KLK7, KLK10, and KLK11 in Papillary Thyroid Cancer: Bioinformatic Analysis and Experimental Validation.

Despite many studies on papillary thyroid carcinoma (PTC) in the past few decades, some critical and significant genes remain undiscovered. To explore genes that may play crucial roles in PTC, a detailed analysis of the expression levels, mutations, and clinical significance of Kallikrein-related peptidases (KLKs) family genes in PTC was undertaken to provide new targets for the precise treatment of the disease. A comprehensive analysis of KLK family genes was performed using various online tools, such as GEPIA, Kaplan-Meier Plotter, LinkedOmics, GSCA, TIMER, and Cluego. KLK7, KLK10, and KLK11 were critical factors of KLK family genes. Then, functional assays were carried out on KLK7/10/11 to determine their proliferation, migration, and invasion capabilities in PTC. The mRNA expression levels of KLK7, KLK10, KLK11, and KLK13 were significantly elevated in thyroid carcinoma, while KLK1, KLK2, KLK3 and KLK4 mRNA levels were decreased compared to normal tissues. Correlations between KLK2/7-12/15 expression levels and tumor stage were also observed in thyroid carcinoma. Survival analysis demonstrated that KLK4/5/7/9-12/14 was associated with overall survival in patients with thyroid cancer. Not only were KLK genes strongly associated with cancer-related pathways, but also KLK7/10/11 was associated with immune-cell infiltration. Finally, silencing KLK7/10/11 impaired human papillary thyroid carcinoma cells' growth, migration ability, and invasiveness. The increased expression of KLK7, KLK10, and KLK11 may serve as molecular markers to identify PTC patients. KLK7, KLK10, and KLK11 could be potential prognostic indicators and targets for precision therapy against PTC.

Intrinsically disordered CsoS2 acts as a general molecular thread for α-carboxysome shell assembly.

Carboxysomes are a paradigm of self-assembling proteinaceous organelles found in nature, offering compartmentalisation of enzymes and pathways to enhance carbon fixation. In α-carboxysomes, the disordered linker protein CsoS2 plays an essential role in carboxysome assembly and Rubisco encapsulation. Its mechanism of action, however, is not fully understood. Here we synthetically engineer α-carboxysome shells using minimal shell components and determine cryoEM structures of these to decipher the principle of shell assembly and encapsulation. The structures reveal that the intrinsically disordered CsoS2 C-terminus is well-structured and acts as a universal "molecular thread" stitching through multiple shell protein interfaces. We further uncover in CsoS2 a highly conserved repetitive key interaction motif, [IV]TG, which is critical to the shell assembly and architecture. Our study provides a general mechanism for the CsoS2-governed carboxysome shell assembly and cargo encapsulation and further advances synthetic engineering of carboxysomes for diverse biotechnological applications.

ChAdOx1 COVID vaccines express RBD open prefusion SARS-CoV-2 spikes on the cell surface.

Vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been proven to be an effective means of decreasing COVID-19 mortality, hospitalization rates, and transmission. One of the vaccines deployed worldwide is ChAdOx1 nCoV-19, which uses an adenovirus vector to drive the expression of the original SARS-CoV-2 spike on the surface of transduced cells. Using cryo-electron tomography and subtomogram averaging, we determined the native structures of the vaccine product expressed on cell surfaces in situ. We show that ChAdOx1-vectored vaccines expressing the Beta SARS-CoV-2 variant produce abundant native prefusion spikes predominantly in one-RBD-up conformation. Furthermore, the ChAdOx1-vectored HexaPro-stabilized spike yields higher cell surface expression, enhanced RBD exposure, and reduced shedding of S1 compared to the wild type. We demonstrate in situ structure determination as a powerful means for studying antigen design options in future vaccine development against emerging novel SARS-CoV-2 variants and broadly against other infectious viruses.

Towards in situ high-resolution imaging of viruses and macromolecular complexes using cryo-electron tomography.

Cryo-electron tomography and subtomogram averaging are rising and fast-evolving imaging techniques to study biological events, providing structural information at an unprecedented resolution while preserving spatial correlation in their native contexts. The latest technology and methodology development ranging from sample preparation to data collection and data processing, has enabled significant advancement in its applications to various biological systems. This review provides an overview of the current technology development enabling high-resolution structural study in situ, highlighting the use of a priori information of biological samples to assess the quality of subtomogram averaging pipeline. We exemplify the applications of this technique to understanding viruses and principles of macromolecule assembly using different biological systems, ranging from in vitro to in situ samples, which provide structural information at different resolutions and contexts.

Parameter adaptive sliding mode trajectory tracking strategy with initial value identification for the swing in a hydraulic construction robot.

A novel trajectory tracking strategy is developed for a double actuated swing in a hydraulic construction robot. Specifically, a nonlinear hydraulic dynamics model of a double actuated swing is established, and a parameter adaptive sliding mode control strategy is designed to enhance the trajectory tracking performance. When an object is grabbed and unloaded, the moment of inertia of a swing considerably changes, and the performance of the estimation algorithm is generally inadequate. Thus, it is necessary to establish an algorithm to identify the initial value of the moment of inertia of the object. To this end, this paper proposes a novel initial value identification algorithm based on a two-DOF robot gravity force identification method combined with stereo vision information. The performance of the identification algorithm is enhanced. Simulations and experiments are performed to verify the effect of the novel control scheme.

Investigation of Anomalous Degradation Tendency of Low-Frequency Noise in Irradiated SOI-NMOSFETs.

In this work, we present new evidence of the physical mechanism behind the generation of low-frequency noise with high interface-trap density by measuring the low-frequency noise magnitudes of partially depleted (PD) silicon-on-insulator (SOI) NMOSFETs as a function of irradiation dose. We measure the DC electrical characteristics of the devices at different irradiation doses and separate the threshold-voltage shifts caused by the oxide-trap charge and interface-trap charge. Moreover, the increased densities of the oxide-trap charge projected to the Si/SiO2 interface and interface-trap charge are calculated. The results of our experiment suggest that the magnitudes of low-frequency noise do not necessarily increase with the increase in border-trap density. A novel physical explanation for the low-frequency noise in SOI-NMOSFETs with high interface-trap density is proposed. We reveal that the presence of high-density interface traps after irradiation has a repressing effect on the generation of low-frequency noise. Furthermore, the exchange of some carriers between border traps and interface traps can cause a decrease in the magnitude of low-frequency noise when the interface-trap density is high.

Analysis of Degradation of Electromigration Reliability of Au-Al and OPM Wire Bonded Contacts at 250 °C Using Resistance Monitoring Method.

The ongoing trend towards miniaturization and increased packaging density has exacerbated the reliability problem of Au-Al heterogeneous metal bonding structures in high-temperature environments, where extreme temperatures and high current pose a serious challenge. In order to address this issue, the present study aims to investigate the electromigration reliability of Au-Al bonding by comparing the conventional heterogeneous contacts with OPM structures, which are homogeneous contacts. A novel bonding layout was developed to precisely detect the resistance and obtain stage changes in electromigration. The experimental results demonstrated that the relative resistance shift of Au-Al bonding at 250 °C was 98.7%, while CrAu and NiPdAu OPM structures exhibited only 46.1% and 2.93% shifts, which suggests that the reliability of OPM structures was improved by a factor of 2.14 and 33.6, respectively. The degradation of Au-Al bonding was attributed to the large cracks observed at the bonding interface and lateral consumption of Al elements. In contrast, OPM structures only exhibited tiny voids and maintained a better bonding state overall, indicating that homogeneous metal contacts have better immunity to electromigration. Furthermore, this study also observed the polarity effect of electromigration and analyzed the impact of NiPdAu thickness on reliability. Overall, this research provides a novel approach and an insightful theoretical reference for addressing the bottleneck of high-temperature electromigration reliability in high-temperature sensor packaging.

A Fast Design Method of Anisotropic Dielectric Lens for Vortex Electromagnetic Wave Based on Deep Learning.

Orbital angular momentum (OAM) has made it possible to regulate classical waves in novel ways, which is more energy- or information-efficient than conventional plane wave technology. This work aims to realize the transition of antenna radiation mode through the rapid design of an anisotropic dielectric lens. The deep learning neural network (DNN) is used to train the electromagnetic properties of dielectric cell structures. Nine variable parameters for changing the dielectric unit structure are present in the input layer of the DNN network. The trained network can predict the transmission phase of the unit cell structure with greater than 98% accuracy within a specific range. Then, to build the corresponding relationship between the phase and the parameters, the gray wolf optimization algorithm is applied. In less than 0.3 s, the trained network can predict the transmission coefficients of the 31 × 31 unit structure in the arrays with great accuracy. Finally, we provide two examples of neural network-based rapid anisotropic dielectric lens design. Dielectric lenses produce the OAM modes +1, -1, and -1, +2 under TE and TM wave irradiation, respectively. This approach resolves the difficult phase matching and time-consuming design issues associated with producing a dielectric lens.

Experimental and Hybrid FEM/Peridynamic Study on the Fracture of Ultra-High-Performance Concretes Reinforced by Different Volume Fractions of Polyvinyl Alcohol Fibers.

In this study, a series of three-point bending tests were carried out with notched beam structures made of polyvinyl alcohol (PVA) fiber-reinforced ultra-high-performance concrete (UHPC) to study the effect of volume fractions of PVA fibers on the fracture characteristics of the UHPC-PVAs. Furthermore, in order to meet the increasing demand for time- and cost-saving design methods related to research and design experimentation for the UHPC structures, a relevant hybrid finite element and extended bond-based peridynamic numerical modeling approach is proposed to numerically analyze the fracture behaviors of the UHPC-PVA structures in 3D. In the proposed method, the random distribution of the fibers is considered according to their corresponding volume fractions. The predicted peak values of the applied force agree well with the experimental results, which validates the effectiveness and accuracy of the present method. Both the experimental and numerical results indicate that, increasing the PVA fiber volume fraction, the strength of the produced UHPC-PVAs will increase approximately linearly.

A peridynamic approach to simulating fatigue crack propagation in composite materials.

In this article, a numerical tool is proposed in the framework of bond-based peridynamics to simulate fatigue crack propagation in composite materials and structures. The cycle-dependent damage-cumulative model derived from Peerlings' law and applied to a bilinear constitutive law is used to evaluate the fatigue degradation of the bond stiffness. Several benchmark cases are studied to validate the proposed approach. Finally, static and fatigue crack propagations in composite systems with single or multi-inclusions are simulated to illustrate the capabilities and characteristics of the developed approach. This article is part of the theme issue 'Ageing and durability of composite materials'.

Cryo-EM structures of perforin-2 in isolation and assembled on a membrane suggest a mechanism for pore formation.

Perforin-2 (PFN2, MPEG1) is a key pore-forming protein in mammalian innate immunity restricting intracellular bacteria proliferation. It forms a membrane-bound pre-pore complex that converts to a pore-forming structure upon acidification; but its mechanism of conformational transition has been debated. Here we used cryo-electron microscopy, tomography and subtomogram averaging to determine structures of PFN2 in pre-pore and pore conformations in isolation and bound to liposomes. In isolation and upon acidification, the pre-assembled complete pre-pore rings convert to pores in both flat ring and twisted conformations. On membranes, in situ assembled PFN2 pre-pores display various degrees of completeness; whereas PFN2 pores are mainly incomplete arc structures that follow the same subunit packing arrangements as found in isolation. Both assemblies on membranes use their P2 ß-hairpin for binding to the lipid membrane surface. Overall, these structural snapshots suggest a molecular mechanism for PFN2 pre-pore to pore transition on a targeted membrane, potentially using the twisted pore as an intermediate or alternative state to the flat conformation, with the capacity to cause bilayer distortion during membrane insertion.

Structure and activity of particulate methane monooxygenase arrays in methanotrophs.

Methane-oxidizing bacteria play a central role in greenhouse gas mitigation and have potential applications in biomanufacturing. Their primary metabolic enzyme, particulate methane monooxygenase (pMMO), is housed in copper-induced intracytoplasmic membranes (ICMs), of which the function and biogenesis are not known. We show by serial cryo-focused ion beam (cryoFIB) milling/scanning electron microscope (SEM) volume imaging and lamellae-based cellular cryo-electron tomography (cryoET) that these ICMs are derived from the inner cell membrane. The pMMO trimer, resolved by cryoET and subtomogram averaging to 4.8 Å in the ICM, forms higher-order hexagonal arrays in intact cells. Array formation correlates with increased enzymatic activity, highlighting the importance of studying the enzyme in its native environment. These findings also demonstrate the power of cryoET to structurally characterize native membrane enzymes in the cellular context.

Perforin-2 clockwise hand-over-hand pre-pore to pore transition mechanism.

Perforin-2 (PFN2, MPEG1) is a pore-forming protein that acts as a first line of defense in the mammalian immune system, rapidly killing engulfed microbes within the phagolysosome in macrophages. PFN2 self-assembles into hexadecameric pre-pore rings that transition upon acidification into pores damaging target cell membranes. Here, using high-speed atomic force microscopy (HS-AFM) imaging and line-scanning and molecular dynamics simulation, we elucidate PFN2 pre-pore to pore transition pathways and dynamics. Upon acidification, the pre-pore rings (pre-pore-I) display frequent, 1.8 s-1, ring-opening dynamics that eventually, 0.2 s-1, initiate transition into an intermediate, short-lived, ~75 ms, pre-pore-II state, inducing a clockwise pre-pore-I to pre-pore-II propagation. Concomitantly, the first pre-pore-II subunit, undergoes a major conformational change to the pore state that propagates also clockwise at a rate ~15 s-1. Thus, the pre-pore to pore transition is a clockwise hand-over-hand mechanism that is accomplished within ~1.3 s. Our findings suggest a clockwise mechanism of membrane insertion that with variations may be general for the MACPF/CDC superfamily.

Diastereo- and Enantioselective Synthesis of Bisbenzannulated Spiroketals and Spiroaminals by Ir/Ag/Acid Ternary Catalysis.

We reported herein an iridium/silver/acid ternary catalytic system to access bisbenzannulated [6,6]-spiroketals in high efficiency with generally high diastereo- and enantioselectivities (up to >20 : 1 dr, >99 % ee). In this procedure, readily available o-alkynylacetophenones undergo cycloisomerization to generate isochromenes in situ that participate in stereoselective allylation/spiroketalization sequence with 2-(1-hydroxyallyl)phenols. Meanwhile, 2-(1-hydroxyallyl)anilines were also compatible in this cascade reaction, furnishing structurally novel bisbenzannulated [6,6]-spiroaminals with good diastereoselectivities (8 : 1-12 : 1 dr) and excellent enantioselectivities (98 %->99 % ee). Moreover, experimental studies and theoretical calculations were performed to illustrate the reaction mechanism and stereochemistry.

Structure and assembly of cargo Rubisco in two native α-carboxysomes.

Carboxysomes are a family of bacterial microcompartments in cyanobacteria and chemoautotrophs. They encapsulate Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase catalyzing carbon fixation inside a proteinaceous shell. How Rubisco complexes pack within the carboxysomes is unknown. Using cryo-electron tomography, we determine the distinct 3D organization of Rubisco inside two distant α-carboxysomes from a marine α-cyanobacterium Cyanobium sp. PCC 7001 where Rubiscos are organized in three concentric layers, and from a chemoautotrophic bacterium Halothiobacillus neapolitanus where they form intertwining spirals. We further resolve the structures of native Rubisco as well as its higher-order assembly at near-atomic resolutions by subtomogram averaging. The structures surprisingly reveal that the authentic intrinsically disordered linker protein CsoS2 interacts with Rubiscos in native carboxysomes but functions distinctively in the two α-carboxysomes. In contrast to the uniform Rubisco-CsoS2 association in the Cyanobium α-carboxysome, CsoS2 binds only to the Rubiscos close to the shell in the Halo α-carboxysome. Our findings provide critical knowledge of the assembly principles of α-carboxysomes, which may aid in the rational design and repurposing of carboxysome structures for new functions.

MicroRNA-1224-5p Aggravates Sepsis-Related Acute Lung Injury in Mice.

Oxidative stress and inflammation are implicated in the development of sepsis-related acute lung injury (ALI). MicroRNA-1224-5p (miR-1224-5p) plays critical roles in regulating inflammatory response and reactive oxygen species (ROS) production. The present study is aimed at investigating the role and underlying mechanisms of miR-1224-5p in sepsis-related ALI. Mice were intratracheally injected with lipopolysaccharide (LPS, 5 mg/kg) for 12 h to induce sepsis-related ALI. To manipulate miR-1224-5p level, mice were intravenously injected with the agomir, antagomir, or matched controls for 3 consecutive days. Murine peritoneal macrophages were stimulated with LPS (100 ng/mL) for 6 h to further validate the role of miR-1224-5p in vitro. To inhibit adenosine 5'-monophosphate-activated protein kinase alpha (AMPKα) or peroxisome proliferator activated receptor-gamma (PPAR-γ), compound C or GW9662 was used in vivo and in vitro. We found that miR-1224-5p levels in lungs were elevated by LPS injection, and that the miR-1224-5p antagomir significantly alleviated LPS-induced inflammation, oxidative stress, and ALI in mice. Conversely, the miR-1224-5p agomir aggravated inflammatory response, ROS generation, and pulmonary dysfunction in LPS-treated mice. In addition, the miR-1224-5p antagomir reduced, while the miR-1224-5p agomir aggravated LPS-induced inflammation and oxidative stress in murine peritoneal macrophages. Further findings revealed that miR-1224-5p is directly bound to the 3'-untranslated regions of PPAR-γ and subsequently suppressed PPAR-γ/AMPKα axis, thereby aggravating LPS-induced ALI in vivo and in vitro. We demonstrate for the first time that endogenous miR-1224-5p is a critical pathogenic factor for inflammation and oxidative damage during LPS-induced ALI through inactivating PPAR-γ/AMPKα axis. Targeting miR-1224-5p may help to develop novel approaches to treat sepsis-related ALI.

The 532 nm Laser Treatment Promotes the Proliferation of Tendon-Derived Stem Cells and Upregulates Nr4a1 to Stimulate Tenogenic Differentiation.

Objective: This study aimed to verify the effect of photobiomodulation therapy (PBMT) with a wavelength of 532 nm on the proliferation and differentiation of tendon-derived stem cells (TDSCs) of Sprague-Dawley (SD) rats. Background: The combination of PBMT and stem cell transplantation with TDSCs provides a new treatment strategy for tendon injury. Nevertheless, the effect of PBMT on the biological behavior of TDSCs and its internal mechanisms remain unclear. Methods: TDSCs were isolated from Achilles tendons of SD rats and identified by cell morphology and flow cytometric analysis. Energy density gradient experiment was performed to determine the ideal energy. Then, TDSCs were treated with PBMT using a wavelength of 532 nm at a fluence of 15 J/cm2 in 532 nm laser group, and the TDSC in control group were not treated with 532 nm laser. Cell response after irradiation was observed to ascertain cell morphology and cell proliferation in the 532 nm laser group and the control group. The RNA expression levels of the key genes of TDSC differentiation, including scleraxis (Scx), tenomodulin (Tnmd), Mohawk homeobox (Mkx), Decorin (Dcn), peroxisome proliferator-activated receptor gamma (PPARγ), SRY-box transcription factor 9 (Sox9), and RUNX family transcription factor 2 (Runx2), were detected by reverse transcription-polymerase chain reaction. Then, gene chip microarray was used to detect the expression of differential genes after 532 nm laser intervention in TDSCs, and the target genes were screened out to verify the role in this process in vitro and in vivo. Results: When the 532 nm laser energy density was 15 J/cm2, the proliferation capacity of TDSCs was improved (2.73 ± 0.24 vs. 1.81 ± 0.71, p < 0.05), and the expression of genes related to tenogenic differentiation of TDSCs was significantly increased (p < 0.01). After RNA sequencing and bioinformatics analyses, we speculated that nuclear receptor subfamily 4 group A member 1 (Nr4a1) was involved in the tenogenic differentiation process of TDSCs regulated by 532 nm laser treatment. Subsequent experiments confirmed that Nr4a1 regulated the expression of the tenogenic differentiation genes Scx and Tnmd in TDSCs. Conclusions: A 532 nm laser with 15 J/cm2 regulated the process of TDSC proliferation and upregulated Nr4a1 to stimulate tenogenic differentiation.

Analysis of and Experimental Research on a Hydraulic Traction System Based on a Digital Hydraulic Transformer.

In this study, we designed a new type of digital hydraulic transformer using four gear-pump/motor units with a displacement ratio of 20:21:22:23 and two control valve groups that consist of four solenoid directional valves. The driving gear shafts of the four gear-pump/motor units are fixedly connected to achieve synchronous rotation. The two control valve groups are respectively installed through an integrated valve block on the inlet and outlet of each gear-pump/motor unit. With the objective of reducing the installed power and energy consumption of hydraulic traction systems, we propose a new energy-saving hydraulic system based on a digital hydraulic transformer. This hydraulic system uses a digital hydraulic transformer as a pressure/flow control element. By controlling the power on/off states of eight solenoid directional valves, the digital hydraulic transformer can realize a change in output flow and then a change in speed of the hydraulic cylinder piston rod. Through the theoretical derivation and simulation analysis of the hydraulic system pressure/flow change process, and the experimental verification of the built hydraulic traction system based on the experimental platform, a conclusion is drawn that the proposed digital hydraulic transformer can change the output pressure/flow of a hydraulic system through a binary digital control, verifying the feasibility of the pressure change principle of the designed digital hydraulic transformer and the rationality of the hydraulic traction system circuit.

Structural, Functional and Computational Studies of Membrane Recognition by Plasmodium Perforin-Like Proteins 1 and 2.

Perforin-like proteins (PLPs) play key roles in mechanisms associated with parasitic disease caused by the apicomplexan parasites Plasmodium and Toxoplasma. The T. gondii PLP1 (TgPLP1) mediates tachyzoite egress from cells, while the five Plasmodium PLPs carry out various roles in the life cycle of the parasite and with respect to the molecular basis of disease. Here we focus on Plasmodium vivax PLP1 and PLP2 (PvPLP1 and PvPLP2) compared to TgPLP1. Determination of the crystal structure of the membrane-binding APCß domain of PvPLP1 reveals notable differences with TgPLP1, reflected in its inability to bind lipid bilayers as TgPLP1 and PvPLP2 do. Molecular dynamics simulations combined with site-directed mutagenesis and functional assays allow dissection of the binding interactions of TgPLP1 and PvPLP2 on lipid bilayers, and reveal similar tropisms for lipids enriched in the inner leaflet of the mammalian plasma membrane. In addition PvPLP2 displays a secondary synergistic interaction side-on from its principal bilayer interface. This study underlines the substantial differences between the biophysical properties of the APCß domains of apicomplexan PLPs, which reflect their significant sequence diversity. Such differences will be important factors in determining the cell targeting and membrane-binding activity of the different proteins in parasitic life cycles and disease.

High-resolution in situ structure determination by cryo-electron tomography and subtomogram averaging using emClarity.

Cryo-electron tomography and subtomogram averaging (STA) has developed rapidly in recent years. It provides structures of macromolecular complexes in situ and in cellular context at or below subnanometer resolution and has led to unprecedented insights into the inner working of molecular machines in their native environment, as well as their functional relevant conformations and spatial distribution within biological cells or tissues. Given the tremendous potential of cryo-electron tomography STA in in situ structural cell biology, we previously developed emClarity, a graphics processing unit-accelerated image-processing software that offers STA and classification of macromolecular complexes at high resolution. However, the workflow remains challenging, especially for newcomers to the field. In this protocol, we describe a detailed workflow, processing and parameters associated with each step, from initial tomography tilt-series data to the final 3D density map, with several features unique to emClarity. We use four different samples, including human immunodeficiency virus type 1 Gag assemblies, ribosome and apoferritin, to illustrate the procedure and results of STA and classification. Following the processing steps described in this protocol, along with a comprehensive tutorial and guidelines for troubleshooting and parameter optimization, one can obtain density maps up to 2.8 Å resolution from six tilt series by cryo-electron tomography STA.