Chimeric Peptides from Californiconus californicus and Heterodontus francisci with Antigen-Binding Capacity: A Conotoxin Scaffold to Create Non-Natural Antibodies (NoNaBodies).

Research into various proteins capable of blocking metabolic pathways has improved the detection and treatment of multiple pathologies associated with the malfunction and overexpression of different metabolites. However, antigen-binding proteins have limitations. To overcome the disadvantages of the available antigen-binding proteins, the present investigation aims to provide chimeric antigen-binding peptides by binding a complementarity-determining region 3 (CDR3) of variable domains of new antigen receptors (VNARs) with a conotoxin. Six non-natural antibodies (NoNaBodies) were obtained from the complexes of conotoxin cal14.1a with six CDR3s from the VNARs of Heterodontus francisci and two NoNaBodies from the VNARs of other shark species. The peptides cal_P98Y vs. vascular endothelial growth factor 165 (VEGF165), cal_T10 vs. transforming growth factor beta (TGF-ß), and cal_CV043 vs. carcinoembryonic antigen (CEA) showed in-silico and in vitro recognition capacity. Likewise, cal_P98Y and cal_CV043 demonstrated the capacity to neutralize the antigens for which they were designed.

First pan-specific vNAR against human TGF-ß as a potential therapeutic application: in silico modeling assessment.

Immunotherapies based on antibody fragments have been developed and applied to human diseases, describing novel antibody formats. The vNAR domains have a potential therapeutic use related to their unique properties. This work used a non-immunized Heterodontus francisci shark library to obtain a vNAR with recognition of TGF-ß isoforms. The isolated vNAR T1 selected by phage display demonstrated binding of the vNAR T1 to TGF-ß isoforms (-ß1, -ß2, -ß3) by direct ELISA assay. These results are supported by using for the first time the Single-Cycle kinetics (SCK) method for Surface plasmon resonance (SPR) analysis for a vNAR. Also, the vNAR T1 shows an equilibrium dissociation constant (KD) of 9.61 × 10-8 M against rhTGF-ß1. Furthermore, the molecular docking analysis revealed that the vNAR T1 interacts with amino acid residues of TGF-ß1, which are essential for interaction with type I and II TGF-ß receptors. The vNAR T1 is the first pan-specific shark domain reported against the three hTGF-ß isoforms and a potential alternative to overcome the challenges related to the modulation of TGF-ß levels implicated in several human diseases such as fibrosis, cancer, and COVID-19.

Neutralizing Ability of a Single Domain VNAR Antibody: In Vitro Neutralization of SARS-CoV-2 Variants of Concern.

Severe Acute Respiratory Syndrome Coronavirus 2 is the causal pathogen of coronavirus disease 2019 (COVID-19). The emergence of new variants with different mutational patterns has limited the therapeutic options available and complicated the development of effective neutralizing antibodies targeting the spike (S) protein. Variable New Antigen Receptors (VNARs) constitute a neutralizing antibody technology that has been introduced into the list of possible therapeutic options against SARS-CoV-2. The unique qualities of VNARs, such as high affinities for target molecules, capacity for paratope reformatting, and relatively high stability, make them attractive molecules to counteract the emerging SARS-CoV-2 variants. In this study, we characterized a VNAR antibody (SP240) that was isolated from a synthetic phage library of VNAR domains. In the phage display, a plasma with high antibody titers against SARS-CoV-2 was used to selectively displace the VNAR antibodies bound to the antigen SARS-CoV-2 receptor binding domain (RBD). In silico data suggested that the SP240 binding epitopes are located within the ACE2 binding interface. The neutralizing ability of SP240 was tested against live Delta and Omicron SARS-CoV-2 variants and was found to clear the infection of both variants in the lung cell line A549-ACE2-TMPRSS2. This study highlights the potential of VNARs to act as neutralizing antibodies against emerging SARS-CoV-2 variants.

Memory Effects in Nanolaminates of Hafnium and Iron Oxide Films Structured by Atomic Layer Deposition.

HfO2 and Fe2O3 thin films and laminated stacks were grown by atomic layer deposition at 350 °C from hafnium tetrachloride, ferrocene, and ozone. Nonlinear, saturating, and hysteretic magnetization was recorded in the films. Magnetization was expectedly dominated by increasing the content of Fe2O3. However, coercive force could also be enhanced by the choice of appropriate ratios of HfO2 and Fe2O3 in nanolaminated structures. Saturation magnetization was observed in the measurement temperature range of 5-350 K, decreasing towards higher temperatures and increasing with the films' thicknesses and crystal growth. Coercive force tended to increase with a decrease in the thickness of crystallized layers. The films containing insulating HfO2 layers grown alternately with magnetic Fe2O3 exhibited abilities to both switch resistively and magnetize at room temperature. Resistive switching was unipolar in all the oxides mounted between Ti and TiN electrodes.

Preparation of Immune and Synthetic VNAR Libraries as Sources of High-Affinity Binders.

The shark-derived autonomous variable antibody domains known as VNARs are attractive tools for therapeutic and diagnostic applications due to their favorable properties like small size (approximately 12 kDa), high thermal and chemical stability, and good tissue penetration. Currently, different techniques have been reported to generate VNAR domains against targets of therapeutic interest. Here, we describe methods for the preparation of an immune VNAR library based on bacteriophage display, and for the preparation of a synthetic library of VNAR domains using a modified protocol based on Kunkel mutagenesis. Finally, we describe procedures for in silico maturation of a VNAR using a bioinformatic approach to obtain higher affinity binders.

Structure and Electrical Behavior of Hafnium-Praseodymium Oxide Thin Films Grown by Atomic Layer Deposition.

Crystal structure and electrical properties of hafnium-praseodymium oxide thin films grown by atomic layer deposition on ruthenium substrate electrodes were characterized and compared with those of undoped HfO2 films. The HfO2 reference films crystallized in the stable monoclinic phase of HfO2. Mixing HfO2 and PrOx resulted in the growth of nanocrystalline metastable tetragonal HfO2. The highest relative permittivities reaching 37-40 were measured for the films with tetragonal structures that were grown using HfO2:PrOx cycle ratio of 5:1 and possessed Pr/(Pr + Hf) atomic ratios of 0.09-0.10. All the HfO2:PrOx films exhibited resistive switching behavior. Lower commutation voltages and current values, promising in terms of reduced power consumption, were achieved for the films grown with HfO2:PrOx cycle ratios of 3:1 and 2:1 and showing Pr/(Pr + Hf) atomic ratios of 0.16-0.23. Differently from the undoped HfO2 films, the Pr-doped films showed low variability of resistance state currents and stable endurance behavior, extending over 104 switching cycles.

Standards for the Characterization of Endurance in Resistive Switching Devices.

Resistive switching (RS) devices are emerging electronic components that could have applications in multiple types of integrated circuits, including electronic memories, true random number generators, radiofrequency switches, neuromorphic vision sensors, and artificial neural networks. The main factor hindering the massive employment of RS devices in commercial circuits is related to variability and reliability issues, which are usually evaluated through switching endurance tests. However, we note that most studies that claimed high endurances >106 cycles were based on resistance versus cycle plots that contain very few data points (in many cases even <20), and which are collected in only one device. We recommend not to use such a characterization method because it is highly inaccurate and unreliable (i.e., it cannot reliably demonstrate that the device effectively switches in every cycle and it ignores cycle-to-cycle and device-to-device variability). This has created a blurry vision of the real performance of RS devices and in many cases has exaggerated their potential. This article proposes and describes a method for the correct characterization of switching endurance in RS devices; this method aims to construct endurance plots showing one data point per cycle and resistive state and combine data from multiple devices. Adopting this recommended method should result in more reliable literature in the field of RS technologies, which should accelerate their integration in commercial products.

Atomic layer deposited nanolaminates of zirconium oxide and manganese oxide from manganese(III)acetylacetonate and ozone.

Atomic layer deposition method was used to grow thin films consisting of ZrO2and MnOxlayers. Magnetic and electric properties were studied of films deposited at 300 °C. Some deposition characteristics of the manganese(III)acetylacetonate and ozone process were investigated, such as the dependence of growth rate on the deposition temperature and film crystallinity. All films were partly crystalline in their as-deposited state. Zirconium oxide contained cubic and tetragonal phases of ZrO2, while the manganese oxide was shown to consist of cubic Mn2O3and tetragonal Mn3O4phases. All the films exhibited nonlinear saturative magnetization with hysteresis, as well as resistive switching characteristics.

Silicon oxide-niobium oxide mixture films and nanolaminates grown by atomic layer deposition from niobium pentaethoxide and hexakis(ethylamino) disilane.

Amorphous SiO2-Nb2O5 nanolaminates and mixture films were grown by atomic layer deposition. The films were grown at 300 °C from Nb(OC2H5)5, Si2(NHC2H5)6, and O3 to thicknesses ranging from 13 to 130 nm. The niobium to silicon atomic ratio was varied in the range of 0.11-7.20. After optimizing the composition, resistive switching properties could be observed in the form of characteristic current-voltage behavior. Switching parameters in the conventional regime were well defined only in a SiO2:Nb2O5 mixture at certain, optimized, composition with Nb:Si atomic ratio of 0.13, whereas low-reading voltage measurements allowed recording memory effects in a wider composition range.

Synthetic libraries of shark vNAR domains with different cysteine numbers within the CDR3.

The variable domain of New Antigen Receptors (vNAR) from sharks, present special characteristics in comparison to the conventional antibody molecules such as: small size (12-15 kDa), thermal and chemical stability and great tissue penetration, that makes them a good alternative source as therapeutic or diagnostic agents. Therefore, it is essential to improve techniques used for the development and selection of vNAR antibodies that recognize distinct antigens. The development of synthetic antibody libraries offers a fast option for the generation of antibodies with the desired characteristics. In this work three synthetic antibody libraries were constructed; without cysteines (Cys), with one Cys and with two Cys residues within its CDR3, with the objective of determining whether the presence or absence of Cys in the CDR3 favors the isolation of vNAR clones from a synthetic library. The libraries were validated selecting against six mammalian proteins. At least one vNAR was found for each of the antigens, and a clone coming from the library without Cys in the CDR3 was selected with all the antigens. In vitro angiogenesis assay with the isolated anti-VEGF antibodies, suggest that these vNARs are capable of inhibiting in vitro angiogenesis. In silico analysis of anti-VEGF antibodies showed that vNARs from synthetic libraries could rival antibodies with affinity maturation by in silico modeling.

The Diversified O-Superfamily in Californiconus californicus Presents a Conotoxin with Antimycobacterial Activity.

Californiconus californicus, previously named Conus californicus, has always been considered a unique species within cone snails, because of its molecular, toxicological and morphological singularities; including the wide range of its diet, since it is capable of preying indifferently on fish, snails, octopus, shrimps, and worms. We report here a new cysteine pattern conotoxin assigned to the O1-superfamily capable of inhibiting the growth of Mycobacterium tuberculosis (Mtb). The conotoxin was tested on a pathogen reference strain (H37Rv) and multidrug-resistant strains, having an inhibition effect on growth with a minimal inhibitory concentration (MIC) range of 3.52⁻0.22 µM, similar concentrations to drugs used in clinics. The peptide was purified from the venom using reverse phase high-performance liquid chromatography (RP-HPLC), a partial sequence was constructed by Edman degradation, completed by RACE and confirmed with venom gland transcriptome. The 32-mer peptide containing eight cysteine residues was named O1_cal29b, according to the current nomenclature for this type of molecule. Moreover, transcriptomic analysis of O-superfamily toxins present in the venom gland of the snail allowed us to assign several signal peptides to O2 and O3 superfamilies not described before in C. californicus, with new conotoxins frameworks.

In silico-designed mutations increase variable new-antigen receptor single-domain antibodies for VEGF165 neutralization.

The stability, binding, and tissue penetration of variable new-antigen receptor (VNAR) single-domain antibodies have been tested as part of an investigation into their ability to serve as novel therapeutics. V13 is a VNAR that recognizes vascular endothelial growth factor 165 (VEGF165). In the present study V13 was used as a parental molecule into which we introduced mutations designed in silico. Two of the designed VNAR mutants were expressed, and their ability to recognize VEGF165 was assessed in vitro and in vivo. One mutation (Pro98Tyr) was designed to increase VEGF165 recognition, while the other (Arg97Ala) was designed to inhibit VEGF165 binding. Compared to parental V13, the Pro98Tyr mutant showed enhanced VEGF165 recognition and neutralization, as indicated by inhibition of angiogenesis and tumor growth. This molecule thus appears to have therapeutic potential for neutralizing VEGF165 in cancer treatment.

Atomic layer deposition and properties of ZrO2/Fe2O3 thin films.

Thin solid films consisting of ZrO2 and Fe2O3 were grown by atomic layer deposition (ALD) at 400 °C. Metastable phases of ZrO2 were stabilized by Fe2O3 doping. The number of alternating ZrO2 and Fe2O3 deposition cycles were varied in order to achieve films with different cation ratios. The influence of annealing on the composition and structure of the thin films was investigated. Additionally, the influence of composition and structure on electrical and magnetic properties was studied. Several samples exhibited a measurable saturation magnetization and most of the samples exhibited a charge polarization. Both phenomena were observed in the sample with a Zr/Fe atomic ratio of 2.0.

A workflow for in silico design of hIL-10 and ebvIL-10 inhibitors using well-known miniprotein scaffolds.

The over-expression of immune-suppressors such as IL-10 is a crucial landmark in both tumor progression, and latent viral and parasite infection. IL-10 is a multifunctional protein. Besides its immune-cell suppressive function, it also promotes B-cell tumorigenesis of lymphomas and melanoma. Human pathogens like unicellular parasites and viruses that remain latent inside B cells promote the over-expression of hIL-10 upon infection, which inhibits cell-mediated immune surveillance, and at the same time mediates B cell proliferation. The B-cell specific oncogenic latent virus Epstein-Barr virus (EBV) encodes a viral homologue of hIL-10 (ebvIL-10), expressed during lytic viral proliferation. Once expressed, ebvIL-10 inhibits cell-mediated immune surveillance, assuring EBV re-infection. During long-term latency, EBV-infected B cells over-express hIL-10 to assure B-cell proliferation, occasionally inducing EBV-mediated lymphomas. The amino acid sequences of hIL-10 and ebvIL-10 are more than 80% identical and thus have a very similar tridimensional structure. Based on their published crystallographic structures bound to their human receptor IL10R1, we report a structure-based design of hIL-10 and ebvIL-10 inhibitors based on 3 loops from IL10R1 that establish specific hydrogen bonds with the two IL10s. We have grafted these loops onto a permissible loop in three well-known miniprotein scaffolds-the Conus snail toxin MVIIA, the plant-derived trypsin inhibitor EETI, and the human appetite modulator AgRP. Our computational workflow described in detail below was invigorated by the negative and positive controls implemented, and therefore paves the way for future in vitro and in vivo validation assays of the IL-10 inhibitors engineered.

Magnetic and Electrical Performance of Atomic Layer Deposited Iron Erbium Oxide Thin Films.

Mixed films of a high-permittivity oxide, Er2O3, and a magnetic material, Fe2O3, were grown by atomic layer deposition on silicon and titanium nitride at 375 °C using erbium diketonate, ferrocene, and ozone as precursors. Crystalline phases of erbium and iron oxides were formed. Growth into three-dimensional trenched structures was demonstrated. A structure deposited using tens to hundreds subsequent cycles for both constituent metal oxide layers promoted both charge polarization and saturative magnetization compared to those in the more homogeneously mixed films.

Electrical Characterization of Amorphous Silicon MIS-Based Structures for HIT Solar Cell Applications.

A complete electrical characterization of hydrogenated amorphous silicon layers (a-Si:H) deposited on crystalline silicon (c-Si) substrates by electron cyclotron resonance chemical vapor deposition (ECR-CVD) was carried out. These structures are of interest for photovoltaic applications. Different growth temperatures between 30 and 200 °C were used. A rapid thermal annealing in forming gas atmosphere at 200 °C during 10 min was applied after the metallization process. The evolution of interfacial state density with the deposition temperature indicates a better interface passivation at higher growth temperatures. However, in these cases, an important contribution of slow states is detected as well. Thus, using intermediate growth temperatures (100-150 °C) might be the best choice.

In Silico Identification of Protein Disulfide Isomerase Gene Families in the De Novo Assembled Transcriptomes of Four Different Species of the Genus Conus.

Small peptides isolated from the venom of the marine snails belonging to the genus Conus have been largely studied because of their therapeutic value. These peptides can be classified in two groups. The largest one is composed by peptides rich in disulfide bonds, and referred to as conotoxins. Despite the importance of conotoxins given their pharmacology value, little is known about the protein disulfide isomerase (PDI) enzymes that are required to catalyze their correct folding. To discover the PDIs that may participate in the folding and structural maturation of conotoxins, the transcriptomes of the venom duct of four different species of Conus from the peninsula of Baja California (Mexico) were assembled. Complementary DNA (cDNA) libraries were constructed for each species and sequenced using a Genome Analyzer Illumina platform. The raw RNA-seq data was converted into transcript sequences using Trinity, a de novo assembler that allows the grouping of reads into contigs without a reference genome. An N50 value of 605 was established as a reference for future assemblies of Conus transcriptomes using this software. Transdecoder was used to extract likely coding sequences from Trinity transcripts, and PDI-specific sequence motif "APWCGHCK" was used to capture potential PDIs. An in silico analysis was performed to characterize the group of PDI protein sequences encoded by the duct-transcriptome of each species. The computational approach entailed a structural homology characterization, based on the presence of functional Thioredoxin-like domains. Four different PDI families were characterized, which are constituted by a total of 41 different gene sequences. The sequences had an average of 65% identity with other PDIs. Using MODELLER 9.14, the homology-based three-dimensional structure prediction of a subset of the sequences reported, showed the expected thioredoxin fold which was confirmed by a "simulated annealing" method.