Trimeric gp120-specific bovine monoclonal antibodies require cysteine and aromatic residues in CDRH3 for high affinity binding to HIV Env.

We isolated HIV-1 Envelope (Env)-specific memory B cells from a cow that had developed high titer polyclonal immunoglobulin G (IgG) with broad neutralizing activity after a long duration vaccination with HIV-1AD8 Env gp140 trimers. We cloned the bovine IgG matched heavy (H) and light (L) chain variable (V) genes from these memory B cells and constructed IgG monoclonal antibodies (mAbs) with either a human constant (C)-region/bovine V-region chimeric or fully bovine C and V regions. Among 42 selected Ig+ memory B cells, two mAbs (6A and 8C) showed high affinity binding to gp140 Env. Characterization of both the fully bovine and human chimeric isoforms of these two mAbs revealed them as highly type-specific and capable of binding only to soluble AD8 uncleaved gp140 trimers and covalently stabilized AD8 SOSIP gp140 cleaved trimers, but not monomeric gp120. Genomic sequence analysis of the V genes showed the third heavy complementarity-determining region (CDRH3) of 6A mAb was 21 amino acids in length while 8C CDRH3 was 14 amino acids long. The entire V heavy (VH) region was 27% and 25% diverged for 6A and 8C, respectively, from the best matched germline V genes available, and the CDRH3 regions of 6A and 8C were 47.62% and 78.57% somatically mutated, respectively, suggesting a high level of somatic hypermutation compared with CDRH3 of other species. Alanine mutagenesis of the VH genes of 6A and 8C, showed that CDRH3 cysteine and tryptophan amino acids were crucial for antigen binding. Therefore, these bovine vaccine-induced anti-HIV antibodies shared some of the notable structural features of elite human broadly neutralizing antibodies, such as CDRH3 size and somatic mutation during affinity-maturation. However, while the 6A and 8C mAbs inhibited soluble CD4 binding to gp140 Env, they did not recapitulate the neutralizing activity of the polyclonal antibodies against HIV infection.

Repeated Vaccination of Cows with HIV Env gp140 during Subsequent Pregnancies Elicits and Sustains an Enduring Strong Env-Binding and Neutralising Antibody Response.

An important feature of a potential vaccine against HIV is the production of broadly neutralising antibodies (BrNAbs) capable of potentially blocking infectivity of a diverse array of HIV strains. BrNAbs naturally arise in some HIV infected individuals after several years of infection and their serum IgG can neutralise various HIV strains across different subtypes. We previously showed that vaccination of cows with HIV gp140 AD8 trimers resulted in a high titre of serum IgG against HIV envelope (Env) that had strong BrNAb activity. These polyclonal BrNAbs concentrated into the colostrum during the late stage of pregnancy and can be harvested in vast quantities immediately after calving. In this study, we investigated the effect of prolonged HIV gp140 vaccination on bovine colostrum IgG HIV Env-binding and BrNAb activity over subsequent pregnancies. Repeated immunisation led to a maintained high titre of HIV Env specific IgG in the colostrum batches, but this did not increase through repeated cycles. Colostrum IgG from all batches also strongly competed with sCD4 binding to gp140 Env trimer and with human-derived monoclonal VRC01 and b12 BrNAbs that bind the CD4 binding site (CD4bs). Furthermore, competition neutralisation assays using RSC3 Env gp120 protein core and a derivative CD4bs mutant, RSC3 Δ371I/P363N, showed that CD4bs neutralising antibodies contribute to the neutralising activity of all batches of purified bovine colostrum IgG. This result indicates that the high IgG titre/avidity of anti-CD4bs antibodies with BrNAb activity was achieved during the first year of vaccination and was sustained throughout the years of repeated vaccinations in the cow tested. Although IgG of subsequent colostrum batches may have a higher avidity towards the CD4bs, the overall breadth in neutralisation was not enhanced. This implies that the boosting vaccinations over 4 years elicited a polyclonal antibody response that maintained the proportion of both neutralising and non-neutralising CD4bs antibodies.

Extended Aromatic and Heteroaromatic Ring Systems in the Chalcone-Flavanone Molecular Switch Scaffold.

Previous work on the o-hydroxychalcone/flavanone molecular switching scaffold showed that simple substitutions alter the pH range in which rapid interconversion occurs. Herein, more impactful structural modifications were performed via alteration of the characteristic phenyl rings to alternative aromatic systems. It was determined that the scaffold was still viable after these changes and that the range of accessible midpoint pH values was markedly increased. To further explore the switch's scope, scaffolds able to have multiple switching events were also investigated.

Impact of mono- and disubstitution on the colorimetric dynamic covalent switching chalcone/flavanone scaffold.

The effect of aryl substitution on various aspects of the interconversion of ortho-hydroxychalcones and flavanones has been studied using multiple spectroscopic techniques. Derivatization of the core scaffold predictably alters the midpoint pH of this equilibration process suggesting its viability for application as a functional colorimetric molecular switch.

Towards a dynamic covalent molecular switch: substituent effects in chalcone/flavanone isomerism.

Chalcone/flavanone interconversion occurs facilely under aqueous alkaline conditions making it a promising scaffold for the development of a covalent molecular switch. In this study, a single methoxy substituent is shown to have a significant impact on the equilibrium dynamics of this reaction; this impact is dependent on the site of substitution.

Stress profiling of longevity mutants identifies Afg3 as a mitochondrial determinant of cytoplasmic mRNA translation and aging.

Although environmental stress likely plays a significant role in promoting aging, the relationship remains poorly understood. To characterize this interaction in a more comprehensive manner, we examined the stress response profiles for 46 long-lived yeast mutant strains across four different stress conditions (oxidative, ER, DNA damage, and thermal), grouping genes based on their associated stress response profiles. Unexpectedly, cells lacking the mitochondrial AAA protease gene AFG3 clustered strongly with long-lived strains lacking cytosolic ribosomal proteins of the large subunit. Similar to these ribosomal protein mutants, afg3Δ cells show reduced cytoplasmic mRNA translation, enhanced resistance to tunicamycin that is independent of the ER unfolded protein response, and Sir2-independent but Gcn4-dependent lifespan extension. These data demonstrate an unexpected link between a mitochondrial protease, cytoplasmic mRNA translation, and aging.

Alleviation of insulin resistance and liver damage by oral administration of Imm124-E is mediated by increased Tregs and associated with increased serum GLP-1 and adiponectin: results of a phase I/II clinical trial in NASH.

BACKGROUND: Nonalcoholic steatohepatitis (NASH) is considered to be part of the nonalcoholic fatty liver disorders and its incidence is increasing. Imm124-E (Immuron Ltd, Melbourne, Australia), containing hyperimmune bovine colostrum, has been shown to exert an immunomodulatory effect and to alleviate target organ damage in animal models of NASH. The aim of our study was to determine the safety and efficacy of oral administration of Imm124-E to patients with insulin resistance and NASH. METHODS: In an open-label trial, ten patients with biopsy-proven NASH and insulin resistance were orally treated with Imm124-E for 30 days. RESULTS: Oral administration of Imm124-E was safe, and no side effects were noted. Alleviation of insulin resistance was reflected by significantly improved hemoglobin A(1c) (HbA(1c)) values in all ten treated patients. For between five and eight responders, the following effects were noted: a decrease in fasting glucose levels; improved oral glucose tolerance test (OGGT) and homeostatic model assessment insulin resistance (HOMA) scores; and alleviation in lipid profile. These effects were accompanied by increased serum levels of glucagon-like peptide 1 (GLP-1), adiponectin and T regulatory cells. CONCLUSION: Hyperimmune colostrum alleviates NASH.

Prevention and treatment of influenza with hyperimmune bovine colostrum antibody.

BACKGROUND: Despite the availability of specific vaccines and antiviral drugs, influenza continues to impose a heavy toll on human health worldwide. Passive transfer of specific antibody (Ab) may provide a useful means of preventing or treating disease in unvaccinated individuals or those failing to adequately seroconvert, especially now that resistance to antiviral drugs is on the rise. However, preparation of appropriate Ab in large scale, quickly and on a yearly basis is viewed as a significant logistical hurdle for this approach to control seasonal influenza. METHODOLOGY/PRINCIPAL FINDINGS: In this study, bovine colostrum, which contains approximately 500 g of IgG per milking per animal, has been investigated as a source of polyclonal antibody for delivery to the respiratory tract. IgG and F(ab')2 were purified from the hyperimmune colostrum of cows vaccinated with influenza A/Puerto Rico/8/34 (PR8) vaccine and were shown to have high hemagglutination-inhibitory and virus-neutralizing titers. In BALB/c mice, a single administration of either IgG or F(ab')2 could prevent the establishment of infection with a sublethal dose of PR8 virus when given as early as 7 days prior to exposure to virus. Pre-treated mice also survived an otherwise lethal dose of virus, the IgG- but not the F(ab')2-treated mice showing no weight loss. Successful reduction of established infection with this highly virulent virus was also observed with a single treatment 24 hr after virus exposure. CONCLUSIONS/SIGNIFICANCE: These data suggest that a novel and commercially-scalable technique for preparing Ab from hyperimmune bovine colostrum could allow production of a valuable substitute for antiviral drugs to control influenza with the advantage of eliminating the need for daily administration.

Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph.

MOTIVATION: The results of initial analyses for many high-throughput technologies commonly take the form of gene or protein sets, and one of the ensuing tasks is to evaluate the functional coherence of these sets. The study of gene set function most commonly makes use of controlled vocabulary in the form of ontology annotations. For a given gene set, the statistical significance of observing these annotations or 'enrichment' may be tested using a number of methods. Instead of testing for significance of individual terms, this study is concerned with the task of assessing the global functional coherence of gene sets, for which novel metrics and statistical methods have been devised. RESULTS: The metrics of this study are based on the topological properties of graphs comprised of genes and their Gene Ontology annotations. A novel aspect of these methods is that both the enrichment of annotations and the relationships among annotations are considered when determining the significance of functional coherence. We applied our methods to perform analyses on an existing database and on microarray experimental results. Here, we demonstrated that our approach is highly discriminative in terms of differentiating coherent gene sets from random ones and that it provides biologically sensible evaluations in microarray analysis. We further used examples to show the utility of graph visualization as a tool for studying the functional coherence of gene sets. AVAILABILITY: The implementation is provided as a freely accessible web application at: http://projects.dbbe.musc.edu/gosteiner. Additionally, the source code written in the Python programming language, is available under the General Public License of the Free Software Foundation. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

GOGrapher: A Python library for GO graph representation and analysis.

BACKGROUND: The Gene Ontology is the most commonly used controlled vocabulary for annotating proteins. The concepts in the ontology are organized as a directed acyclic graph, in which a node corresponds to a biological concept and a directed edge denotes the parent-child semantic relationship between a pair of terms. A large number of protein annotations further create links between proteins and their functional annotations, reflecting the contemporary knowledge about proteins and their functional relationships. This leads to a complex graph consisting of interleaved biological concepts and their associated proteins. What is needed is a simple, open source library that provides tools to not only create and view the Gene Ontology graph, but to analyze and manipulate it as well. Here we describe the development and use of GOGrapher, a Python library that can be used for the creation, analysis, manipulation, and visualization of Gene Ontology related graphs. FINDINGS: An object-oriented approach was adopted to organize the hierarchy of the graphs types and associated classes. An Application Programming Interface is provided through which different types of graphs can be pragmatically created, manipulated, and visualized. GOGrapher has been successfully utilized in multiple research projects, e.g., a graph-based multi-label text classifier for protein annotation. CONCLUSION: The GOGrapher project provides a reusable programming library designed for the manipulation and analysis of Gene Ontology graphs. The library is freely available for the scientific community to use and improve.

Multi-label literature classification based on the Gene Ontology graph.

BACKGROUND: The Gene Ontology is a controlled vocabulary for representing knowledge related to genes and proteins in a computable form. The current effort of manually annotating proteins with the Gene Ontology is outpaced by the rate of accumulation of biomedical knowledge in literature, which urges the development of text mining approaches to facilitate the process by automatically extracting the Gene Ontology annotation from literature. The task is usually cast as a text classification problem, and contemporary methods are confronted with unbalanced training data and the difficulties associated with multi-label classification. RESULTS: In this research, we investigated the methods of enhancing automatic multi-label classification of biomedical literature by utilizing the structure of the Gene Ontology graph. We have studied three graph-based multi-label classification algorithms, including a novel stochastic algorithm and two top-down hierarchical classification methods for multi-label literature classification. We systematically evaluated and compared these graph-based classification algorithms to a conventional flat multi-label algorithm. The results indicate that, through utilizing the information from the structure of the Gene Ontology graph, the graph-based multi-label classification methods can significantly improve predictions of the Gene Ontology terms implied by the analyzed text. Furthermore, the graph-based multi-label classifiers are capable of suggesting Gene Ontology annotations (to curators) that are closely related to the true annotations even if they fail to predict the true ones directly. A software package implementing the studied algorithms is available for the research community. CONCLUSION: Through utilizing the information from the structure of the Gene Ontology graph, the graph-based multi-label classification methods have better potential than the conventional flat multi-label classification approach to facilitate protein annotation based on the literature.

The cytotoxic effect of anthrax lethal toxin on human lung cells in vitro and the protective action of bovine antibodies to PA and LF.

The excretion of protein toxins by vegetative cells of Bacillus anthracis is critical to the development of the lethal consequences of anthrax, particularly inhalational anthrax. Whilst the lung macrophages and other phagocytic cells transfer the spores from the lung cavities into the lymphatic system, and provide an initial germination site for the proliferation of the vegetative cells, it appears that much of the tissue pathology at the time of the host's death could be due to the action of the toxins, especially lethal toxin-protective antigen (PA) plus lethal factor (LF). The widespread tissue oedema and hypoxia may in part reflect a direct attack by lethal toxin on vascular endothelial cells. Also the distribution of the receptor for PA on a variety of cell types including epithelial cells as well as endothelial cells, and the involvement of the lungs in the pathology raises the question of whether lung epithelial cells are also susceptible to lethal toxin. To investigate this possibility a series of in vitro cytotoxicity experiments were carried out with human lung epithelial cells and microvascular endothelial cells. In these experiments lethal toxin (PA 500 ng ml(-1) plus 10-100 ng ml(-1) LF) was shown to cause a progressive loss of cell viability that developed slowly over at least 3 days. Affinity purified bovine colostrum antibodies for both PA and LF were equally effective in providing a 100% protection for epithelial cells from this cytotoxic action of lethal toxin. This was achieved at a 10:1 molar ratio of the particular antibody to its respective target.

Determining particle size distributions in the inhalable size range for wood dust collected by air samplers.

In the absence of methods for determining particle size distributions in the inhalable size range with good discrimination, the samples collected by personal air sampling devices can only be characterized by their total mass. This parameter gives no information regarding the size distribution of the aerosol or the size-selection characteristics of different samplers in field use conditions. A method is described where the particles collected by a sampler are removed, suspended, and re-deposited on a mixed cellulose-ester filter, and examined by optical microscopy to determine particle aerodynamic diameters. This method is particularly appropriate to wood dust particles which are generally large and close to rectangular prisms in shape. Over 200 wood dust samples have been collected in three different wood-products industries, using the traditional closed-face polystyrene/acrylonitrile cassette, the Institute of Occupational Medicine inhalable sampler, and the Button sampler developed by the University of Cincinnati. A portion of these samples has been analyzed to determine the limitations of this method. Extensive quality control measures are being developed to improve the robustness of the procedure, and preliminary results suggest the method has an accuracy similar to that required of National Institute for Occupational Safety and Health (NIOSH) methods. The results should provide valuable insights into the collection characteristics of the samplers and the impact of these characteristics on comparison of sampler results to present and potential future limit values. The NIOSH Deep South Education and Research Center has a focus on research into hazards of the forestry and associated wood-products industry, and it is hoped to expand this activity in the future.

An evaluation of total and inhalable samplers for the collection of wood dust in three wood products industries.

In 1998 the American Conference for Governmental Industrial Hygienists (ACGIH) proposed size selective sampling for wood dust based on the inhalable fraction. Thus the proposed threshold limit values (TLVs) require the use of a sampler whose performance matches the inhalable convention. The Institute of Occupational Medicine (IOM) sampler has shown good agreement with the inhalable convention under controlled conditions, and the Button sampler, developed by the University of Cincinnati, has shown reasonable agreement in at least one laboratory study. The Button sampler has not been previously evaluated under wood working conditions, and the IOM has been shown to sample more mass than expected when compared to the standard closed-face cassette, which may be due to the collection of very large particles in wood working environments. Some projectile particles may be > 100 microm aerodynamic diameter and thus outside the range of the convention. Such particles, if present, can bias the estimates of concentration considerably. This study is part of an on-going research focus into selecting the most appropriate inhalable sampler for use in these industries, and to examine the impact of TLV changes. This study compared gravimetric analyses (National Institute of Occupational Safety and Health Method 0500) of side-by-side personal samples using the Button, IOM, and 37 mm closed-face cassette (CFC) under field-use conditions. A total of 51 good sample pairs were collected from three wood products industries involved in the manufacturing of cabinets, furniture, and shutters. Paired t-tests were run on each sample pair using Statistical Package for the Social Sciences (SPSS) version 10. The IOM and the CFC measured statistically different concentrations (p < 0.0005, n = 16). The IOM and Button measured statistically different concentrations (p = 0.020, n = 12). The Button and CFC did not measure statistically different concentrations of wood dust (p = 0.098, n = 23). Sampler ratios for IOM/CFC pairs ranged from 1.19-19 (median 3.35). Sampler ratios for IOM/Button pairs ranged from 0.49-163 (median 3.15). Sampler ratios for CFC/Button pairs ranged from 0.36-27 (median 1.2). In all cases, higher ratios were associated with higher concentrations. The median relative difference between the IOM's and CFC's is in accord with prior field studies in woodworking environments, and, taken together, the data imply a conversion factor greater than the 2.5 normally applied to CFC results to approximate inhalable values, as measured by the IOM. Raising the limit values by approximately 50% appears warranted for this particular situation of inhalable wood dust measured by the IOM. The IOM/Button and CFC/Button ratios were unexpectedly low, which may be due to the exclusion of very large particles, collected by the IOM and CFC samplers. Further work is required to explain these results.