ARTICLE | doi:10.20944/preprints202210.0134.v1
Subject: Medicine And Pharmacology, Obstetrics And Gynaecology Keywords: endometriosis; endometrium; ErbB receptors; immunoprecipitation; implantation stage; infertility
Online: 11 October 2022 (03:30:29 CEST)
Several lines of evidence indicate that high proliferative bias in eutopic endometrium during secretory phase is a hallmark of endometriosis and that high occurrence of implantation failure in patients resulting in infertility is often associated with endometriosis. ErbB family of proteins, which regulate the proliferation capacity in mammalian cells, appear as potential group of proteins to cause higher proliferation and endometrial hostility to implantation process in endometriosis. However, we have no concrete knowledge regarding the involvement of ErbB family in human endometrium during the ‘implantation window’, i.e., days 20-24 of a typical ovulatory cycle in endometriosis associated infertility. In the present study, the cellular profiles of immunopositive ErbBs-1 to -4 in endometrium of endometriosis-free, infertile women (Group 1; n=11), and in eutopic endometrium of infertile women diagnosed with stage IV ovarian endometriosis (Group 2; n=13) during mid-secretory phase were examined and compared using standardized WERF EPHect guidelines. Computer-aided standardized combinative analysis of immunoprecipitation in different compartments revealed an overexpression of ErbB-1 in the epithelial, stromal and vascular compartments along with marginally higher ErbB-3 expressions (P< 0.06) in the vascular compartment and ErbB-4 expression (P< 0.05) in the glandular epithelium and stroma in endometrium during the window of implantation of women with primary infertility associated with stage IV ovarian endometriosis compared with disease-free endometrium from women. A global overexpression of ErbB-1 in the endometrium during implantation window may induce anomalous proliferative, inflammatory and angiogenic activities in it, which antagonizes endometrial preparation for embryo implantation.
ARTICLE | doi:10.20944/preprints202303.0253.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: ASFV; humoral responses; ASFV capsid proteins; ASFV vaccines; ASFV immunity; antigen discovery; luciferase antibody capture assay; luciferase immunoprecipitation assay; viral hemorrhagic fever.
Online: 14 March 2023 (09:43:57 CET)
African swine fever (ASF) is a lethal disease in pigs that has grave socio-economic implications worldwide. For the development of vaccines against African swine fever virus (ASFV), immunogenic antigens that generate protective immune responses need to be identified. There are over 150 viral proteins - many of which are uncharacterized – and humoral immunity to ASFV has not been closely examined. To profile antigen specific antibody responses, we developed luciferase-linked antibody capture assays (LACAs) for a panel of ASFV capsid proteins and screened sera from inbred and outbred animals that were previously immunized with low virulent ASFV before challenge with virulent ASFV. Antibodies to B646L/p72, D117L/p17, M1249L and E120R/p14.5 were detected in this study; however, we were unable to detect B438L specific antibodies. Although OURT88/1 induced viremia was observed in the presence of anti-B646L/p72 antibodies as well as B602L antibodies they were associated with recovery from lethal disease in inbred and outbred animals. However, these antibodies did not correlate with protection against Georgia 2007/1 infection. Antibody responses against M1249L and E120R/p14.5 were observed in animals with reduced clinical signs and viremia. Here we present LACAs as a tool for targeted profiling of antigen specific antibody responses to inform vaccine development.
ARTICLE | doi:10.20944/preprints202311.1617.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Chromatin immunoprecipitation followed by sequencing; transcription factors binding sites prediction; cooperative binding of transcription factors; motifs conservation; classification of transcription factors; direct binding of transcription factors
Online: 27 November 2023 (07:26:54 CET)
(1) Background: Transcription factors (TFs) are main regulators of eukaryotic gene expression. The cooperative binding of at least two TFs to genomic DNA is the widespread mechanism of transcription regulation. Massive analysis of co-occurrence of overrepresented pairs of motifs (composite elements, CEs) for different target TFs studied in ChIP-seq experiments can clarify the mechanisms of TF cooperation. (2) Methods: We focused on homotypic CEs representing the same motif models and considered only CEs with spacers. We improved the capability of the Motifs Co-Occurrence Tool (MCOT) to predict asymmetric homotypic CEs in which one of par-ticipating motifs has higher conservation than the other. We categorized the target TFs from the data of M. musculus ChIP-seq and A. thaliana ChIP-seq/DAP-seq according to the structure of DNA-binding domains (DBDs) into classes. (3) Results: For all TF classes the predominance of asymmetric CEs over both symmetric and those with no enrichment in both directions was re-vealed. Target TFs from classes Basic helix-loop-helix factors (bHLH) and Basic leucine zipper factors (bZIP) showed the highest fractions of datasets with asymmetric CEs. We showed that pioneer TFs, despite their DBD types, have a higher significance of asymmetry within homotyp-ic CEs compared to other TFs. (4) Conclusion: Asymmetry within homotypic CEs is a promising new feature decrypting the mechanisms of gene transcription regulation.
ARTICLE | doi:10.20944/preprints201904.0205.v1
Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: antibody coating; proximity-enhanced reaction; immunoglobulins; IgG; protein A; protein G; bio-interaction; immunoprecipitation; pull-down assay; immunocapture; stabilization; yield; regeneration; nanoparticles; microparticles; biochips; immunosensor; photochemical crosslinker; click chemistry; herceptin; trastuzumab
Online: 18 April 2019 (07:55:11 CEST)
Crosslinking of proteins for their irreversible immobilization on surfaces is a proven and popular method. However, many protocols lead to random orientation and the formation of undefined or even inactive by-products. Most concepts to obtain a more targeted conjugation or immobilization requires the recombinant modification of at least one binding partner, which is often impractical or prohibitively expensive. Here a novel method is presented, which is based on the chemical preactivation of Protein A or G with selected conventional crosslinkers. In a second step, the antibody is added, which is subsequently crosslinked in the Fc part. This leads to an oriented and covalent immobilization of the immunoglobulin with a very high yield. Protocols for Protein A and Protein G with murine and human IgG are presented. This method may be useful for the preparation of columns for affinity chromatography, immunoprecipitation, antibodies conjugated to magnetic particles, permanent and oriented immobilization of antibodies in biosensor systems, microarrays, microtitration plates or any other system, where the loss of antibodies needs to be avoided, and maximum binding capacity is desired. This method is directly applicable even to antibodies in crude cell culture supernatants, raw sera or protein-stabilized antibody preparations without any purification nor enrichment of the IgG. This new method delivered much higher signals as a traditional method and, hence, seems to be preferable in many applications.
ARTICLE | doi:10.20944/preprints202208.0004.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: protein affinity enrichment; bioseparation; immunoprecipitation; immunocapture; affinity chro-matography; solid phase; carrier; material; corundum; polyglycerol; aromatic amino acid analysis; self-assembled monolayers (SAM), periodate oxidation; reductive amination; antibodies; IgG; im-munoglobulins; glutaraldehyde; polyglycerol; hyperbranched polymer
Online: 1 August 2022 (04:42:41 CEST)
Nonporous corundum powder, known as an abrasive material in the industry, was functionalized covalently with protein binders to isolate and enrich specific proteins from complex matrices. The materials based on corundum were characterized by TEM, ESEM, BET, DLS, and zeta potential measurements. The strong Al-O-P bonds between the corundum surface and amino phosphonic acids are used to introduce functional groups for further conjugations. The common crosslinker glutaraldehyde was compared with a hyperbranched polyglycerol (PG) of around 10 kDa. The latter is oxidized with periodate to generate aldehyde groups that can covalently react with the amines of the surface and the amino groups from the protein via a reductive amination process. The amount of bound protein was quantified via aromatic amino acid analysis (AAAA). This work shows that oxidized polyglycerol can be used as an alternative to glutaraldehyde. With polyglycerol, more of the model protein bovine serum albumin (BSA) could be attached to the surface under the same conditions, and lower nonspecific binding (NSB) was observed. As a proof of concept, IgG was extracted with protein A from crude human plasma. The purity of the product was examined by SDS-PAGE. A binding capacity of 1.8 mg IgG per g of corundum powder was achieved. The advantages of corundum are the very low price, extremely high physical and chemical stability, pressure resistance, favorable binding kinetics, and flexible application.
ARTICLE | doi:10.20944/preprints202007.0639.v2
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: chromatin immunoprecipitation with massively parallel sequencing, transcription factors binding sites prediction; cooperative binding of transcription factors; composite elements; motifs conservation; classification of transcription factors; ETS transcription factor family; direct binding of transcription factors; overlap of motifs
Online: 20 August 2020 (13:43:09 CEST)
Background: Transcription factors (TFs) are main regulators of eukaryotic gene expression. The cooperative binding to genomic DNA of at least two TFs is the widespread mechanism of transcription regulation. Cooperating TFs can be revealed through the analysis of co-occurrence of their motifs. Methods: We applied Motifs Co-Occurrence Tool (MCOT) that predicted pairs of spaced or overlapped motifs (composite elements, CEs) for a single ChIP-seq dataset. We improved MCOT capability for prediction of asymmetric CEs with one of participating motifs possessing higher conservation than another does. Results: Analysis of 119 ChIP-seq datasets for 45 human TFs revealed that almost for all families of TFs the co-occurrence with an overlap between motifs of target TFs and more conserved partner motifs was significantly higher than that for less conserved partner motifs. The asymmetry toward partner TFs was the most clear for partner motifs of TFs from ETS family. Conclusion: Co-occurrence with an overlap of less conserved motif of a target TF and more conserved motifs of partner TFs explained a substantial portion of ChIP-seq data lacking conserved motifs of target TFs. Among other TF families, conservative motifs of TFs from ETS family were the most prone to mediate interaction of target TFs with its weak motifs in ChIP-seq.