A rapid and sensitive CRISPR-Cas12a for the detection of Fusobacterium nucleatum.

Fusobacterium nucleatum (Fn), as a conditional pathogen, can cause a range of oral and gastrointestinal diseases. However, existing clinical detection methods require expensive equipment and complex procedures, which are inconvenient for large-scale screening in epidemiological research. The purpose of this study was to establish a reliable, rapid, and inexpensive detection method based on CRISPR/Cas12a technology for the detection of Fn. Specific recombinase polymerase amplification (RPA) primer sequences and crRNA sequences were designed based on the nusG gene of Fn. Subsequently, a fluorescence assay and a lateral flow immunoassay were established using the RPA and CRISPR-Cas12a system (RPA-CRISPR-Cas12a). Sensitivity validation revealed a limit of detection of 5 copies/µL. This method could distinguish Fn from other pathogens with excellent specificity. Furthermore, the RPA-CRISPR-Cas12a assay was highly consistent with the classical quantitative real-time PCR method when testing periodontal pocket samples. This makes it a promising method for the detection of Fn and has the potential to play an increasingly important role in infectious disease testing.IMPORTANCEFusobacterium nucleatum (Fn) naturally exists in the microbial communities of the oral and gastrointestinal tracts of healthy individuals and can cause inflammatory diseases in the oral and gastrointestinal tracts. Recent studies have shown that Fn is closely associated with the occurrence and development of gastrointestinal cancer. Therefore, the detection of Fn is very important. Unlike the existing clinical detection methods, this study established a fluorescence-based assay and lateral flow immunoassay based on the RPA and CRISPR-Cas12a system (RPA-CRISPR-Cas12a), which is fast, reliable, and inexpensive and can complete the detection within 30-40 minutes. This makes it a promising method for the detection of Fn and has the potential to play an increasingly important role in infectious disease testing.

Interaction between membrane curvature sensitive factors SpoVM and SpoIVA in Bicelle condition.

SpoVM and SpoIVA are essential proteins for coat assembly in Bacillus subtilis. SpoVM is a membrane curvature sensor, specifically localized on the forespore membrane. SpoIVA is an ATP hydrolase that self-assembles by hydrolyzing ATP. In this work, SpoVM and its mutant SpoVMP9A were obtained by cyanogen bromide cleavage and reconstituted into bicelles. The purification of SpoIVA was achieved through a rigorous process involving Ni-NTA chromatography column and size exclusion chromatography. This study utilized Biacore to obtain a direct determination of the kinetic parameters of interaction between SpoVM (SpoVMP9A) and SpoIVA in Bicelle conditions.

Study on Corrosion Behavior of Porous Pure Copper Based on Electrochemistry and Scanning Kelvin Probe.

Porous metals are widely used in filtration and separation, flame retardant explosion-proof, biomedical application, etc. Compared with its corresponding dense metal, the presence of porous structures also leads to different corrosive performances in porous metal. Some studies have utilized the weight loss method, electrochemical impedance to evaluate porous metal corrosion behavior; however, the influence of pore structure on metal corrosion is still ambiguous, and present methods used for analyses of porous metal corrosion are statistical averages of the corrosion behavior of the entire porous material, which cannot accurately reflect the corrosion behavior inside the pores. Herein, we prepare the porous copper samples with 0, 24, 72, and 96 pores using a mechanical process, and employ scanning Kelvin probe combined with electrochemical polarization and impedance spectroscopy to test the corrosion performance of the porous copper in static and dynamic NaCl solutions. The relevant results indicate that in the static solution, the corrosion resistance of the samples gradually increases with the rise in the number of pores. By contrast, in the dynamic solution, the 24-pore sample is more susceptible to corrosion than the sample without the pore.

A Trimeric Hydrophobic Zipper Mediates the Intramembrane Assembly of SARS-CoV-2 Spike.

The S protein of SARS-CoV-2 is a type I membrane protein that mediates membrane fusion and viral entry. A vast amount of structural information is available for the ectodomain of S, a primary target by the host immune system, but much less is known regarding its transmembrane domain (TMD) and its membrane-proximal regions. Here, we determined the NMR structure of the S protein TMD in bicelles that closely mimic a lipid bilayer. The TMD structure is a transmembrane α-helix (TMH) trimer that assembles spontaneously in a membrane. The trimer structure shows an extensive hydrophobic core along the 3-fold axis that resembles that of a trimeric leucine/isoleucine zipper, but with tetrad, not heptad, repeats. The trimeric core is strong in bicelles, resisting hydrogen-deuterium exchange for weeks. Although highly stable, structural guided mutagenesis identified single mutations that can completely dissociate the TMD trimer. Multiple studies have shown that the membrane anchors of viral fusion proteins can form highly specific oligomers, but the exact function of these oligomers remains unclear. Our findings should guide future experiments to address the above question for SARS coronaviruses.

A trimeric hydrophobic zipper mediates the intramembrane assembly of SARS-CoV-2 spike.

The S protein of the SARS-CoV-2 is a Type I membrane protein that mediates membrane fusion and viral entry. A vast amount of structural information is available for the ectodomain of S, a primary target by the host immune system, but much less is known regarding its transmembrane domain (TMD) and its membrane-proximal regions. Here, we determined the nuclear magnetic resonance (NMR) structure of the S protein TMD in bicelles that closely mimic a lipid bilayer. The TMD structure is a transmembrane α-helix (TMH) trimer that assembles spontaneously in membrane. The trimer structure shows an extensive hydrophobic core along the 3-fold axis that resembles that of a trimeric leucine/isoleucine zipper, but with tetrad, not heptad, repeat. The trimeric core is strong in bicelles, resisting hydrogen-deuterium exchange for weeks. Although highly stable, structural guided mutagenesis identified single mutations that can completely dissociate the TMD trimer. Multiple studies have shown that the membrane anchor of viral fusion protein can form highly specific oligomers, but the exact function of these oligomers remain unclear. Our findings should guide future experiments to address the above question for SARS coronaviruses.

NMR Model of the Entire Membrane-Interacting Region of the HIV-1 Fusion Protein and Its Perturbation of Membrane Morphology.

HIV-1 envelope glycoprotein (Env) is a transmembrane protein that mediates membrane fusion and viral entry. The membrane-interacting regions of the Env, including the membrane-proximal external region (MPER), the transmembrane domain (TMD), and the cytoplasmic tail (CT), not only are essential for fusion and Env incorporation but also can strongly influence the antigenicity of the Env. Previous studies have incrementally revealed the structures of the MPER, the TMD, and the KS-LLP2 regions of the CT. Here, we determined the NMR structure of the full-length CT using a protein fragment comprising the TMD and the CT in bicelles that mimic a lipid bilayer, and by integrating the new NMR data and those acquired previously on other gp41 fragments, we derived a model of the entire membrane-interacting region of the Env. The structure shows that the CT forms a large trimeric baseplate around the TMD trimer, and by residing in the headgroup region of the lipid bilayer, the baseplate causes severe exclusion of lipid in the cytoleaflet of the bilayer. All-atom molecular dynamics simulations showed that the overall structure of the MPER-TMD-CT can be stable in a viral membrane and that a concerted movement of the KS-LLP2 region compensates for the lipid exclusion in order to maintain both structure and membrane integrity. Our structural and simulation results provide a framework for future research to manipulate the membrane structure to modulate the antigenicity of the Env for vaccine development and for mutagenesis studies for investigating membrane fusion and Env interaction with the matrix proteins.

Synergy between vinorelbine and afatinib in the inhibition of non-small cell lung cancer progression by EGFR and p53 signaling pathways.

Currently, epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) were approved for the treatment of non-small cell lung cancer (NSCLC) patients harboring EGFR mutation. However, some lung cancer patients fail to respond and eventually develop drug resistance. Therefore, new therapeutic strategies are needed to improve the outcomes for substantial clinical benefit. Here we aimed to explore the combination of vinorelbine with the second EGFR-TKI afatinib in NSCLC cells with or without EGFR mutation. The three cells of H1975, HCC827, and H460 were assessed for the combination of vinorelbine and afatinib. Vinorelbine combined with afatinib synergistically inhibited the three lung cancer cells growth without aggravating adverse effect on the normal lung cells. The combination of low doses of vinorelbine and afatinib suppressed the cancer cell proliferation by cell colony formation assay and significantly induced cell apoptosis. The anti-apoptotic proteins Bcl-xL and Bcl-2 showed significant reduction after the drug combination treatment, while the pro-apoptotic protein Bax as well as apoptosis indicators cytochrome C and cleaved PARP were observed a notable increasing. EGFR downstream pathways including AKT, ERK, JNK, and p38 were highly active and p53 was inactive in the three lung cancer cells, favoring tumor growth. The low doses of vinorelbine plus afatinib blocked the phosphorylation of AKT, ERK, JNK, and p38, but restored the expression of p53. Our findings suggested that the combination of vinorelbine and afatinib could be recommended as a therapeutic regimen for treatment of NSCLC with or without EGFR mutation.

Effect of Fe substitution on structure and exchange interactions within and between the sublattices of frustrated CoCr2O4.

Obtaining tunable magnetic states in geometrically frustrated multiferroic compound CoCr2O4 by tuning the sublattice magnetic coupling is indeed of high interest from the fundamental and applied points of view. In this work, Fe substitution effects in Co(Cr1-xFex)2O4 (0 ≤ x ≤0.5) are experimentally investigated through detailed measurements of the crystalline structure and magnetization. Our experiments reveal that the samples undergo a magnetic transition characterized by a sharp variation in magnetization from 94 K at x = 0 to 317 K at x = 0.5. The field-cooled process shows that a magnetization reversal phenomenon is observed under a stable positive magnetic field when the measurement undergoes the compensation temperature. A magnetic field-assisted switching effect is realized near the compensation temperature, which possesses the characteristics of high repeatability and stability. The molecular field coefficients are evaluated based on the ferrimagnetic Curie-Weiss fitting, and the exchange interactions within and between the sublattices show a relationship of |JAA| < |JAB| < |JBB|. The magnetization reversal in Co(Cr1-xFex)2O4 is considered to be attributed to the coexistence and competition of A-A, A-B and B-B magnetic interactions, as well as the weakening of spin frustration.

The Diversity and Similarity of Transmembrane Trimerization of TNF Receptors.

Receptors in the tumor necrosis factor receptor superfamily (TNFRSF) regulate proliferation of immune cells or induce programmed cell death, and many of them are candidates for antibody-based immunotherapy. Previous studies on several death receptors in the TNFRSF including Fas, p75NTR, and DR5 showed that the transmembrane helix (TMH) of these receptors can specifically oligomerize and their oligomeric states have direct consequences on receptor activation, suggesting a much more active role of TMH in receptor signaling than previously appreciated. Here, we report the structure of the TMH of TNFR1, another well studied member of the TNFRSF, in neutral bicelles that mimic a lipid bilayer. We find that TNFR1 TMH forms a defined trimeric complex in bicelles, and no evidences of higher-order clustering of trimers have been detected. Unexpectedly, a conserved proline, which is critical for Fas TMH trimerization, does not appear to play an important role in TNFR1 TMH trimerization, which is instead mediated by a glycine near the middle of the TMH. Further, TNFR1 TMH trimer shows a larger hydrophobic core than that of Fas or DR5, with four layers of hydrophobic interaction along the threefold axis. Comparison of the TNFR1 TMH structure with that of Fas and DR5 reveals reassuring similarities that have functional implications but also significant structural diversity that warrants systematic investigation of TMH oligomerization property for other members of the TNFRSF.

Ice- and MOF-templated porous carbonaceous monoliths for adsorptive removal of dyes in water with easy recycling.

Various nanoporous particles, nanofibers have been employed for adsorptive removal of dyes from wastewater. However, these nanomaterials are difficult in separation from solution, generally by centrifugation or filtration. These processes are tedious and will limit the upscale applications. Herein, a hierarchically porous carbon monolith has been fabricated on grounds of ice and metal organic framework (MOF) templating method. The prepared carbonaceous monolith exhibited abundant ice-templated macropores, MOF-templated micropores and mesopores, and a high BET (Brunauer-Emmett-Teller) special surface area (530 m2 g-1). The monolith achieved an MB (methylene blue) adsorption capacity of 95.82 mg g-1 (10 mg adsorbent/5 mL aqueous dye solution) and a theoretic maximum value of 179.86 mg g-1 by the Langmuir model. Compared with MB, the adsorption capacity for MO (methyl orange) was lower. Several adsorption kinetics and isotherms models were used for analysis of adsorptive data, and the results demonstrated the adsorption of MB and MO on the porous carbon monolith is a spontaneous endothermic physisorption process, which was mainly controlled by electrostatic reaction. Importantly, the monolith could be easily picked up using tweezers and used for recycling tests. After four cycles, the 94% of the initial adsorption capacity for MB can be retained.

Anti-tubulin agent vinorelbine inhibits metastasis of cancer cells by regulating epithelial-mesenchymal transition.

Cancer invasion and metastasis are the leading causes of death. The process of metastasis or tumor cell dissemination is still much of a mystery. Emerging evidence has shown that epithelial-mesenchymal transition (EMT) plays a vital role in the progression of malignant tumor including the inducing cell invasion and metastasis as well as promoting drug resistance. Vinorelbine is a traditional chemotherapeutic agent for treatment of lung cancer and breast cancer by the selectivity to mitotic microtubules. The aim of this study was to investigate the effect of vinorelbine on three metastatic cancer cells including lung cancer (H1975), liver cancer (HepG2), and colon cancer (HCT116) cells through inhibition of metastatic abilities and EMT program. Vinorelbine inhibited the cancer cell proliferation by MTT and colony formation assays and inducing G2/M arrest and cell apoptosis via regulation of Bax, Bcl-2, and Bcl-xL. Vinorelbine decrease the migration and invasion ability of the cancer cells by wound healing assay and Tran swell test. The molecular mechanisms of vinorelbine suppressing the metastatic phenotypes of cancer cells through modulation of E-cadherin, N-cadherin, vimentin and transcription factors Snail, MMP-2 and MMP-9. Our results demonstrated that vinorelbine inhibited the cancer cell metastasis through a reduction in metastatic mobility, such as migration, invasion, and the EMT. It provided the evidence that vinorelbine can be used alone or with other agents for treatment of metastatic lung cancer, liver cancer and colon cancer.

Structural basis of transmembrane coupling of the HIV-1 envelope glycoprotein.

The prefusion conformation of HIV-1 envelope protein (Env) is recognized by most broadly neutralizing antibodies (bnAbs). Studies showed that alterations of its membrane-related components, including the transmembrane domain (TMD) and cytoplasmic tail (CT), can reshape the antigenic structure of the Env ectodomain. Using nuclear magnetic resonance (NMR) spectroscopy, we determine the structure of an Env segment encompassing the TMD and a large portion of the CT in bicelles. The structure reveals that the CT folds into amphipathic helices that wrap around the C-terminal end of the TMD, thereby forming a support baseplate for the rest of Env. NMR dynamics measurements provide evidences of dynamic coupling across the TMD between the ectodomain and CT. Pseudovirus-based neutralization assays suggest that CT-TMD interaction preferentially affects antigenic structure near the apex of the Env trimer. These results explain why the CT can modulate the Env antigenic properties and may facilitate HIV-1 Env-based vaccine design.

HIV-1 fusion inhibitors targeting the membrane-proximal external region of Env spikes.

Combination antiretroviral therapy has transformed HIV-1 infection, once a fatal illness, into a manageable chronic condition. Drug resistance, severe side effects and treatment noncompliance bring challenges to combination antiretroviral therapy implementation in clinical settings and indicate the need for additional molecular targets. Here, we have identified several small-molecule fusion inhibitors, guided by a neutralizing antibody, against an extensively studied vaccine target-the membrane proximal external region (MPER) of the HIV-1 envelope spike. These compounds specifically inhibit the HIV-1 envelope-mediated membrane fusion by blocking CD4-induced conformational changes. An NMR structure of one compound complexed with a trimeric MPER construct reveals that the compound partially inserts into a hydrophobic pocket formed exclusively by the MPER residues, thereby stabilizing its prefusion conformation. These results suggest that the MPER is a potential therapeutic target for developing fusion inhibitors and that strategies employing an antibody-guided search for novel therapeutics may be applied to other human diseases.

Size Dependence of the Integral Melting Enthalpy and Entropy of Nanoparticles.

Precise thermodynamic relations to describe the size-dependent integral melting enthalpy and entropy of nanoparticles were deduced by virtue of designing a thermochemical cycle. The differences between integral and differential melting enthalpy and integral and differential melting entropy of nanoparticles were discussed. Nano-Sn of different sizes was prepared by means of chemical reduction, and differential scanning calorimetry (DSC) was utilized to obtain the melting temperature, melting enthalpy, and melting entropy. The experimental results agree with the theoretical predictions and literature results, demonstrating that the melting temperature, enthalpy, and entropy decrease with decreasing particle size and linearly vary with the reciprocal of particle size within the experimental size range. The variations of melting enthalpy and entropy with particle size mainly depend on the molar surface area, the interfacial tension, and the temperature coefficient of interfacial tension. These findings offer a better understanding of the effect of particle size on the melting thermodynamic behaviors of nanoparticles at different melting stages.

Structure determination protocol for transmembrane domain oligomers.

The transmembrane (TM) anchors of cell surface proteins have been one of the 'blind spots' in structural biology because they are generally very hydrophobic, sometimes dynamic, and thus difficult targets for structural characterization. A plethora of examples show these membrane anchors are not merely anchors but can multimerize specifically to activate signaling receptors on the cell surface or to stabilize envelope proteins in viruses. Through a series of studies of the TM domains (TMDs) of immune receptors and viral membrane proteins, we have established a robust protocol for determining atomic-resolution structures of TM oligomers by NMR in bicelles that closely mimic a lipid bilayer. Our protocol overcomes hurdles typically encountered by structural biology techniques such as X-ray crystallography and cryo-electron microscopy (cryo-EM) when studying small TMDs. Here, we provide the details of the protocol, covering five major technical aspects: (i) a general method for producing isotopically labeled TM or membrane-proximal (MP) protein fragments that involves expression of the protein (which is fused to TrpLE) into inclusion bodies and releasing the target protein by cyanogen bromide (CNBr) cleavage; (ii) determination of the oligomeric state of TMDs in bicelles; (iii) detection of intermolecular contacts using nuclear Overhauser effect (NOE) experiments; (iv) structure determination; and (v) paramagnetic probe titration (PPT) to characterize the membrane partition of the TM oligomers. This protocol is broadly applicable for filling structural gaps of many type I/II membrane proteins. The procedures may take 3-6 months to complete, depending on the complexity and stability of the protein sample.

Unidirectional Presentation of Membrane Proteins in Nanoparticle-Supported Liposomes.

Presentation of membrane proteins to host immune systems has been a challenging problem owing to complexity arising from the poor in vivo stability of the membrane-mimetic media often used for solubilizing the membrane proteins. The use of functionalized, biocompatible nanoparticles as substrates is shown to guide the formation of proteoliposomes, which can present many copies of membrane proteins in a unidirectional manner. The approach was demonstrated to present the membrane-proximal region of the HIV-1 envelope glycoprotein. These nanoparticle-supported liposomes are broadly applicable as membrane antigen vehicles for inducing host immune responses.

Higher-Order Clustering of the Transmembrane Anchor of DR5 Drives Signaling.

Receptor clustering on the cell membrane is critical in the signaling of many immunoreceptors, and this mechanism has previously been attributed to the extracellular and/or the intracellular interactions. Here, we report an unexpected finding that for death receptor 5 (DR5), a receptor in the tumor necrosis factor receptor superfamily, the transmembrane helix (TMH) alone in the receptor directly assembles a higher-order structure to drive signaling and that this structure is inhibited by the unliganded ectodomain. Nuclear magnetic resonance structure of the TMH in bicelles shows distinct trimerization and dimerization faces, allowing formation of dimer-trimer interaction networks. Single-TMH mutations that disrupt either trimerization or dimerization abolish ligand-induced receptor activation. Surprisingly, proteolytic removal of the DR5 ectodomain can fully activate downstream signaling in the absence of ligand. Our data suggest a receptor activation mechanism in which binding of ligand or antibodies to overcome the pre-ligand autoinhibition allows TMH clustering and thus signaling.

Structure of the membrane proximal external region of HIV-1 envelope glycoprotein.

The membrane-proximal external region (MPER) of the HIV-1 envelope glycoprotein (Env) bears epitopes of broadly neutralizing antibodies (bnAbs) from infected individuals; it is thus a potential vaccine target. We report an NMR structure of the MPER and its adjacent transmembrane domain in bicelles that mimic a lipid-bilayer membrane. The MPER lies largely outside the lipid bilayer. It folds into a threefold cluster, stabilized mainly by conserved hydrophobic residues and potentially by interaction with phospholipid headgroups. Antigenic analysis and comparison with published images from electron cryotomography of HIV-1 Env on the virion surface suggest that the structure may represent a prefusion conformation of the MPER, distinct from the fusion-intermediate state targeted by several well-studied bnAbs. Very slow bnAb binding indicates that infrequent fluctuations of the MPER structure give these antibodies occasional access to alternative conformations of MPER epitopes. Mutations in the MPER not only impede membrane fusion but also influence presentation of bnAb epitopes in other regions. These results suggest strategies for developing MPER-based vaccine candidates.

Determination Method and Size Dependence of Interfacial Tension between Nanoparticles and a Solution.

Interfacial tension plays an important role in the processes of preparation, research, and application of nanomaterials. Because the interfacial tension is fairly difficult to be determined by experiments, it is still unclear about the effect of particle size on interfacial tension. In this paper, we proposed a method to determine the interfacial tensions and its temperature coefficients by determining the electrode potential of the nanoparticle electrode. Nano-Au with different radii (from 0.9 to 37.4 nm) in an aqueous solution was taken as a research system; we determined the interfacial tension and its temperature coefficient of the interface and discussed the size dependence. At the same time, we found surprisingly that this method can also be applied to determine the Tolman length and the atomic radius. The results show that the particle size of nano-Au has remarkable influences on the interfacial tension and its temperature coefficient. As the particle size decreases, the interfacial tension and the absolute value of its temperature coefficient increase. With the decrease of radius, the influences of the particle size on the interfacial tension and its temperature coefficient become more significant, whereas the influences can be neglected when the radius exceeds 10 nm. In addition, the results also show that the Tolman length is a negative value, and temperature has little effect on the Tolman length. This research can provide a new method to conveniently and reliably determine the interfacial tension on interfaces between nanoparticles and solutions, the temperature coefficients, the Tolman lengths, and the atomic radii; and the size dependences can provide important references for preparation, research, and application of nanomaterials.

Stability and Water Accessibility of the Trimeric Membrane Anchors of the HIV-1 Envelope Spikes.

HIV-1 envelope spike (Env) is a type I membrane protein that mediates viral entry. Recent studies showed that its transmembrane domain (TMD) forms a trimer in lipid bilayer whose structure has several peculiar features that remain difficult to explain. One is the presence of an arginine R696 in the middle of the TM helix. Additionally, the N- and C-terminal halves of the TM helix form trimeric cores of opposite nature (hydrophobic and hydrophilic, respectively). Here we determined the membrane partition and solvent accessibility of the TMD in bicelles that mimic a lipid bilayer. Solvent paramagnetic relaxation enhancement analysis showed that the R696 is indeed positioned close to the center of the bilayer, but, surprisingly, can exchange rapidly with water as indicated by hydrogen-deuterium exchange measurements. The solvent accessibility of R696 is likely mediated by the hydrophilic core, which also showed fast water exchange. In contrast, the N-terminal hydrophobic core showed extremely slow solvent exchange, suggesting the trimer formed by this region is extraordinarily stable. Our data explain how R696 is accommodated in the middle of the membrane while reporting the overall stability of the Env TMD trimer in lipid bilayer.