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-β), 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-β 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-β isoforms. The isolated vNAR T1 selected by phage display demonstrated binding of the vNAR T1 to TGF-β isoforms (-β1, -β2, -β3) 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 (K_D) of 9.61 × 10^-8 M against rhTGF-β1. Furthermore, the molecular docking analysis revealed that the vNAR T1 interacts with amino acid residues of TGF-β1, which are essential for interaction with type I and II TGF-β receptors. The vNAR T1 is the first pan-specific shark domain reported against the three hTGF-β isoforms and a potential alternative to overcome the challenges related to the modulation of TGF-β 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.

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.

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 MnO_xlayers. 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.

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.

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.

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.

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.

Autofluorescence as a tool to study mucus secretion in Eisenia foetida

Autofluorescence in living cells is due to the presence of endogenous substances that emit fluorescence upon excitation by incidental light. A type of fluorescence, bioluminescence, has been suggested to be linked to mucus secretion in earthworms; however, the origin and the physiological function of this fluorescence are not clear. The aims of this work were to describe autofluorescence in the earthworm Eisenia foetida by SEM, CLSM, and fluorescence microscopy and to examine the possible mechanism of mucus secretion by video microscopy. Earthworms were stimulated either chemically or electrically to induce the secretion of yellow mucus, which was subsequently studied by video microscopy. Mucus was released from the body wall and near the mouth. This phenomenon was associated with autofluorescence and involved at least four distinct stages: release of vesicles, formation of granules, muscular contraction, and organization of strands. The fluorescent molecules were stored in vesicles bound to the membranes. These vesicles were intact when shed from the body. The vesicles were stable but also changed to a granular material or formed strands. Video analyses demonstrated that secretion was dependent on the type of stimulus.

Sites of action of segmental and descending control of transmission on pathways mediating PAD of Ia- and Ib-afferent fibers in cat spinal cord

The present series of investigations was aimed to disclose the possible sites of action of excitatory and inhibitory inputs on tho-interneuron pathway mediating the primary afferent depolarization (PAD) of group I afferents of extensor muscles in the cat spinal cord. To this end we compared the effects produced by stimulation of segmental and descending pathways on the PAD generated either by stimulation of group I fibers of flexor muscles or by intraspinal microstimulation. It was assumed that under the appropriate conditions the PAD produced by intraspinal microstimulation results from the activation of the last-order interneurons in the PAD pathway and may, therefore, allow detection pathway. The PAD of single group I afferent fibers was determined in barbiturate-anesthetized preparations by measuring the test stimulus current required to maintain a constant probability of antidromic firing. This was achieved by means of a feedback system that continuously adjusted the test stimulus current to the required values. The PAD of individual group Ia gastrocnemius soleus (GS) fibers that is produced by activation of the low-threshold afferents of the posterior biceps and semitendinosus nerve was found to be inhibited by conditioning stimulation of the relatively low-threshold cutaneous fibers and also by stimulation of supraspinal structures such as the ipsilateral brain stem reticular formation, the contralateral red nucleus, and the contralateral pyramidal tract. In contrast, the PAD of group Ia fibers produced by microstimulation applied in the intermediate nucleus could be inhibited only by stimulation of the brain stem reticular formation but not by stimulation of the other descending inputs presently tested or by stimulation of cutaneous nerves. PAD of group Ia fibers was produced also by microstimulation applied within the motor nucleus. However, in most fibers the resulting PAD could not be inhibited either by stimulation of the brain stem reticular formation, the red nucleus, the pyramidal tract, or cutaneous nerves. Stimulation of cutaneous and of flexor muscle nerves of the brain stem reticular formation, the red nucleus, and the pyramidal tract all produced PAD of the group Ib GS fibers.(ABSTRACT TRUNCATED AT 400 WORDS)