SIV Viral Variation; Implications for Vaccines and Transmission
PART 1 Viral diversity at mucosal transmission
-determine if vaginal SIV inoculation of rhesus macaques
recapitulates HIV-1 variant transmission
PART 2 Viral diversity in vaccine setting
-Characterize the replication levels and anatomic distribution of vaccine (SHIV 89.6) and challenge (SIVmac239) virus in monkeys prior to and after challenge.
-Characterize evolution of SIV env population complexity of SIV DNA in PBMC of SHIV immunized and control animals
Recombinant low-seroprevalent adenoviral vectors Ad26 and Ad35Arun kumar
RSV is an important cause of lower respiratory tract infections in children, the elderly and in those with
underlying medical conditions. Although the high disease burden indicates an urgent need for a vaccine
against RSV, no licensed RSV vaccine is currently available. We developed an RSV vaccine candidate
based on the low-seroprevalent human adenovirus serotypes 26 and 35 (Ad26 and Ad35) encoding the
RSV fusion (F) gene. Single immunization of mice with either one of these vectors induced high titers of
RSV neutralizing antibodies and high levels of F specific interferon-gamma-producing T cells. A Th1-type
immune response was indicated by a high IgG2a/IgG1 ratio of RSV-specific antibodies, strong induction
of RSV-specific interferon-gamma and tumor necrosis factor-alpha cytokine producing CD8 Tcells, and
low RSV-specific CD4 T-cell induction. Both humoral and cellular responses were increased upon a boost
with RSV-F expressing heterologous adenovirus vector (Ad35 boost after Ad26 prime or vice versa). Both
single immunization and prime-boost immunization of cotton rats induced high and long-lasting RSV
neutralizing antibody titers and protective immunity against lung and nasal RSV A2 virus load up to at
least 30 weeks after immunization. Cotton rats were also completely protected against challenge with
a RSV B strain (B15/97) after heterologous prime-boost immunization. Lungs from vaccinated animals
showed minimal damage or inflammatory infiltrates post-challenge, in contrast to animals vaccinated
with formalin-inactivated virus. Our results suggest that recombinant human adenoviral Ad26 and Ad35
vectors encoding the RSV F gene have the potential to provide broad and durable protection against RSV
in humans, and appear safe to be investigated in infants.
This document describes the development of reporter Dengue virus (DENV) strains that express green fluorescent protein (GFP) or firefly luciferase (Fluc). The reporter DENV strains were characterized in vitro and in vivo. In vitro, the reporter DENV strains were infectious, sensitive to antiviral compounds and interferons, and allowed screening of a library of interferon-stimulated genes. In vivo bioluminescence imaging in mice revealed that DENV localized predominantly to lymphoid and gut tissues. A mutation (NS4B L52F) was required to confer virulence of the reporter DENV strain in mice. The reporter DENV strains provide a platform for applications such as antiviral discovery and vaccine validation.
Creative Biogene provides world-class packaging services for a variety of viral types using our QVirusTM platform. Creative Biogene's state-of-the-art facilities and highly experienced staff are available in order to assist in all areas of virus vector design and construction, as well as the generation of the virus in a quick turnaround. Our custom viral services are highlighted by a consistent high titer and large delivery viral counts.
Vancomycin Resistance Genes in Various Organisms- An Insilico StudyCSCJournals
Abstract Glycopeptide antibiotics are widely used to treat many serious infections caused by gram positive bacteria particularly, methicillin resistant Enterococci and Staphyllococcus sp. Emergence of commonly acquired resistance in bacterial pathogens has lead to clinical complications and threat to human health. The resistance in these organisms is conferred by several Van genes like VanA, VanB, VanD, VanC and VanM. Knowledge of presence of Van genes in various organisms was felt necessary prior to molecular investigation. Therefore, in this insilico study the DNA sequence information was used and screening was carried out for Van gene sequences. Results indicate that many pathogenic and non-pathogenic bacteria, fungal, viral and protozoan pathogens, other organisms like fishes, mammals possess Van like sequences. The present findings provide first hand information on extent of Vancomycin antibiotic resistance in many organisms and emphasize further investigation of the significance of these genes using molecular and bioinformatics tools to help minimize human sufferings.
1. A study analyzed genetic and immune response differences between P. vivax circumsporozoite (CS) genotypes VK210 and P. vivax-like.
2. Phylogenetic analysis of 18S rRNA and CytB genes found high similarity between the genotypes, with zero nucleotide diversity, placing them in the same clade.
3. Individuals infected with P. vivax-like had a lower antibody response against CS repetitive region peptides than those with VK210, suggesting variation is limited to the CS repetitive region.
Alexander Gold - CAEV Literature Review for IndustryAlexander Gold
Caprine Arthritis Encephalitis Virus (CAEV) is a lentivirus that infects goats and causes arthritis, mastitis, and encephalitis. It is transmitted from mother goats to kids through colostrum and milk. While infection can also occur in utero or through contact, milk-borne transmission is the primary route. The virus infects white blood cells and travels to joints, mammary glands, and brain tissue, causing inflammation and disease. Diagnosis is through ELISA antibody tests and PCR DNA detection. There is no treatment, so control relies on identification and separation of infected animals.
The document summarizes efforts to develop an HIV vaccine by inducing broadly neutralizing antibodies (bnAbs) through structure-based immunogen design. It describes how bnAbs isolated from infected individuals can inform design of immunogens that expose conserved vulnerabilities on HIV. Challenges include guiding antibody maturation along pathways to bnAbs and understanding how bnAbs develop naturally. Ongoing work includes defining HIV vulnerabilities with additional bnAbs and structures, understanding natural bnAb responses, epitope-directed and trimer-based immunogen design, and evaluating immunogens in collaboration between multiple research institutions. The goal is to develop an HIV vaccine to help curb the global AIDS pandemic.
Porcine Reproductive and Respiratory Syndrome Viruskkrimetz
This document summarizes information about Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), including its history, etiology, prevalence, risk factors, transmission, immune response, pathogenesis, clinical signs, diagnosis, treatment, control and prevention. PRRSV causes reproductive losses and respiratory disease in pigs. It is endemic in many pig herds worldwide. Control and prevention strategies include vaccination, biosecurity measures, and managing exposure to reduce stress.
Recombinant low-seroprevalent adenoviral vectors Ad26 and Ad35Arun kumar
RSV is an important cause of lower respiratory tract infections in children, the elderly and in those with
underlying medical conditions. Although the high disease burden indicates an urgent need for a vaccine
against RSV, no licensed RSV vaccine is currently available. We developed an RSV vaccine candidate
based on the low-seroprevalent human adenovirus serotypes 26 and 35 (Ad26 and Ad35) encoding the
RSV fusion (F) gene. Single immunization of mice with either one of these vectors induced high titers of
RSV neutralizing antibodies and high levels of F specific interferon-gamma-producing T cells. A Th1-type
immune response was indicated by a high IgG2a/IgG1 ratio of RSV-specific antibodies, strong induction
of RSV-specific interferon-gamma and tumor necrosis factor-alpha cytokine producing CD8 Tcells, and
low RSV-specific CD4 T-cell induction. Both humoral and cellular responses were increased upon a boost
with RSV-F expressing heterologous adenovirus vector (Ad35 boost after Ad26 prime or vice versa). Both
single immunization and prime-boost immunization of cotton rats induced high and long-lasting RSV
neutralizing antibody titers and protective immunity against lung and nasal RSV A2 virus load up to at
least 30 weeks after immunization. Cotton rats were also completely protected against challenge with
a RSV B strain (B15/97) after heterologous prime-boost immunization. Lungs from vaccinated animals
showed minimal damage or inflammatory infiltrates post-challenge, in contrast to animals vaccinated
with formalin-inactivated virus. Our results suggest that recombinant human adenoviral Ad26 and Ad35
vectors encoding the RSV F gene have the potential to provide broad and durable protection against RSV
in humans, and appear safe to be investigated in infants.
This document describes the development of reporter Dengue virus (DENV) strains that express green fluorescent protein (GFP) or firefly luciferase (Fluc). The reporter DENV strains were characterized in vitro and in vivo. In vitro, the reporter DENV strains were infectious, sensitive to antiviral compounds and interferons, and allowed screening of a library of interferon-stimulated genes. In vivo bioluminescence imaging in mice revealed that DENV localized predominantly to lymphoid and gut tissues. A mutation (NS4B L52F) was required to confer virulence of the reporter DENV strain in mice. The reporter DENV strains provide a platform for applications such as antiviral discovery and vaccine validation.
Creative Biogene provides world-class packaging services for a variety of viral types using our QVirusTM platform. Creative Biogene's state-of-the-art facilities and highly experienced staff are available in order to assist in all areas of virus vector design and construction, as well as the generation of the virus in a quick turnaround. Our custom viral services are highlighted by a consistent high titer and large delivery viral counts.
Vancomycin Resistance Genes in Various Organisms- An Insilico StudyCSCJournals
Abstract Glycopeptide antibiotics are widely used to treat many serious infections caused by gram positive bacteria particularly, methicillin resistant Enterococci and Staphyllococcus sp. Emergence of commonly acquired resistance in bacterial pathogens has lead to clinical complications and threat to human health. The resistance in these organisms is conferred by several Van genes like VanA, VanB, VanD, VanC and VanM. Knowledge of presence of Van genes in various organisms was felt necessary prior to molecular investigation. Therefore, in this insilico study the DNA sequence information was used and screening was carried out for Van gene sequences. Results indicate that many pathogenic and non-pathogenic bacteria, fungal, viral and protozoan pathogens, other organisms like fishes, mammals possess Van like sequences. The present findings provide first hand information on extent of Vancomycin antibiotic resistance in many organisms and emphasize further investigation of the significance of these genes using molecular and bioinformatics tools to help minimize human sufferings.
1. A study analyzed genetic and immune response differences between P. vivax circumsporozoite (CS) genotypes VK210 and P. vivax-like.
2. Phylogenetic analysis of 18S rRNA and CytB genes found high similarity between the genotypes, with zero nucleotide diversity, placing them in the same clade.
3. Individuals infected with P. vivax-like had a lower antibody response against CS repetitive region peptides than those with VK210, suggesting variation is limited to the CS repetitive region.
Alexander Gold - CAEV Literature Review for IndustryAlexander Gold
Caprine Arthritis Encephalitis Virus (CAEV) is a lentivirus that infects goats and causes arthritis, mastitis, and encephalitis. It is transmitted from mother goats to kids through colostrum and milk. While infection can also occur in utero or through contact, milk-borne transmission is the primary route. The virus infects white blood cells and travels to joints, mammary glands, and brain tissue, causing inflammation and disease. Diagnosis is through ELISA antibody tests and PCR DNA detection. There is no treatment, so control relies on identification and separation of infected animals.
The document summarizes efforts to develop an HIV vaccine by inducing broadly neutralizing antibodies (bnAbs) through structure-based immunogen design. It describes how bnAbs isolated from infected individuals can inform design of immunogens that expose conserved vulnerabilities on HIV. Challenges include guiding antibody maturation along pathways to bnAbs and understanding how bnAbs develop naturally. Ongoing work includes defining HIV vulnerabilities with additional bnAbs and structures, understanding natural bnAb responses, epitope-directed and trimer-based immunogen design, and evaluating immunogens in collaboration between multiple research institutions. The goal is to develop an HIV vaccine to help curb the global AIDS pandemic.
Porcine Reproductive and Respiratory Syndrome Viruskkrimetz
This document summarizes information about Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), including its history, etiology, prevalence, risk factors, transmission, immune response, pathogenesis, clinical signs, diagnosis, treatment, control and prevention. PRRSV causes reproductive losses and respiratory disease in pigs. It is endemic in many pig herds worldwide. Control and prevention strategies include vaccination, biosecurity measures, and managing exposure to reduce stress.
Kimberly Carter evaluated the efficacy of multivalent virus-like particle (VLP) antigens in enzyme-linked immunosorbent assays (ELISAs) for detecting antibodies against infectious bursal disease virus (IBDV) strains. Multivalent VLPs containing VP3, a classic strain pVP2, and a variant strain pVP2 were produced. ELISAs using these antigens yielded positive results at low serum dilutions but not higher dilutions. Antigens containing a single VP3 and pVP2 appeared more effective. While multivalent VLP ELISAs showed some ability to detect antibodies, commercial ELISA kits still need testing for superior performance.
1. RNA viruses like SFV and VSV are effective oncolytic viruses but their replication is inhibited by type I interferons, limiting their efficacy.
2. Vaccinia virus has greater potential as an oncolytic virus because it produces a protein called B18R that allows it to evade type I interferon inhibition.
3. The study shows that vaccinia virus or B18R can boost the replication of RNA viruses like SFV and VSV in cancer cells by overcoming the antiviral effects of type I interferons. This dual viral therapy leads to enhanced oncolytic activity.
Virus-like particles (VLPs) are non-infectious nanoparticles that resemble viruses but lack the viral genome. They are formed through the self-assembly of viral structural proteins. VLPs mimic the structure of viruses and can effectively deliver antigens and stimulate immune responses, making them a promising platform for vaccine development. VLP vaccines in clinical trials include ones against HPV, malaria, influenza, and HIV. VLPs can also be used to deliver therapeutic proteins to cells for applications such as cancer treatment.
Presented by Etienne de Villiers at the African Swine Fever Diagnostics, Surveillance, Epidemiology and Control Workshop, Nairobi, Kenya, 20-21 July 2011
This document summarizes work to construct an infectious clone of the squirrel monkey strain of simian foamy virus (SFVsqu). The researchers amplified fragments of the SFVsqu genome using PCR and plan to fuse the fragments together using Gibson assembly to generate a full-length circular viral genome. This cloned genome can then be transfected into mammalian cells to produce virus particles and allow study of the viral lifecycle. The researchers acknowledge funding sources and cite relevant references. Construction of this infectious clone will enable future study of how the human immune system responds to infection with New World Monkey strains of SFV.
This document discusses adenoviral cloning vectors. It begins by defining a cloning vector as a small piece of DNA that can be stably maintained in an organism and have foreign DNA inserted into it for cloning purposes. It then discusses viral vectors, noting that they are commonly used to deliver genetic material into cells through transduction. The document focuses on properties of viral vectors, specifically safety features and targeting abilities. It provides details on adenoviruses, noting they can efficiently transfer genes, their structure, applications in gene therapy and vaccination, and their DNA genome capacity. Adeno-associated viruses are also mentioned as attractive for gene therapy due to mild immune response.
Genomic surveillance of the Rift Valley fever: From sequencing to Lineage ass...ILRI
Poster prepared John Juma, Vagner Fonseca, Samson Limbaso, Peter van Heusden, Kristina Roesel, Bernard Bett, Rosemary Sang, Alan Christoffels, Tulio de Oliveira and Samuel Oyola for the Kenya One Health Online Conference, 6-8 December 2021
Global repeated replacement of bacterial symbionts by fungal pathogens in cic...erg55
This document summarizes research on symbiotic relationships between cicadas and bacteria or fungi. The research found that in some cicada species, the bacterial symbiont Hodgkinia has been replaced at least 16 times by fungal pathogens from the genus Ophiocordyceps. These fungal pathogens then take on the role of the bacterial symbiont. Additionally, the complexity and fragmentation of Hodgkinia does not seem to correlate with likelihood of replacement by the fungal symbiont. Host diversification and changes in co-primary symbiont evolution also do not consistently correlate with Hodgkinia complexity or symbiont shifts. Further research is needed to better understand the patterns and prevalence of symbiont
Virus-like particles (VLPs) have significant applications in veterinary vaccine research. VLPs mimic the structure of viruses but lack the viral genome, making them non-infectious and safer vaccine candidates. There are three main types of VLP structures: monolayered non-enveloped VLPs composed of a single capsid protein, multilayered non-enveloped VLPs composed of multiple capsid proteins, and enveloped VLPs containing viral surface proteins embedded in a membrane. VLPs induce strong humoral and cellular immune responses through repetitive epitopes on their surface. They can also serve as carriers to present foreign epitopes and induce immunity against heterologous pathogens
This document discusses a thesis presented by Priyanka Rughwani to the USC Graduate School examining factors that contribute to outcomes of Staphylococcus aureus bacteremia. The introduction provides background on the increasing incidence of S. aureus infections including methicillin-resistant S. aureus. It describes how S. aureus has developed resistance to multiple antibiotic classes and discusses the role of virulence factors and their impact on infection outcomes. The study aims to analyze the contribution of microbial resistance and virulence factors like agr functionality, protein A, and extracellular adherence protein towards persistent SAB or death.
This document reviews the current status of natural virus resistance genes and prospects for deploying these genes against virus infections. It discusses dominant resistance genes that confer monogenic resistance through recognition of viral avirulence factors. To date, 12 examples have been characterized that fall into the nucleotide binding site-leucine rich repeat class. Recessive resistance genes that cause impaired susceptibility by disrupting host factors required for virus infection are also described. These include mutations in translation initiation factors that cause resistance to various potyviruses and other viruses. Advances in genomics and molecular techniques are improving prospects for identifying and utilizing natural virus resistance genes in crop breeding programs.
This document summarizes a presentation on applying replication-defective West Nile virus vectors to non-flavivirus vaccine targets. The presentation discusses how flavivirus genomes are highly immunogenic and effective vaccines. It describes a methodology where envelope proteins from other viruses were expressed in place of structural proteins from West Nile virus, eliciting antibody and T-cell responses. Some challenges discussed are production issues, efficiency, stability, and dosage requirements. References are provided on using defective flaviviruses for vaccine development and characterization of the RepliVax vaccine platform.
This document describes a study conducted at Los Alamos National Laboratory to investigate the evolution of influenza A virus (IAV) under artificial selection pressure. The researchers engineered host cells to express IAV proteins and infected these "supplemented" cells with IAV over multiple passages. They hypothesized that the virus would evolve to efficiently infect the supplemented cells while losing ability to infect unmodified cells. Preliminary results found measurable viral replication in supplemented cells expressing one IAV protein (PB1C1) over generations, but limited replication in cells expressing another protein (M1), suggesting it may interfere with virion packaging. The goal is to better understand viral evolution and identify novel antiviral strategies.
Adenovirus, a DNA virus, was first isolated in the 1950s in adenoid tissue-derived cell cultures, hence the name. A large number of acute respiratory, gastrointestinal and eye infections in humans are caused by adenoviruses.
https://www.creative-biogene.com/Support/Virus.html
Adenoviruses are DNA viruses that are powerful research tools for investigating cellular events and can infect a wide range of mammalian cells with high efficiency, making them a versatile vector for gene delivery and expression. Creative Biogene is a biotechnology company that offers custom adenovirus services including vector design, construction, amplification, and purification to produce high-titer recombinant adenoviruses for use in research applications both in vitro and in vivo. Their services streamline the adenovirus production process which can otherwise be time-consuming and labor-intensive for researchers.
Oncolytic viruses(OVs)are viral strains that can infect and kill malignant cells without harming normal cells, while simultaneously stimulate the immune system and creating system antitumor immunity. Oncolytic viruses have become one of the aglare immunotherapies that have been extensively studied and developed.
Creative Biolabs is a world-renowned service provider for immunotherapy. Taking advantage of the OncoVirapy™ platform, Creative Biolabs provides a comprehensive overview on the basic biology that support OVs as cancer therapeutic agents, including properties of inherent and engineered oncolytic viruses, mechanisms of viral targeting cancer cells, mechanisms of action of viruses killing cancer cells (induction of local and systemic anti-tumor immunity). Based on this basic knowledge review, we hope you can have a comprehensive understanding of OVs and quickly capture one of the frontiers of immunotherapy research.
This document discusses a meta-analysis of multiple datasets examining features of viral RNA that correlate with activation of the innate immune system. The analysis found that "A" nucleotide content and minimum folding energy (MFE) were good predictors of immune system activation, more so than other proposed indicators like CpG enrichment. As RNA composition and structure are correlated, further experiments using synthetic sequences are needed to identify the specific viral RNA sensing mechanisms of immune system receptors.
- Comprehensive peptide libraries were designed for immune profiling of Zika virus and related flaviviruses like dengue virus.
- The libraries include PepStar peptide arrays for profiling humoral immune responses using minimal serum, and PepMix peptide pools for stimulating antigen-specific T cell responses.
- The libraries were designed using bioinformatics to select peptides providing optimal coverage of sequence diversity within and between viruses. The libraries have been used to monitor immune responses to Zika virus vaccine candidates in animal studies.
Five attenuated Francisella novicida transposon mutants (with mutations corresponding to dsbB, FTT0742, pdpB, fumA, and carB in F. tularensis) were identified that provided protection against challenge with over 8 x 105 CFU of wild-type F. novicida in mice. The mutants were screened by examining their ability to grow in mouse macrophages and their virulence in mice. These attenuated mutants were then tested for their ability to protect mice against challenge with high doses of wild-type bacteria. The findings from this study could be useful in the design of a vaccine against tularemia.
The study aimed to recapitulate key findings from the Phase IIb Step Trial of a Merck Ad5 HIV-1 vaccine in rhesus macaques. Rhesus macaques were infected with Ad5hr and immunized with an Ad5 SIV vaccine or empty vector. They were then challenged with escalating doses of penile SIV exposure. The Ad5 SIV vaccine induced CD8+ T cell responses in 70% of monkeys, similar to humans in the Step Trial, but did not protect against SIV infection. At the lowest SIV dose, 2/9 Ad5-seropositive monkeys immunized with the Ad5 SIV vaccine became infected compared to 0/34 in
Dr. X.J. Meng - Designing PRRSV Vaccines for Heterologous ProtectionJohn Blue
1) PRRSV remains a major problem for the global swine industry, causing $664 million in losses annually in the US alone. The emergence of more virulent strains and heterogeneity have complicated vaccine development.
2) DNA shuffling techniques are being used to generate chimeric PRRSV vaccines containing structural genes from multiple heterologous strains, which have shown promise in inducing cross-neutralizing antibodies and protection against diverse strains.
3) Targeting shuffled PRRSV antigens to dendritic cells through DC-SIGN enhances antigen-specific CD4+ and CD8+ T cell immune responses in pigs. These approaches aim to overcome obstacles in developing a broadly protective PRRSV vaccine.
Kimberly Carter evaluated the efficacy of multivalent virus-like particle (VLP) antigens in enzyme-linked immunosorbent assays (ELISAs) for detecting antibodies against infectious bursal disease virus (IBDV) strains. Multivalent VLPs containing VP3, a classic strain pVP2, and a variant strain pVP2 were produced. ELISAs using these antigens yielded positive results at low serum dilutions but not higher dilutions. Antigens containing a single VP3 and pVP2 appeared more effective. While multivalent VLP ELISAs showed some ability to detect antibodies, commercial ELISA kits still need testing for superior performance.
1. RNA viruses like SFV and VSV are effective oncolytic viruses but their replication is inhibited by type I interferons, limiting their efficacy.
2. Vaccinia virus has greater potential as an oncolytic virus because it produces a protein called B18R that allows it to evade type I interferon inhibition.
3. The study shows that vaccinia virus or B18R can boost the replication of RNA viruses like SFV and VSV in cancer cells by overcoming the antiviral effects of type I interferons. This dual viral therapy leads to enhanced oncolytic activity.
Virus-like particles (VLPs) are non-infectious nanoparticles that resemble viruses but lack the viral genome. They are formed through the self-assembly of viral structural proteins. VLPs mimic the structure of viruses and can effectively deliver antigens and stimulate immune responses, making them a promising platform for vaccine development. VLP vaccines in clinical trials include ones against HPV, malaria, influenza, and HIV. VLPs can also be used to deliver therapeutic proteins to cells for applications such as cancer treatment.
Presented by Etienne de Villiers at the African Swine Fever Diagnostics, Surveillance, Epidemiology and Control Workshop, Nairobi, Kenya, 20-21 July 2011
This document summarizes work to construct an infectious clone of the squirrel monkey strain of simian foamy virus (SFVsqu). The researchers amplified fragments of the SFVsqu genome using PCR and plan to fuse the fragments together using Gibson assembly to generate a full-length circular viral genome. This cloned genome can then be transfected into mammalian cells to produce virus particles and allow study of the viral lifecycle. The researchers acknowledge funding sources and cite relevant references. Construction of this infectious clone will enable future study of how the human immune system responds to infection with New World Monkey strains of SFV.
This document discusses adenoviral cloning vectors. It begins by defining a cloning vector as a small piece of DNA that can be stably maintained in an organism and have foreign DNA inserted into it for cloning purposes. It then discusses viral vectors, noting that they are commonly used to deliver genetic material into cells through transduction. The document focuses on properties of viral vectors, specifically safety features and targeting abilities. It provides details on adenoviruses, noting they can efficiently transfer genes, their structure, applications in gene therapy and vaccination, and their DNA genome capacity. Adeno-associated viruses are also mentioned as attractive for gene therapy due to mild immune response.
Genomic surveillance of the Rift Valley fever: From sequencing to Lineage ass...ILRI
Poster prepared John Juma, Vagner Fonseca, Samson Limbaso, Peter van Heusden, Kristina Roesel, Bernard Bett, Rosemary Sang, Alan Christoffels, Tulio de Oliveira and Samuel Oyola for the Kenya One Health Online Conference, 6-8 December 2021
Global repeated replacement of bacterial symbionts by fungal pathogens in cic...erg55
This document summarizes research on symbiotic relationships between cicadas and bacteria or fungi. The research found that in some cicada species, the bacterial symbiont Hodgkinia has been replaced at least 16 times by fungal pathogens from the genus Ophiocordyceps. These fungal pathogens then take on the role of the bacterial symbiont. Additionally, the complexity and fragmentation of Hodgkinia does not seem to correlate with likelihood of replacement by the fungal symbiont. Host diversification and changes in co-primary symbiont evolution also do not consistently correlate with Hodgkinia complexity or symbiont shifts. Further research is needed to better understand the patterns and prevalence of symbiont
Virus-like particles (VLPs) have significant applications in veterinary vaccine research. VLPs mimic the structure of viruses but lack the viral genome, making them non-infectious and safer vaccine candidates. There are three main types of VLP structures: monolayered non-enveloped VLPs composed of a single capsid protein, multilayered non-enveloped VLPs composed of multiple capsid proteins, and enveloped VLPs containing viral surface proteins embedded in a membrane. VLPs induce strong humoral and cellular immune responses through repetitive epitopes on their surface. They can also serve as carriers to present foreign epitopes and induce immunity against heterologous pathogens
This document discusses a thesis presented by Priyanka Rughwani to the USC Graduate School examining factors that contribute to outcomes of Staphylococcus aureus bacteremia. The introduction provides background on the increasing incidence of S. aureus infections including methicillin-resistant S. aureus. It describes how S. aureus has developed resistance to multiple antibiotic classes and discusses the role of virulence factors and their impact on infection outcomes. The study aims to analyze the contribution of microbial resistance and virulence factors like agr functionality, protein A, and extracellular adherence protein towards persistent SAB or death.
This document reviews the current status of natural virus resistance genes and prospects for deploying these genes against virus infections. It discusses dominant resistance genes that confer monogenic resistance through recognition of viral avirulence factors. To date, 12 examples have been characterized that fall into the nucleotide binding site-leucine rich repeat class. Recessive resistance genes that cause impaired susceptibility by disrupting host factors required for virus infection are also described. These include mutations in translation initiation factors that cause resistance to various potyviruses and other viruses. Advances in genomics and molecular techniques are improving prospects for identifying and utilizing natural virus resistance genes in crop breeding programs.
This document summarizes a presentation on applying replication-defective West Nile virus vectors to non-flavivirus vaccine targets. The presentation discusses how flavivirus genomes are highly immunogenic and effective vaccines. It describes a methodology where envelope proteins from other viruses were expressed in place of structural proteins from West Nile virus, eliciting antibody and T-cell responses. Some challenges discussed are production issues, efficiency, stability, and dosage requirements. References are provided on using defective flaviviruses for vaccine development and characterization of the RepliVax vaccine platform.
This document describes a study conducted at Los Alamos National Laboratory to investigate the evolution of influenza A virus (IAV) under artificial selection pressure. The researchers engineered host cells to express IAV proteins and infected these "supplemented" cells with IAV over multiple passages. They hypothesized that the virus would evolve to efficiently infect the supplemented cells while losing ability to infect unmodified cells. Preliminary results found measurable viral replication in supplemented cells expressing one IAV protein (PB1C1) over generations, but limited replication in cells expressing another protein (M1), suggesting it may interfere with virion packaging. The goal is to better understand viral evolution and identify novel antiviral strategies.
Adenovirus, a DNA virus, was first isolated in the 1950s in adenoid tissue-derived cell cultures, hence the name. A large number of acute respiratory, gastrointestinal and eye infections in humans are caused by adenoviruses.
https://www.creative-biogene.com/Support/Virus.html
Adenoviruses are DNA viruses that are powerful research tools for investigating cellular events and can infect a wide range of mammalian cells with high efficiency, making them a versatile vector for gene delivery and expression. Creative Biogene is a biotechnology company that offers custom adenovirus services including vector design, construction, amplification, and purification to produce high-titer recombinant adenoviruses for use in research applications both in vitro and in vivo. Their services streamline the adenovirus production process which can otherwise be time-consuming and labor-intensive for researchers.
Oncolytic viruses(OVs)are viral strains that can infect and kill malignant cells without harming normal cells, while simultaneously stimulate the immune system and creating system antitumor immunity. Oncolytic viruses have become one of the aglare immunotherapies that have been extensively studied and developed.
Creative Biolabs is a world-renowned service provider for immunotherapy. Taking advantage of the OncoVirapy™ platform, Creative Biolabs provides a comprehensive overview on the basic biology that support OVs as cancer therapeutic agents, including properties of inherent and engineered oncolytic viruses, mechanisms of viral targeting cancer cells, mechanisms of action of viruses killing cancer cells (induction of local and systemic anti-tumor immunity). Based on this basic knowledge review, we hope you can have a comprehensive understanding of OVs and quickly capture one of the frontiers of immunotherapy research.
This document discusses a meta-analysis of multiple datasets examining features of viral RNA that correlate with activation of the innate immune system. The analysis found that "A" nucleotide content and minimum folding energy (MFE) were good predictors of immune system activation, more so than other proposed indicators like CpG enrichment. As RNA composition and structure are correlated, further experiments using synthetic sequences are needed to identify the specific viral RNA sensing mechanisms of immune system receptors.
- Comprehensive peptide libraries were designed for immune profiling of Zika virus and related flaviviruses like dengue virus.
- The libraries include PepStar peptide arrays for profiling humoral immune responses using minimal serum, and PepMix peptide pools for stimulating antigen-specific T cell responses.
- The libraries were designed using bioinformatics to select peptides providing optimal coverage of sequence diversity within and between viruses. The libraries have been used to monitor immune responses to Zika virus vaccine candidates in animal studies.
Five attenuated Francisella novicida transposon mutants (with mutations corresponding to dsbB, FTT0742, pdpB, fumA, and carB in F. tularensis) were identified that provided protection against challenge with over 8 x 105 CFU of wild-type F. novicida in mice. The mutants were screened by examining their ability to grow in mouse macrophages and their virulence in mice. These attenuated mutants were then tested for their ability to protect mice against challenge with high doses of wild-type bacteria. The findings from this study could be useful in the design of a vaccine against tularemia.
The study aimed to recapitulate key findings from the Phase IIb Step Trial of a Merck Ad5 HIV-1 vaccine in rhesus macaques. Rhesus macaques were infected with Ad5hr and immunized with an Ad5 SIV vaccine or empty vector. They were then challenged with escalating doses of penile SIV exposure. The Ad5 SIV vaccine induced CD8+ T cell responses in 70% of monkeys, similar to humans in the Step Trial, but did not protect against SIV infection. At the lowest SIV dose, 2/9 Ad5-seropositive monkeys immunized with the Ad5 SIV vaccine became infected compared to 0/34 in
Dr. X.J. Meng - Designing PRRSV Vaccines for Heterologous ProtectionJohn Blue
1) PRRSV remains a major problem for the global swine industry, causing $664 million in losses annually in the US alone. The emergence of more virulent strains and heterogeneity have complicated vaccine development.
2) DNA shuffling techniques are being used to generate chimeric PRRSV vaccines containing structural genes from multiple heterologous strains, which have shown promise in inducing cross-neutralizing antibodies and protection against diverse strains.
3) Targeting shuffled PRRSV antigens to dendritic cells through DC-SIGN enhances antigen-specific CD4+ and CD8+ T cell immune responses in pigs. These approaches aim to overcome obstacles in developing a broadly protective PRRSV vaccine.
HIV is a retrovirus that infects and destroys CD4+ immune cells. It has high genetic variability due to a lack of proofreading during replication. There are three main groups of HIV (M, O, N) with group M causing the global epidemic and consisting of nine genetic subtypes. Natural infection progresses from asymptomatic infection to AIDS without treatment over many years. Some individuals are able to control virus levels long-term. Diagnosis involves antibody and viral load testing. While antiretroviral therapy can suppress the virus, developing an effective vaccine has proven difficult due to HIV's ability to mutate and evade the immune system.
Dr. Jay Calvert - Viral genetics and application to vaccine developmentJohn Blue
Viral genetics and application to vaccine development - Dr. Jay Calvert, Zoetis, Inc, from the 2017 North American PRRS/National Swine Improvement Federation Joint Meeting, December 1‐3, 2017, Chicago, Illinois, USA.
More presentations at http://www.swinecast.com/2017-north-american-prrs-nsif-joint-meeting
This document provides an overview of virological tests for virus detection and diagnosis. There are three main categories of tests: direct examination to detect viral antigens or genomes, indirect examination using cell culture or animals to isolate viruses, and serology to detect antibodies. Direct methods include antigen detection by immunofluorescence, electron microscopy, PCR and hybridization probes. Indirect methods involve culturing viruses in cell lines or eggs and observing cytopathic effects or hemagglutination. Serology detects rising antibody titers between acute and convalescent patient samples or presence of IgM. Newer molecular techniques like PCR have increased sensitivity but require skill and specialized equipment. Proper specimen collection and a combination of direct, culture and serology tests
Novel research aimed at finding a cure for AIDS requires animal models responding to human antiretroviral drugs. However, there have been few antiretrovirals cross-active against the simian viruses. In this study, we expanded the arsenal of drugs active against the simian retrovirus SIVmac251 and showed that this virus is inhibited by the protease inhibitor, darunavir, and the CCR5 blocker, maraviroc. Administration of these two drugs in combination with the reverse transcriptase inhibitors, tenofovir and emtricitabine, and the integrase inhibitor, raltegravir, resulted in prolonged plasma viral loads below assay detection limits, and, surprisingly, restricted the viral reservoir, a marker of which is viral DNA. We then decided to employ this multidrug regimen (termed “highly intensified ART”) in order to increase the potency of a previous strategy based on the gold drug auranofin, which recently proved able to restrict the viral reservoir in vivo. A short course of highly intensified ART following the previous treatment resulted, upon therapy suspension, in a remarkably spontaneous control of the infection, that may pave the way to a persistent suppression of viremia in the absence of ART. These results corroborate the robustness of the macaque AIDS model as a vanguard for potentially future treatments for HIV in humans.
This document describes a study comparing cytokine and chemokine responses during acute infection with progressive and non-progressive strains of SIV in nonhuman primates. Rhesus macaques were infected with either pathogenic SIVmac251 or attenuated SIVmac239Δnef, while African green monkeys were infected with non-pathogenic SIVsab9315BR. Levels of various cytokines and chemokines were measured longitudinally and correlated with acute and chronic phase viremia. The magnitude of cytokine responses during acute infection correlated with both acute and chronic viremia levels. However, the specific cytokines elevated differed between progressive and non-progressive infections.
1) Chimpanzees vaccinated with HIV neutralizing antibodies were resistant to homologous virus challenge but the challenge dose and route were important factors in determining protection.
2) SIV vaccination studies in monkeys showed protection against SIV challenge, even when the vaccine did not contain SIV, possibly due to antibodies against host proteins in the virus envelope.
3) An adenovirus-based vaccine aimed at cytotoxic T lymphocytes failed to prevent HIV infection in a clinical trial, possibly due to pre-existing antibodies against the viral vector.
Case study on human papilloma virus vaccineZohaib HUSSAIN
Sarah received the HPV vaccine Gardasil at age 15 through her school's immunization program to reduce her risk of cervical cancer later in life. The HPV vaccine works by using virus-like particles (VLPs) that are similar in structure to actual HPV viruses but are non-infectious and non-cancer causing. When exposed to these VLPs, the immune system mounts a strong antibody response against the types of HPV targeted by the vaccine. If Sarah were exposed to one of these HPV types later, her immune system would launch a rapid response from memory cells, preventing infection and damage to her cervical tissue.
Presentation on conventional vaccine (Quality Control and Production aspects)Sunny Rathee
The document discusses the production and quality control of vaccines. It begins by introducing vaccines and their purpose of stimulating immunity. It then covers the history of vaccines, classifications of vaccines, and properties of an ideal vaccine. The document discusses the differences between conventional and novel vaccines. It provides details on the preparation and standardization of several common vaccines, including polio, smallpox, typhoid, BCG, and cholera vaccines. The production process of vaccines is summarized as selecting strains, growing microorganisms, isolating and purifying the product, inactivating microorganisms, and formulating and testing the final vaccine.
MVI is working with ICGEB in India to develop a vaccine against Plasmodium vivax. This effort includes Bharat Biotech, which will manufacture the vaccine for preclinical and initial safety trials in adults. The vaccine aims to prevent infection, decrease infection intensity, and prevent malaria transmission.
Virology is the study of viruses and their relationship with hosts. Viruses are acellular organisms that can only replicate inside host cells. They have nucleic acid genomes and use host cell machinery to assemble new viral particles. Viruses come in a variety of shapes and sizes, and some have envelopes derived from host cell membranes. They enter host cells, express their genes, replicate their genomes, assemble new viral particles, and exit host cells to infect new targets. Viruses are cultivated using various methods including cell cultures, embryonated eggs, and animal models to study viral replication and pathogenesis.
This study assessed the protective efficacy of a vaccine composed of three vaccinia virus proteins - A27L, B5R, and D8L - expressed in E. coli. Mice were vaccinated with the proteins in an adjuvant. Vaccination induced neutralizing antibodies and protected mice from lethal vaccinia virus challenge. Passive transfer of serum from vaccinated mice also protected naive mice, suggesting antibodies were important for protection. Several epitopes in the proteins were recognized by sera from vaccinated mice. Cellular immune responses to peptides from the proteins were also detected. The results suggest a subunit vaccine containing these proteins can stimulate immune responses and protect against vaccinia virus.
The document discusses various aspects of vaccines including:
1. It defines what a vaccine is and how it works to provide immunity.
2. It outlines several key properties and factors that are important for an ideal vaccine, including safety, effectiveness, ease of administration, stability and cost.
3. It describes some common reasons why producing certain vaccines can fail, such as rapid pathogen evolution or a disease not conferring immunity upon exposure.
4. It provides details on different methods used to develop live attenuated vaccines including serial passaging, chemical mutagenesis, and genetic engineering. It gives examples for each method.
This document discusses rotavirus prevention and control. It begins with an introduction stating that rotavirus is the leading cause of severe diarrhea in children under 5 globally, resulting in over 500,000 child deaths annually. The majority of these deaths occur in low-income countries.
It then covers the epidemiology and disease burden, describing rotavirus as the top cause of death in children under 5 worldwide. Clinical presentation is discussed, outlining the typical timeline and symptoms of rotavirus infection.
Prevention and control methods are summarized as infection control practices and vaccination. Two oral rotavirus vaccines currently available are described and their efficacy and safety are discussed. WHO recommendations for rotavirus vaccination through national immunization
This dissertation defense presentation summarizes the candidate's work developing a recombinant measles virus vaccine cocktail expressing Dengue virus antigens to prime anti-flaviviral immunity in young infants. The presentation covers: 1) the global threat of Dengue virus, 2) broad neutralizing responses generated during flavivirus infections, and 3) generation and characterization of recombinant measles viruses expressing Dengue virus antigens that effectively replicate and induce neutralizing antibody responses against measles and Dengue in mouse models. The candidate hypothesizes that this vaccine strategy could robustly enhance subsequent Dengue virus vaccines in young children.
The document summarizes the development of three types of LAB-based (lactic acid bacteria-based) vaccines described in a Ph.D. thesis. It describes (1) the development of a safer plasmid DNA vaccine using L. lactis that obtained comparable antibody responses to an E. coli vector but lower CD8+ T cell activation, (2) the production of the peanut allergen Ara h 2 in L. lactis and its authenticity, and (3) the use of LAB for antigen delivery by presenting antigens on their surface and through adhesion mechanisms aided by molecules like the mannose-binding adhesin.
Immunology and Detection of Acute HIV-1 InfectionRongpong Plongla
This document summarizes key aspects of acute HIV infection, including transmission routes, early immune responses, detection challenges, and prevention opportunities. It discusses how a small number of viruses can establish infection and the rapid spread throughout lymph tissue. Early treatment may help reduce transmission by suppressing viral load during this acute phase when contagiousness is highest. Ongoing research aims to better understand transmission dynamics and develop optimal testing and prevention strategies to interrupt spread during this critical early window.
This document discusses rabies, a zoonotic viral disease spread through contact with infected saliva. It is caused by the rabies virus (RABV) and can infect wild and domestic animals like dogs, bats, cats, jackals and wolves. The virus enters nerves at the site of exposure and travels through neurons to the central nervous system. Symptoms vary depending on exposure but include pain, encephalitis, and eventually death from respiratory failure if left untreated. The document discusses the history of rabies vaccine development including the use of nerve tissue and different cell cultures to produce safer and more effective vaccines for human and veterinary use. Purification methods including various chromatography columns are also outlined.
Gene Olinger, USAMRIID, Fort Detrick USA, presents at the ProImmune Antigen Characterization and Biomarker Discovery Summit, January 2011.
Protective Immune Reponses to Ebola Virus
Similar to SIV Viral Variation; Implications for Vaccines and Transmission - Mars Stone PhD (20)
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...Leonel Morgado
Current descriptions of immersive learning cases are often difficult or impossible to compare. This is due to a myriad of different options on what details to include, which aspects are relevant, and on the descriptive approaches employed. Also, these aspects often combine very specific details with more general guidelines or indicate intents and rationales without clarifying their implementation. In this paper we provide a method to describe immersive learning cases that is structured to enable comparisons, yet flexible enough to allow researchers and practitioners to decide which aspects to include. This method leverages a taxonomy that classifies educational aspects at three levels (uses, practices, and strategies) and then utilizes two frameworks, the Immersive Learning Brain and the Immersion Cube, to enable a structured description and interpretation of immersive learning cases. The method is then demonstrated on a published immersive learning case on training for wind turbine maintenance using virtual reality. Applying the method results in a structured artifact, the Immersive Learning Case Sheet, that tags the case with its proximal uses, practices, and strategies, and refines the free text case description to ensure that matching details are included. This contribution is thus a case description method in support of future comparative research of immersive learning cases. We then discuss how the resulting description and interpretation can be leveraged to change immersion learning cases, by enriching them (considering low-effort changes or additions) or innovating (exploring more challenging avenues of transformation). The method holds significant promise to support better-grounded research in immersive learning.
When I was asked to give a companion lecture in support of ‘The Philosophy of Science’ (https://shorturl.at/4pUXz) I decided not to walk through the detail of the many methodologies in order of use. Instead, I chose to employ a long standing, and ongoing, scientific development as an exemplar. And so, I chose the ever evolving story of Thermodynamics as a scientific investigation at its best.
Conducted over a period of >200 years, Thermodynamics R&D, and application, benefitted from the highest levels of professionalism, collaboration, and technical thoroughness. New layers of application, methodology, and practice were made possible by the progressive advance of technology. In turn, this has seen measurement and modelling accuracy continually improved at a micro and macro level.
Perhaps most importantly, Thermodynamics rapidly became a primary tool in the advance of applied science/engineering/technology, spanning micro-tech, to aerospace and cosmology. I can think of no better a story to illustrate the breadth of scientific methodologies and applications at their best.
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
Phenomics assisted breeding in crop improvementIshaGoswami9
As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional
genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding
the complex characteristics of multiple gene, owing to a lack of crop phenotypic data. Efficient, automatic, and accurate technologies and platforms that can capture phenotypic data that can
be linked to genomics information for crop improvement at all growth stages have become as important as genotyping. Thus,
high-throughput phenotyping has become the major bottleneck restricting crop breeding. Plant phenomics has been defined as the high-throughput, accurate acquisition and analysis of multi-dimensional phenotypes
during crop growing stages at the organism level, including the cell, tissue, organ, individual plant, plot, and field levels. With the rapid development of novel sensors, imaging technology,
and analysis methods, numerous infrastructure platforms have been developed for phenotyping.
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...AbdullaAlAsif1
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/
Immersive Learning That Works: Research Grounding and Paths ForwardLeonel Morgado
We will metaverse into the essence of immersive learning, into its three dimensions and conceptual models. This approach encompasses elements from teaching methodologies to social involvement, through organizational concerns and technologies. Challenging the perception of learning as knowledge transfer, we introduce a 'Uses, Practices & Strategies' model operationalized by the 'Immersive Learning Brain' and ‘Immersion Cube’ frameworks. This approach offers a comprehensive guide through the intricacies of immersive educational experiences and spotlighting research frontiers, along the immersion dimensions of system, narrative, and agency. Our discourse extends to stakeholders beyond the academic sphere, addressing the interests of technologists, instructional designers, and policymakers. We span various contexts, from formal education to organizational transformation to the new horizon of an AI-pervasive society. This keynote aims to unite the iLRN community in a collaborative journey towards a future where immersive learning research and practice coalesce, paving the way for innovative educational research and practice landscapes.
The debris of the ‘last major merger’ is dynamically youngSérgio Sacani
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
The debris of the ‘last major merger’ is dynamically young
SIV Viral Variation; Implications for Vaccines and Transmission - Mars Stone PhD
1. SIV Viral Variation; Implications
for Vaccines and Transmission
Mars Stone, Ph.D.
California National Primate Research Center
University of California, Davis
2. PART 1 Viral diversity at mucosal transmission
-determine if vaginal SIV inoculation of rhesus macaques
recapitulates HIV-1 variant transmission
PART 2 Viral diversity in vaccine setting
-Characterize the replication levels and anatomic distribution
of vaccine (SHIV 89.6) and challenge (SIVmac239) virus in
monkeys prior to and after challenge.
-Characterize evolution of SIV env population complexity of
SIV DNA in PBMC of SHIV immunized and control animals.
3. Error in Reverse Transcription
leads to Viral Population Complexity
Reverse transcriptase
synthesizes viral DNA from
viral RNA
Error rate of 1.7x105
nucleotide incorporations
Host RNA polymerase II
transcribes the proviral DNA
into RNA which will be packed
into virions.
Mutation can occur during one
or all of these replication steps
~1 error per replication
cycle
4. RNA viruses exist as a quasispecies
Raul Andino, PLoS Pathog. 2010
Every round of replication mutations are
generated, constantly introducing variation as
population expands.
5.
6. Important findings:
Studied 5 seroconverters, 2 linked transmission partners
•Homogeneous HIV env populations within newly infected
patients
•No common signature sequence among transmitted
variants
•Transmitted sequence represented only minor variant in
complex population of chronically infected transmitting
partner
They conclude that the transmitted virus
should be the target of vaccines
8. Single Genome Amplification
Methods were developed to generate and sequence
amplicons derived from a single template,
avoiding artifacts common to basic cloning and
sequencing approach
9. Single Genome Amplification
• Proportional representation of variants
• Excludes PCR induced misincorporation error
• Eliminates PCR-mediated recombination
10. Why env?
• Env is primary determinant of cellular tropism and
selective transmission would likely involve
selection among env variants
• Is the most variable gene in the HIV quasispecies
11. Is the SIVenv variant population
transmitted by vaginal inoculation
• Homogeneous?
• Heterogeneous?
14. Purpose:
1. Determine the number and identity of SIVmac251 env
variants in stock
2. Determine the number and identity of SIVmac251 env
variants transmitted by vaginal inoculation
3. Determine if signature sequence is selected for by
vaginal inoculation
18. Composite NJ
tree of
SIVmac251
stock and
transmitted
variants
-No two low diversity
lineages were identical
-each lineage distributed
throughout the tree
25. Conclusions 1:
-Rhesus macaque/SIV model of HIV-1 vaginal transmission
recapitulates human infection.
•Relatively few genetic variants establish systemic infection
even when exposed to complex inoculum
•A specific viral variant was not consistently transmitted by
i.vag. Inoculations
26. PART 1 Viral diversity at mucosal transmission
-Recapitulate HIV-1 variant transmission in rhesus macaque
model of vaginal SIV infection.
-Explore possible host factors affecting variant transmission
PART 2 Viral diversity in vaccine setting
-Characterize the replication levels and distribution of
vaccine (SHIV 89.6) and challenge (SIVmac239) virus in
monkeys prior to and after challenge.
-Characterize the population complexity of SIV in PBMC
vDNA of SHIV immunized and control animals over time.
27. PART 2 Viral diversity in vaccine setting
• HIV is primarily transmitted mucosally, and a vaccine to prevent mucosal
transmission is the best opportunity to stop the AIDS pandemic
• Live attenuated vaccines have demonstrated the best protection from
pathogenic vaginal SIV challenge
• Live attenuated vaccines are not likely to be used due to safety concerns, but
they do provide a good model to understand the nature of immune protection.
• In unprotected animals it is important to know if there are specific anatomic
sites that are resistant to vaccine-induced immune control of challenge virus
replication.
31. Intravaginal SIVmac239 challenge outcome in
SHIV89.6 vaccinated female macaques
Prior SHIV89.6 infection “protects” 60% of rhesus monkeys from
vaginal challenge with SIVmac239
Abel et al. J Virol, 2003
32. Goals:
AIM 1
• Characterize the replication levels and distribution of vaccine (SHIV
89.6) and challenge (SIVmac239) virus in monkeys prior to and after
challenge.
AIM 2
• Determine relationship between SIV population diversity and viral
replication in control animals and animals that eventually fail vaccine
protection
33. Vaccine or Challenge virus?
In other attenuated lentivirus vaccine models it is unclear if “vaccine
failure” is due to replication of the vaccine virus, the challenge virus,
or both
Display Settings: Abstract
We found 1 article by title matching your search:
J Gen Virol. 2008 Sep;89(Pt 9):2240-51.
Resistance to superinfection by a vigorously replicating,
uncloned stock of simian immunodeficiency virus (SIVmac251)
stimulates replication of a live attenuated virus vaccine
(SIVmacC8).
Berry N, Stebbings R, Ferguson D, Ham C, Alden J, Brown S, Jenkins A, Lines J, Duffy L, Davis L, Elsley W, Page M, Hull R,
Stott J, Almond N.
Division of Retrovirology, National Institute for Biological Standards and Control, Blanche Lane, Sou th Mimms, Potters Bar,
Hertfordshire EN6 3QG, UK. rberry@nibsc.ac.uk
Abstract
Vaccination with live attenuated simian immunodeficiency virus (SIVmacC8) confers potent, reproducibl e protection against
homologous wild-type virus challenge (SIVmacJ5). The ability of SIVmacC8 to confer resistance to supe rinfection with an
uncloned ex vivo derivative of SIVmac251 (SIVmac32H/L28) was investigated. In naïve, Mauritian-derive d cynomolgus
macaques (Macaca fascicularis), SIVmac32H/L28 replicated to high peak titres (>10(8) SIV RNA copies ml(-1)), persisted at
high levels and induced distinctive pathology in lymphoid tissues. In cynomolgus macaques vaccinated with SIVmacC8, no
evidence of detectable superinfection was observed in 3/8 vaccinates following challenge 3 or 20 week s later with
SIVmac32H/L28. Analyses after SIVmac32H/L28 challenge revealed a significant reduction in viral RNA (P<0.001) and DNA
levels between 20 week vaccinates and challenge controls. Amongst 3 week vaccinates, less potent prot ection was
observed. However, analysis of env from breakthrough virus indicated >99% sequence similarity with th e vaccine virus.
Highly sensitive PCR assays that distinguish vaccine and challenge virus stocks demonstrated restimul ation of replication of
the vaccine virus SIVmacC8 in the face of potent protection against a vigorous, homologous challenge virus. Vaccine-induced
antiviral neutralizing antibodies and anti-Nef CD8+ cytotoxic T cell responses did not correlate with the outcome of the
challenge. Defining the mechanism of vaccine protection will need to account for the ef fective control of a genetically closely
related challenge virus whilst remaining unable to suppress replication of the pre-existing vaccine v irus. The role of innate
and intrinsic anti-retroviral immunity in the protection conferred by live attenuated SIV vaccines wa rrants careful study.
PMID: 18753233 [PubMed - indexed for MEDLINE] Free Article
PubMed
U.S. National Library of Medicine
National Institutes of Health
Search: Resistance[Title] AND superinfection[Title] AND vigor ously[Title] AND replicating[Title] AND uncloned[Title]
AND stock[Title] AND simian[Title] AND immunodeficiency[Title]
Publication Types, MeSH Terms, Substances, Grant Support
LinkOut - more resources
References
1 The Recurrent Miscarriage Immunotherapy Trialists Group.
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Department of Obstetrics and Gynaecology, Nagoya City University
Medical School, Nagoya, Japan (K Aoki MD, S Kajiura MD,
Y Matsumoto MD, M Ogasawara MD, S Okada MD,
Prof Y Yagami MD); and Center for Human Reproduction and
Foundation for Reproductive Medicine, Chicago, Illinois, USA
(Prof N Gleicher MD)
Correspondence to: Dr Koji Aoki
Protection by attenuated simian
immunodeficiency virus in macaques
against challenge with virus-infected cells
A vaccine against AIDS will probably have to protect
against challenge both by viable virus-infected cells and by
cell-free virus. Eight cynomolgus macaques infected with
attenuated simian immunodeficiency virus (SIV) were
challenged (four each) with cell-free and cell-associated
SIV. All were protected, whereas eight controls were all
Two molecular clones of SIV, called J5 and C8, have
been isolated. They are identical in sequence, except for
seven differences located in the nef gene or the 3’ long-
terminal-repeat. One of these differences is a 12 basepair
deletion, in C8, where the nef gene overlaps the U3 region
of the repeat.3 We have found by PCR and the persistence
of anti-SIV antibodies that J5 and C8 viruses can infect
cynomolgus macaques chronically. However, the C8 virus
expresses an attenuated phenotype in vivo. 2 weeks after
infection, virus is readily reisolated from the blood of C8-
infected or J5-infected animals, but the proportion of
infected lymphocytes is 10-100 times lower in the former.
By 8-12 weeks, reisolation of C8 virus becomes sporadic
and mean antibody titres are 10-fold lower in C8-infected
than in J5-infected macaques. None of the C8-infected
protect
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require
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whether
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ction is
ee virus
terminal-repeat. basepair
deletion, in C8, where the nef gene overlaps the U3 region
of the repeat.3 We have found by PCR and the persistence
of anti-SIV antibodies that J5 and C8 viruses can infect
cynomolgus macaques chronically. However, the C8 virus
expresses an attenuated phenotype in vivo. 2 weeks after
infection, virus is readily reisolated from the blood of C8-
infected or J5-infected animals, but the proportion of
infected lymphocytes is 10-100 times lower in the former.
By 8-12 weeks, reisolation of C8 virus becomes sporadic
and mean antibody titres are 10-fold lower in C8-infected
than in J5-infected macaques. None of the C8-infected
animals has developed AIDS-like disease even after 2
years (ref 3 and our data).
Four purpose-bred macaques (L103-L106) were
injected intravenously with 104 median tissue-culture
infective doses (TCIDso) of a titrated stock (from the 9/90
pool) of C8 grown in the human T-cell line C8166.3 All
macaques became infected. Although virus was rarely
isolated by co-cultivation of C8166 cells with 107
peripheral blood mononuclear cells after 8 weeks, proviral
DNA was repeatedly detected by PCR. Antibodies to
recombinant SIV p27 and gpl40 reached a plateau by 12
weeks and persisted (mean loglo ELISA 2-8 [SD 01] and
2-9 [0’3], respectively). Neutralising antibodies against J5
reached titres between loglo 1-8 and 2-7 (mean 2-1 [0-4]).
At 39 weeks after infection with C8, these macaques and
four control animals were challenged with 10 median
infective doses (MID50) of J5M, a cell-free stock of J5
virus, prepared in peripheral blood mononuclear cells
from macaques.3 The course of infection was assessed by
virus recovery and a diagnostic PCR in which a region of
nef is amplified and the two clones J5 and C8 can be
distinguished.4 Virus was recovered from all controls after
challenge but not from the animals that had been
preinfected with C8 (table). After challenge, the nef PCR
identified proviral sequences derived from J5 in all
controls. By contrast, no such sequences were detected in
the blood of macaques previously infected with C8.
Furthermore, no anamnestic antibody responses to SIV
envelope were detected by ELISA with recombinant SIV
gpl40 (Repligen)’ in macaques infected with C8 (table).
The Lancet
Display Settings: Abstract
Arch Virol. 2002 Jun;147(6):1091-104.
Characterization of simian and human immunodeficiency
chimeric viruses re-isolated from vaccinated macaque monkeys
after challenge infection.
Kwofie TB, Miura T, Ibuki K, Enose Y, Suzuki H, Ui M, Kuwata T, Hayami M.
Laboratory of Viral Pathogenesis, Research Center for AIDS, Institute for V irus Research, Kyoto University, Japan.
Abstract
Monkeys that have been vaccinated with nef-deleted SHIVs were either fully or partially protected aga inst challenge with
acute pathogenic SHIV-89.6 P. Viruses isolated from these vaccinated monkeys were all found to be the 89.6 P challenge
virus using PCR amplification and restriction enzyme analysis of the env region of the viruses. Analy sis of the 3'-end of the
env region and 5'-half of the nef region using a heteroduplex mobility assay revealed that the parent al 89.6 P and
re-isolated viruses from unvaccinated 89.6 P-infected monkeys had quite an abundant and similar heter ogeneous
quasispecies population. In contrast, the viruses isolated from the vaccinated monkeys had dif ferent and fewer
quasispecies indicating a selective immune pressure in the vaccinated monkeys. The in vitro replicati on of the viruses
isolated from the vaccinated monkeys in human and macaque peripheral blood mononucular cells (PBMCs) as well as in
established cell lines such as M8166 and HSC-F cells, were slow and delayed when compared to the pare ntal 89.6 P and
re-isolated viruses from unvaccinated 89.6 P-infected monkeys. Further comparison revealed that in HS C-F cells the
viruses from vaccinated monkeys again showed delayed and weak CD4(+) cell down-modulation as well as having little or
no effect on cell growth or cell viability on HSC-F cells and monkey PBMC. Thus we noticed that these re-isolated 89.6 P
viruses from the vaccinated monkeys had changed or had been selected for low pathogenic viruses in th e monkeys. This
suggests that though the vaccination did not completely prevent the replication of the challenge viru s in the monkeys it did
contain the challenge virus by suppressing the pathogenic variants. This further enhances the prospec ts of this nef-deleted
SHIV as the bases for effective anti-HIV vaccine candidates.
PubMed
U.S. National Library of Medicine
National Institutes of Health
34. Experimental Design: Acute infection
3 days 7 days 14 days
vaccination
SHIV89.6
IV
pathogenic
SIVmac239
IVAG6 months
Nx time points for
21 SIV controls
Nx time points for
30 SHIV-vaccinated animals
35. Stone et al, Virology 2009
Fig. 1
Fig. 1
Challenge outcome
Plasma vRNA
7 days PC 14 days PC
36. Stone et al, Virology 2009
Fig. 1
Fig. 1
Challenge outcome
Plasma vRNA
7 days PC 14 days PC
40. Nx time point for
5 SHIV-immunized animals,
CD8 depleted animals
anti-CD8
(cM T807;
50mg/kg)
Experimental Design: Acute infection
3 days 7 days 14 days
vaccination
SHIV89.6
IV
pathogenic
SIVmac239
IVAG6 months
Nx time points for
21 SIV controls
Nx time points for
30 SHIV-vaccinated animals
Genescà et al J Virology
What role do CD8+ play in vRNA levels and distribution?
41. CD8+ Depleted
Plasma vRNA levels
after vaginal
SIV challenge
SIVgag
SIVenv
Stone et al, Virology 2009
7 days PC 14 days PC
43. Conclusions 2:
• Pathogenic challenge virus SIVmac239 is responsible for Vaccine
failure
– Although vaccine virus persists in some tissues, it is not responsible for vaccine failure in
this model.
– No anatomic sites the immune system can’t reach to control SIV replication
• In vaccinated animals that control virus replication, dissemination of
SIV beyond the genital lymph nodes is limited
• CD8+ depletion abrogates protective effect of SHIV immunization
– There is increased SIV replication in CD8- SHIV vaccinated animals in the female genital
tract consistent with an increase in target cells
44. Goals:
AIM 1
• Characterize the replication levels and distribution of vaccine (SHIV
89.6) and challenge (SIVmac239) virus in monkeys prior to and after
challenge.
AIM 2
• Determine relationship between SIV population diversity and viral
replication in control animals and animals that eventually fail vaccine
protection
45. IVAG SIVmac239 challenge outcome in
SHIV89.6 vaccinated female macaques
Apply SGA methods to determine if increase in population
diversity precedes increase in viral replication in animals that
eventually fail vaccine protection
47. Why env?
• Env has appropriate properties of molecular
biology and immunology for serving as a marker
of genetic diversity
– Tolerates variability without change in biological
properties
– There is no vaccine – induced immune pressure acting
on env in immunized animals, vaccine and challenge
virus are heterologous.
57. Model of Mucosal Infection with Pre-existing
Immune selection pressures (modified from B. Keele)
R0=1
CD8
CD8
CD8
CD8
CD8
CD8
CD8
CD8
CD8
CD8
CD8
CD8
CD8
CD8
CD8
CD8
CD8
CD8
58. Conclusions 3:
– Although plasma vRNA not detected by our assays, some replication must
be occurring to provide substrate that allows generation of breakthrough
variants
– Competition between parental and mutant variants for target cells leads to
purifying selection that accounts for relatively low levels of diversity in
animals with high viral replication
– Conversely, lack of competition between parental and mutant variants for
target cells in animals with low replication levels allows diversity to
accumulate
Regardless of levels of replication, diversity increases over time in all animals
...so a vaccine must block transmission and prevent establishment of systemic
infection after which the viral quasispecies becomes a complex moving target.
59. Thanks to:
Chris Miller
Mike McChesney
Meritxell Genesca
Zhong-Min Ma
Linda Fritts
Vero deSilva
Joe Dutra
Ding Lu
Tracy Rourke
Lili Guo
Primate Services Unit
NIH/NCI
Brandon Keele
UAB
George Shaw
Beatrice Hahn
University of Nottingham
Liz Bailes
University of California-Davis