Modelling the interplay of SARS-CoV-2 variants in the United Kingdom.

Many COVID-19 vaccines are proving to be highly effective to prevent severe disease and to diminish infections. Their uneven geographical distribution favors the appearance of new variants of concern, as the highly transmissible Delta variant, affecting particularly non-vaccinated people. It is important to device reliable models to analyze the spread of the different variants. A key factor is to consider the effects of vaccination as well as other measures used to contain the pandemic like social behaviour. The stochastic geographical model presented here, fulfills these requirements. It is based on an extended compartmental model that includes various strains and vaccination strategies, allowing to study the emergence and dynamics of the new COVID-19 variants. The model conveniently separates the parameters related to the disease from the ones related to social behavior and mobility restrictions. We applied the model to the United Kingdom by using available data to fit the recurrence of the currently prevalent variants. Our computer simulations allow to describe the appearance of periodic waves and the features that determine the prevalence of certain variants. They also provide useful predictions to help planning future vaccination boosters. We stress that the model could be applied to any other country of interest.

Strategies for COVID-19 vaccination under a shortage scenario: a geo-stochastic modelling approach.

In a world being hit by waves of COVID-19, vaccination is a light on the horizon. However, the roll-out of vaccination strategies and their influence on the pandemic are still open questions. In order to compare the effect of various strategies proposed by the World Health Organization and other authorities, a previously developed SEIRS stochastic model of geographical spreading of the virus is extended by adding a compartment for vaccinated people. The parameters of the model were fitted to describe the pandemic evolution in Argentina, Mexico and Spain to analyze the effect of the proposed vaccination strategies. The mobility parameters allow to simulate different social behaviors (e.g. lock-down interventions). Schemes in which vaccines are applied homogeneously in all the country, or limited to the most densely-populated areas, are simulated and compared. The second strategy is found to be more effective. Moreover, under the current global shortage of vaccines, it should be remarked that immunization is enhanced when mobility is reduced. Additionally, repetition of vaccination campaigns should be timed considering the immunity lapse of the vaccinated (and recovered) people. Finally, the model is extended to include the effect of isolation of detected positive cases, shown to be important to reduce infections.

Detecting infected asymptomatic cases in a stochastic model for spread of Covid-19: the case of Argentina.

We have studied the dynamic evolution of the Covid-19 pandemic in Argentina. The marked heterogeneity in population density and the very extensive geography of the country becomes a challenge itself. Standard compartment models fail when they are implemented in the Argentina case. We extended a previous successful model to describe the geographical spread of the AH1N1 influenza epidemic of 2009 in two essential ways: we added a stochastic local mobility mechanism, and we introduced a new compartment in order to take into account the isolation of infected asymptomatic detected people. Two fundamental parameters drive the dynamics: the time elapsed between contagious and isolation of infected individuals ([Formula: see text]) and the ratio of people isolated over the total infected ones (p). The evolution is more sensitive to the [Formula: see text]parameter. The model not only reproduces the real data but also predicts the second wave before the former vanishes. This effect is intrinsic of extensive countries with heterogeneous population density and interconnection.The model presented has proven to be a reliable predictor of the effects of public policies as, for instance, the unavoidable vaccination campaigns starting at present in the world an particularly in Argentina.

Reduction in CYP1A1 and 2B2 activity at low oxygen tension.

The Cytochrome P450 (CYP) enzyme family comprises a wide array of monooxygenases involved in the oxidation of endobiotic and xenobiotic molecules. The active site of a CYP enzyme contains an iron protoporphyrin center coordinated to a cysteine thiolate, and then, molecular oxygen is associated with the iron to be converted into dioxygen complex plus substrate. Reduction by CYP reductase expedites hydroxylation of the compound. In this oxidation reaction, insufficient oxygen molecules would affect enzyme catalysis. Nevertheless, biochemical data about CYP kinetics at low oxygen concentrations are not available. In this work, we present the results on the variation in rat liver microsomal CYP Vmax app and Km app under normal and hypoxic conditions. Using alkoxyresorufin molecules as substrates, the Vmax/Km ratios for resorufin production decreased from 426 to 393 for CYP1A1 and from 343 to 202 for CYP2B1 at a low oxygen concentration (4.1 ppm) compared to the ratios observed at a normal oxygen concentration (6.5 ppm). Additionally, the bacterial mutagenicity of 2-aminoanthracene and cyclophosphamide, decreased by 32% and 42%, respectively, at low oxygen concentrations. These results support the hypothesis that low oxygen availability is implicated in the low efficiency of substrate oxidation by CYP.

Novel amyloid-beta specific scFv and VH antibody fragments from human and mouse phage display antibody libraries.

Anti-amyloid immunotherapy has been proposed as an appropriate therapeutic approach for Alzheimer's disease (AD). Significant efforts have been made towards the generation and assessment of antibody-based reagents capable of preventing and clearing amyloid aggregates as well as preventing their synaptotoxic effects. In this study, we selected a novel set of human anti-amyloid-beta peptide 1-42 (Abeta1-42) recombinant monoclonal antibodies in a single chain fragment variable (scFv) and a single-domain (VH) format. We demonstrated that these antibody fragments recognize in a specific manner amyloid-beta deposits in APP/Tg mouse brains, inhibit toxicity of oligomeric Abeta1-42 in neuroblastoma cell cultures in a concentration-dependent manner and reduced amyloid deposits in APP/Tg2576 mice after intracranial administration. These antibody fragments recognize epitopes in the middle/C-terminus region of Abeta, which makes them strong therapeutic candidates due to the fact that most of the Abeta species found in the brains of AD patients display extensive N-terminus truncations/modifications.

Immunodominant epitope and properties of pyroglutamate-modified Abeta-specific antibodies produced in rabbits.

N-truncated and N-modified forms of amyloid beta (Abeta) peptide are found in diffused and dense core plaques in Alzheimer's disease (AD) and Down's syndrome patients as well as transgenic mouse models of AD. Although the pathological significance of these shortened forms Abeta is not completely understood, previous studies have demonstrated that these peptides are significantly more resistant to degradation, aggregate more rapidly in vitro and exhibit similar or, in some cases, increased toxicity in hippocampal neuronal cultures compared to the full length peptides. In the present study we further investigated the mechanisms of toxicity of one of the most abundant N-truncated/modified Abeta peptide bearing amino-terminal pyroglutamate at position 3 (AbetaN3(pE)). We demonstrated that AbetaN3(pE) oligomers induce phosphatidyl serine externalization and membrane damage in SH-SY5Y cells. Also, we produced AbetaN3(pE)-specific polyclonal antibodies in rabbit and identified an immunodominant epitope recognized by anti-AbetaN3(pE) antibodies. Our results are important for developing new immunotherapeutic compounds specifically targeting AbetaN3(pE) aggregates since the most commonly used immunogens in the majority of vaccines for AD have been shown to induce antibodies that recognize the N-terminal immunodominant epitope (EFRH) of the full length Abeta, which is absent in N-amino truncated peptides.

Epitope mapping and neuroprotective properties of a human single chain FV antibody that binds an internal epitope of amyloid-beta 1-42.

Active and passive immunotherapy targeted at the amyloid-beta (Abeta) peptide has been proposed as therapeutic approach against Alzheimer's disease (AD), and efforts towards the generation and application of antibody-based reagents that are capable of preventing and clearing amyloid aggregates are currently under active investigation. Previously, we selected and characterized a new anti-Abeta1-42 phage-displayed scFv antibody, designated clone b4.4, using a non-immune human scFv antibody library and demonstrated that a peptide based on the sequence of the Ig heavy chain (VH) complementarity-determining region (HCDR3) of this antibody fragment bound to Abeta1-42)and had neuroprotective potential against Abeta1-42 mediated neurotoxicity in rat hippocampal cultured neurons. In the present study, using novel computational methods and in vitro experiments we demonstrated that b4.4 binds to the central region of Abeta1-42. We also demonstrated that this scFv antibody binds to Abeta-derived diffusible ligands (ADDLs) and neutralizes the toxicity of both fibrillar and oligomeric forms of Abeta1-42 tested in vitro in SH-SY5Y cell cultures.

Human single chain Fv antibodies and a complementarity determining region-derived peptide binding to amyloid-beta 1-42.

A library of phage-displayed human single-chain Fv (scFv) antibodies was selected against the human amyloid-beta peptide (Abeta42). Two new anti-Abeta42 phage-displayed scFvs antibodies were obtained, and the sequences of their V(H) and Vkappa genes were analyzed. A synthetic peptide based on the sequence of Ig heavy chain (V(H)) complementarity-determining region (HCDR3) of the clone with the highest recognition signal was generated and determined to bind to Abeta42 in ELISA. Furthermore, we showed for the first time that an HCDR3-based peptide had neuroprotective potential against Abeta42 neurotoxicity in rat cultured hippocampal neurons. Our results suggest that not only scFvs recognizing Abeta42 but also synthetic peptides based on the V(H) CDR3 sequences of these antibodies may be novel potential candidates for small molecule-based Alzheimer's disease (AD) therapy.

Amyloid-beta peptide-specific single chain Fv antibodies isolated from an immune phage display library.

A single-chain fragment variable (scFv) antibody library displayed on phage was constructed using spleen cells from mice immunized with human amyloid-beta peptide (Abeta42). This first anti-Abeta42 scFv immune antibody library was selected against human Abeta42. A number of positive clones were obtained, and sequences of VH and Vkappa genes were analyzed using ExPASy and BLAST computer tools. This analysis revealed that only two unique clones with identical VH and Vkappa complementarity determining region (CDR) (except HCDR2) and identical germline genes were selected, indicating that oligoclonal immune response was occurring in Abeta42-immunized mice. Abeta42-specific scFv antibodies selected from this first immune anti-Abeta42 phage antibody library may be an important tool for the development of therapeutic molecules for Alzheimer's disease (AD).

Identification of peptide sequences specific for serum antibodies from human papillomavirus-infected patients using phage display libraries.

Three random phage display peptide libraries were screened with sera from human papillomavirus (HPV)-infected patients to characterize the specificities of antibodies present in patients' sera and to identify molecules that correspond to or mimic natural epitopes; 141 phage clones were randomly selected in three rounds of bioselection and their binding properties were analyzed in ELISA using sera from 36 patients with confirmed HPV 16 infection and 24 healthy control female blood donors. Sixteen of 36 (44%) patients' sera reacted with at least 1 phage clone, and only 2 of 24 female donors' sera showed positive reaction with 1 of the selected clones. We conclude that the combination of various disease-specific epitopes generated by screening of phage display peptide libraries may potentially lead to a multicomponent diagnostic assay for the early detection of HPV infection and precancerous cervical lesions, making possible the prevention of one of the most common cancers in women.

Intraspleen DNA inoculation elicits protective cellular immune responses.

DNA immunization or inoculation is a recent vaccination method that induces both humoral and cellular immune responses in a range of hosts. Independent of the route or site of vaccination, the transfer of antigen-presenting cells (APC) or antigens into lymphoid organs is necessary. The aim of this investigation was to test whether intraspleen (i.s.) DNA inoculation is capable of inducing a protective immune response. We immunized mice by a single i.s. injection of a DNA construct expressing the immunoglobulin (Ig) heavy-chain variable domain (VH) in which the complementarity-determining regions (CDR) had been replaced by a Taenia crassiceps T-cell epitope. In these mice, immune responses and protective effects elicited by the vaccine were measured. We have shown here for the first time that i.s. DNA inoculation can induce protective cellular immune responses and activate CD8(+) T cells. Also, Ig V(H) appeared to be the minimal delivery unit of "antigenized" Ig capable of inducing T-cell activation in a lymphoid organ. The strategy of introducing T-cell epitopes into the molecular context of the V(H) domain in combination with i.s. DNA immunization could have important implications and applications for human immunotherapy.

Kinetics and characterization of cellular responses in the peritoneal cavity of mice infected with Taenia crassiceps.

Changes in the leukocyte population of the peritoneal cavity ensue immediately after infection with Taenia crassiceps metacestodes. Basophils and neutrophils decrease, whereas macrophages, monocytes, and lymphocytes increase to reach only modest levels by 6 wk and then diminish to nearly disappear by 15 wk when the parasite begins rapid reproduction. Eosinophils also appear early in infection, but then abate to lower levels that persist. In late infections, when the mass of cysticerci equals that of the mouse, the cysticerci grow among surprisingly few inflammatory cells. Mingling with the peritoneal inflammatory cells is a number of odd-looking cells that could correspond to the metaplasic mesothelial cells of the host or be of parasite origin. These cells are multinucleated, they aggregate in varigerated clusters, and form cystic structures in vitro; they also bind specific anti-T. crassiceps antibodies and specific T. crassiceps DNA probes in their nuclei. When the peritoneal cell exudate is reinjected intraperitoneally into naive mice, the odd-looking cells subsist for months, inducing in the host the synthesis of specific anti-T. crassiceps antibodies and immune resistance to challenge but do not reassemble into cysticerci even after 6 mo of inoculation. The early appearance and the immunogenic and antigenic properties of these odd-looking cells suggest they are important protagonists in the early host-parasite confrontation when the outcome of infection is set.

Identification of mimotopes of platelet autoantigens associated with autoimmune thrombocytopenic purpura.

GPIIb/IIIa, the human platelet glycoprotein complex, is the autoantigen most commonly recognized by autoantibodies in autoimmune thrombocytopenic purpura (AITP). Two murine monoclonal antibodies (mAbs), namely Y2/51 and 5B12, directed against gpIIIa and gpIIb/IIIa, respectively, and rabbit anti-human platelet polyclonal antibodies have been used to select AITP-related epitopes from a phage display peptide library expressing random dodecapeptides in the pIII coat protein of M13 phage. The selected phage clones were tested by ELISA for binding to rabbit anti-human platelet antibodies as well as to sera from AITP patients. Seven clones reacted strongly with rabbit anti-human platelet antibodies, and four clones reacted with sera from AITP patients. Some homology between peptide inserts sequences of selected clones and human platelet gpIIIa and gpIb were found.

Taenia crassiceps cysticercosis: a role for prostaglandin E2 in susceptibility.

Several biological factors are involved in susceptibility and resistance to murine cysticercosis. A substantial body of evidence implies prostaglandins as potent regulators of immune responses during parasitic diseases. Here we evaluated the role played by prostaglandin E2 in cysticercosis. Mice were treated in vivo with prostaglandin E2 or with indomethacin (a prostaglandin E2 synthesis inhibitor) before infection. Parasite growth was enhanced by prostaglandin treatment, which provoked poor Con-A responses, low Th1-type cytokines secretion, and high levels of IL-6 and IL-10. In contrast, mice receiving indomethacin showed a reduction in parasite load parallel to a strong Con-A response and high levels of IL-2 and IFN-gamma, concomitantly with a decrease in IL-4, IL-6 and IL-10 production. Indirect in vitro studies suggest that an important source of prostaglandin E2 production could be related to host's adherent cells. However, prostaglandin E2 from parasite origin cannot be discarded.

DNA pulsed macrophage-mediated cDNA expression library immunization in vaccine development.

cDNA expression library immunization (cDELI), based on the use of a large number of pathogen's cDNA clones, has been previously used in our laboratory in an experimental model of murine Taenia crassiceps cysticercosis. In this study we show that ex vivo immunization of mice with macrophages pulsed in vitro with plasmid DNA containing cDNA expression library (2x10(4) clones) leads to significant reduction of parasite load. Additionally, pathogen-specific proliferation of splenocytes from immunized mice is demonstrated indicating the induction of cellular protective immune response and the efficacy of the proposed strategy to identify vaccine candidate antigens. Our method may represent an attractive tool in vaccine discovery applicable to any host-pathogen system and may be useful especially for the pathogens with large genomes and complicated life cycles.

Phage-displayed T-cell epitope grafted into immunoglobulin heavy-chain complementarity-determining regions: an effective vaccine design tested in murine cysticercosis.

A new type of immunogenic molecule was engineered by replacing all three complementarity-determining-region (CDR) loops of the human immunoglobulin (Ig) heavy-chain variable (V(H)) domain with the Taenia crassiceps epitope PT1 (PPPVDYLYQT) and by displaying this construct on the surfaces of M13 bacteriophage. When BALB/c mice were immunized with such phage particles (PIgphage), a strong protection against challenge infection in very susceptible female hosts was obtained. When specifically stimulated, the in vivo-primed CD4(+) and CD8(+) T cells isolated from mice immunized with PT1, both as a free peptide and as the PIgphage construct, proliferated in vitro, indicating efficient epitope presentation by both major histocompatibility complex class II and class I molecules in the specifically antigen-pulsed macrophages used as antigen-presenting cells. These data demonstrate the immunogenic potential of recombinant phage particles displaying CDR epitope-grafted Ig V(H) domains and establish an alternative approach to the design of an effective subunit vaccine for prevention of cysticercosis. The key advantage of this type of immunogen is that no adjuvant is required for its application. The proposed strategy for immunogen construction is potentially suitable for use in any host-pathogen interaction.

[Numerical analysis of western blot digitalized images. The case of HIV]. / Análisis numérico de imágenes digitalizadas de western blot. El caso del VIH.

The present work explores the use of image digitalization of western blot (WB) aiming to extract more information about the humoral immune response of human immunodeficiency virus (HIV) infected individuals, and to analyze obtained data in a multivariate manner. The digitalization and analysis of WB images was performed on 115 sera. Images were analyzed either qualitatively: dendogram and principal component analysis (PCA) or quantitatively: PCA of the total bands, taking either the antigens, which belong to the virus, or only those which do not. Results show the feasibility of mechanical diagnosis of a large number of WB images. The dendogram and the qualitative PCA satisfactorily separated white images, images with less than four bands, and images with more complex patterns. Quantitative analysis, which keeps more information, separated the images of negative, undetermined and positive diagnosis quite precisely. It was also found that the positive images with complex patterns of antigen recognition correlate better with asymptomatic individuals. Image analysis also revealed various other bands in WB which do not seem to correspond to viral proteins and could represent autoantigens or crossed antigens between HIV and humans which may cause autoimmunity. Digital analysis of WB images is thus demonstrated to be of great usefulness in the diagnosis and of potential great interest in following the evolution and exploring the pathogenesis of AIDS.

Protection against murine cysticercosis using cDNA expression library immunization.

Genetic or DNA-based immunization, including genomic immunization, has shown to be a viable alternative approach to induce protective immunity against a number of pathogens in several disease models. Here we describe a new method, cDNA expression library immunization (cDELI), based on the use of a large number of cDNA clones. This immunization strategy was tested in experimental murine Taenia crassiceps cysticercosis model. A partial cDNA expression library of 2 x 10(4) members was constructed in eukaryotic expression vector pcDNA3 and used to immunize BALB/c female mice subcutaneously (s.c.) and intramuscularly (i.m.). In both cases significant reduction of parasite load (up to 65%) was obtained. We were unable to directly measure T. crassiceps-specific humoral immune response in any of the immunized mice, although the expression of pathogen proteins in vitro in macrophages transfected with cDNA expressing plasmids was demonstrated. Also, in three out of five randomly selected immunized mice detectable levels of interferon-gamma (IFN-gamma) were obtained. cDELI has additional advantages compared with recently developed single gene or genomic immunization approaches because a cDNA population represents only those genes that are being expressed in the pathogen cells and the selection of stage-specific antigens is possible. The use of cDELI could be particularly attractive for the pathogens with complicated life cycles and large genomes.

Identification of autoimmune thrombocytopenic purpura-related epitopes using phage-display peptide library.

A random heptapeptide phage-displayed library was screened with two serum samples from autoimmune thrombocytopenic purpura (AITP) patients to address the repertoire of autoantigenic epitopes involved in platelet destruction. We obtained a panel of affinity-selected phage clones that have been shown to react in enzyme-linked immunosorbent assay with autoantibodies from other AITP patients. None of the peptides obtained has been described previously as possibly being an epitope for antiplatelet antibodies, and the majority of them did not show any homology with known platelet glycoproteins. We conclude that peptides identified in this study could represent discontinuous epitopes or mimotopes of natural autoantigens. Also, they could be present in still-unknown proteins involved in AITP pathogenesis.

Depressed immunity to a Salmonella typhimurium vaccine in mice experimentally parasitized by Taenia crassiceps.

To assess the immunological status of mice parasitized with Taenia crassiceps metacestodes, 6-month old female BALB/c mice experimentally parasitized with T. crassiceps and immunized with Salmonella typhimurium antigens were infected with S. typhimurium virulent bacilli (1.6 x LD50). Both T. crassiceps-parasitized and immunized and parasitized mice showed a very high susceptibility to infection (**P < 0.01) with higher bacteremia than control and immunized-control animals and produced a reduced IgG response to S. typhimurium, antigens (* P < 0.05). This indicates that T. crassiceps is able to preclude development of immunity to S. typhimurium, because appropriate antibody production to a heterologous antigenic stimulus did not take place, and the bacteremia results suggest the parasitosis altered the mononuclear phagocyte system. It has been demonstrated that Taenia solium metacestodes produce a small RNA molecule in culture which suppresses humoral and cellular responses against homologous antigens in mice. We propose that T. crassiceps may be actively synthesizing such a factor, apart from other simultaneously acting immunomodulatory mechanisms, to induce an immunosuppressed state favorable to its development in the host.