamic tibial laxity as measured using the GNRB.

Optical edge detection based on high-efficiency dielectric metasurface.

Optical edge detection is a useful method for characterizing boundaries, which is also in the forefront of image processing for object detection. As the field of metamaterials and metasurface is growing fast in an effort to miniaturize optical devices at unprecedented scales, experimental realization of optical edge detection with metamaterials remains a challenge and lags behind theoretical proposals. Here, we propose a mechanism of edge detection based on a Pancharatnam-Berry-phase metasurface. We experimentally demonstrated broadband edge detection using designed dielectric metasurfaces with high optical efficiency. The metasurfaces were fabricated by scanning a focused laser beam inside glass substrate and can be easily integrated with traditional optical components. The proposed edge-detection mechanism may find important applications in image processing, high-contrast microscopy, and real-time object detection on compact optical platforms such as mobile phones and smart cameras.

Array atomic force microscopy for real-time multiparametric analysis.

Nanoscale multipoint structure-function analysis is essential for deciphering the complexity of multiscale biological and physical systems. Atomic force microscopy (AFM) allows nanoscale structure-function imaging in various operating environments and can be integrated seamlessly with disparate probe-based sensing and manipulation technologies. Conventional AFMs only permit sequential single-point analysis; widespread adoption of array AFMs for simultaneous multipoint study is challenging owing to the intrinsic limitations of existing technological approaches. Here, we describe a prototype dispersive optics-based array AFM capable of simultaneously monitoring multiple probe-sample interactions. A single supercontinuum laser beam is utilized to spatially and spectrally map multiple cantilevers, to isolate and record beam deflection from individual cantilevers using distinct wavelength selection. This design provides a remarkably simplified yet effective solution to overcome the optical cross-talk while maintaining subnanometer sensitivity and compatibility with probe-based sensors. We demonstrate the versatility and robustness of our system on parallel multiparametric imaging at multiscale levels ranging from surface morphology to hydrophobicity and electric potential mapping in both air and liquid, mechanical wave propagation in polymeric films, and the dynamics of living cells. This multiparametric, multiscale approach provides opportunities for studying the emergent properties of atomic-scale mechanical and physicochemical interactions in a wide range of physical and biological networks.

Kerr Metasurface Enabled by Metallic Quantum Wells.

Optical metasurfaces have emerged as promising candidates for multifunctional devices. Dynamically reconfigurable metasurfaces have been introduced by employing phase-change materials or by applying voltage, heat, or strain. While existing metasurfaces exhibit appealing properties, they do not express any significant nonlinear effects due to the negligible nonlinear responses from the typical materials used to build the metasurface. In this work, we propose and experimentally demonstrate one kind of Kerr metasurface that shows strong intensity-dependent responses. The Kerr metasurface is composed of a top layer of gold antennas, a dielectric spacer, and a ground layer of metallic quantum wells (MQWs). Because of the large Kerr nonlinearity supported by the MQWs, the effective optical properties of the MQWs can change from metallic to dielectric with increasing of the input intensity, leading to dramatic modifications of the metasurface responses. This opens up new routes for potential applications in the field of nonlinear optics.

Imaging of Cell Morphology Changes via Metamaterial-Assisted Photobleaching Microscopy.

Determining the axial position of an emitter with nanoscale precision is critical to a fundamental imaging methodology. While there are many advanced optical techniques being applied to high-resolution imaging, high-axial-resolution topography imaging of living cells is particularly challenging. Here, we present an application of metamaterial-assisted photobleaching microscopy (MAPM) with high-axial resolution to characterize morphological properties of living cells. Quantitative imaging of changes in the morphology of live cells is obtained by topographic and statistical analysis. The time-lapse topography image using the metamaterial-induced photostability provides information about growth factor induced changes in the cell morphology with high-axial resolution.

Neural representations of imagined speech revealed by frequency-tagged magnetoencephalography responses.

Speech mental imagery is a quasi-perceptual experience that occurs in the absence of real speech stimulation. How imagined speech with higher-order structures such as words, phrases and sentences is rapidly organized and internally constructed remains elusive. To address this issue, subjects were tasked with imagining and perceiving poems along with a sequence of reference sounds with a presentation rate of 4 Hz while magnetoencephalography (MEG) recording was conducted. Giving that a sentence in a traditional Chinese poem is five syllables, a sentential rhythm was generated at a distinctive frequency of 0.8 Hz. Using the frequency tagging we concurrently tracked the neural processing timescale to the top-down generation of rhythmic constructs embedded in speech mental imagery and the bottom-up sensory-driven activity that were precisely tagged at the sentence-level rate of 0.8 Hz and a stimulus-level rate of 4 Hz, respectively. We found similar neural responses induced by the internal construction of sentences from syllables with both imagined and perceived poems and further revealed shared and distinct cohorts of cortical areas corresponding to the sentence-level rhythm in imagery and perception. This study supports the view of a common mechanism between imagery and perception by illustrating the neural representations of higher-order rhythmic structures embedded in imagined and perceived speech.

Upregulation of TRPC5 in hippocampal excitatory synapses improves memory impairment associated with neuroinflammation in microglia knockout IL-10 mice.

BACKGROUND: Members of the transient receptor potential canonical (TRPC) protein family are widely distributed in the hippocampus of mammals and exert respective and cooperative influences on the functions of neurons. The relationship between specific TRPC subtypes and neuroinflammation is receiving increasing attention. METHODS: Using Cx3cr1CreERIL-10-/- transgenic mice and their littermates to study the relationship between TRPC channels and memory impairment. RESULTS: We demonstrated that Cx3cr1CreERIL-10-/- mice displayed spatial memory deficits in object location recognition (OLR) and Morris water maze (MWM) tasks. The decreased levels of TRPC4 and TRPC5 in the hippocampal regions were verified via reverse transcription polymerase chain reaction, western blotting, and immunofluorescence tests. The expression of postsynaptic density protein 95 (PSD95) and synaptophysin in the hippocampus decreased with an imbalance in the local inflammatory environment in the hippocampus. The number of cells positive for ionized calcium-binding adaptor molecule 1 (Iba1), a glial fibrillary acidic protein (GFAP), increased with the high expression of interleukin 6 (IL-6) in Cx3cr1CreERIL-10-/- mice. The nod-like receptor protein 3 (NLRP3) inflammasome was also involved in this process, and the cytokines IL-1ß and IL-18 activated by NLRP3 were also elevated by western blotting. The co-localization of TRPC5 and calmodulin-dependent protein kinase IIα (CaMKIIα) significantly decreased TRPC5 expression in excitatory neurons. AAV9-CaMKIIα-TRPC5 was used to upregulate TRPC5 in excitatory neurons in the hippocampus. CONCLUSIONS: The results showed that the upregulation of TRPC5 improved the memory performance of Cx3cr1CreERIL-10-/- mice related to inhibiting NLRP3 inflammasome-associated neuroinflammation.

Depression-like behavior associated with E/I imbalance of mPFC and amygdala without TRPC channels in mice of knockout IL-10 from microglia.

Depression has a growing impact on public health. Accumulating evidence supports an association between depression and increased immune system activity. IL-10 is a key cytokine that inhibits excessive inflammatory responses and is related to the anti-inflammatory and protective functions of the central nervous system (CNS). Cx3cr1CreERIL-10-/- mice were used in our study. We aimed to identify the role of IL-10 in microglia in depression and anxiety-like behavior. We performed a series of behavioral tests on the mice; the Cx3cr1CreERIL-10-/- male mice showed depression- and anxiety-like behavior compared with the littermates. The expression of transient receptor potential canonical 5 (TRPC5) decreased in both the medial prefrontal cortex (mPFC) and amygdala regions. The cytokines IL-1ß and IL-6 increased, and IL-10 was decreased by western blotting. The knockout mice showed different trends in the effects of synaptic proteins. In the mPFC, IL-10 knockout induced a decrease in NR2B and synaptophysin; in the amygdala region, there was a significant increase in NR2B and PSD95. IL-10 knockout from microglia induced a decrease in GAD67 and parvalbumin (Pv) in the mPFC, but not in the amygdala. Our results showed enhanced depression and anxiety-like behavior in the Cx3cr1CreER IL-10-/- mice, which could be related to an imbalance in local excitatory and inhibitory transmission, as well as neuroinflammation in the mPFC and amygdala. This imbalance was associated with increased local inflammation. Although many studies have demonstrated the role of TRPC channels in emotional responses, our study showed that TRPC was not involved in this process in Cx3cr1CreERIL-10-/- mice.

LED control of gene expression in a nanobiosystem composed of metallic nanoparticles and a genetically modified E. coli strain.

BACKGROUND: Within the last decade, genetic engineering and synthetic biology have revolutionized society´s ability to mass-produce complex biological products within genetically-modified microorganisms containing elegantly designed genetic circuitry. However, many challenges still exist in developing bioproduction processes involving genetically modified microorganisms with complex or multiple gene circuits. These challenges include the development of external gene expression regulation methods with the following characteristics: spatial-temporal control and scalability, while inducing minimal permanent or irreversible system-wide conditions. Different stimuli have been used to control gene expression and mitigate these challenges, and they can be characterized by the effect they produce in the culture media conditions. Invasive stimuli that cause permanent, irreversible changes (pH and chemical inducers), non-invasive stimuli that cause partially reversible changes (temperature), and non-invasive stimuli that cause reversible changes in the media conditions (ultrasound, magnetic fields, and light). METHODS: Opto-control of gene expression is a non-invasive external trigger that complies with most of the desired characteristics of an external control system. However, the disadvantage relies on the design of the biological photoreceptors and the necessity to design them to respond to a different wavelength for every bioprocess needed to be controlled or regulated in the microorganism. Therefore, this work proposes using biocompatible metallic nanoparticles as external controllers of gene expression, based on their ability to convert light into heat and the capacity of nanotechnology to easily design a wide array of nanostructures capable of absorbing light at different wavelengths and inducing plasmonic photothermal heating. RESULTS: Here, we designed a nanobiosystem that can be opto-thermally triggered using LED light. The nanobiosystem is composed of biocompatible gold nanoparticles and a genetically modified E. coli with a plasmid that allows mCherry fluorescent protein production at 37 °C in response to an RNA thermometer. CONCLUSIONS: The LED-triggered photothermal protein production system here designed offers a new, cheaper, scalable switchable method, non-destructive for living organisms, and contribute toward the evolution of bioprocess production systems.

Influence of Fluorination on Single-Molecule Unfolding and Rupture Pathways of a Mechanostable Protein Adhesion Complex.

We investigated the influence of fluorination on unfolding and unbinding reaction pathways of a mechanostable protein complex comprising the tandem dyad XModule-Dockerin bound to Cohesin. Using single-molecule atomic force spectroscopy, we mapped the energy landscapes governing the unfolding and unbinding reactions. We then used sense codon suppression to substitute trifluoroleucine in place of canonical leucine globally in XMod-Doc. Although TFL substitution thermally destabilized XMod-Doc, it had little effect on XMod-Doc:Coh binding affinity at equilibrium. When we mechanically dissociated global TFL-substituted XMod-Doc from Coh, we observed the emergence of a new unbinding pathway with a lower energy barrier. Counterintuitively, when fluorination was restricted to Doc, we observed mechano-stabilization of the non-fluorinated neighboring XMod domain. This suggests that intramolecular deformation is modulated by fluorination and highlights the differences between equilibrium thermostability and non-equilibrium mechanostability. Future work is poised to investigate fluorination as a means to modulate mechanical properties of synthetic proteins and hydrogels.