Composition of Arkansas Grapes During Maturation

Changes in organic acid and glucose content during maturation and ripening of grapes grown in Arkansas in 1973 are shown for four French hybrid varieties, S5279, S10878, SV23- 657, and S13053, and for four rotundifolia varieties, Scuppernong, Tarheel, Fry, and Magoon. In all varieties the concentrations of malates and tartrates were highest in the early stages of berry growth after veraison. During ripening the titratable acidity decreased and Balling and pH measurements increased. Although varieties reached maturity on different dates, changes in parameters followed similar curves typical for grapes of the species but occurring over a short period (Johnson and Nagel 1976, Winkler 1970). Rotundifolia varieties showed unacceptable Balling-acid ratios as well as irregular maturation progress in the study period

The Relationship of MHC-Peptide Binding and T Cell Activation Probed Using Chemically Defined MHC Class II Oligomers

AbstractA series of novel chemically defined soluble oligomers of the human MHC class II protein HLA-DR1 was constructed to probe the molecular requirements for initiation of T cell activation. MHC dimers, trimers, and tetramers stimulated T cells, as measured by upregulation of the activation markers CD69 and CD25, and by internalization of activated T cell receptor subunits. Monomeric MHC-peptide complexes engaged T cell receptors but did not induce activation. For a given amount of receptor engagement, the extent of activation was equivalent for each of the oligomers and correlated with the number of T cell receptor cross-links induced. These results suggest that formation or rearrangement of a T cell receptor dimer is necessary and sufficient for initiation of T cell signaling

Characterizing antigen-specific CD4⁺ T cells using HLA-DR oligomers

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2002.Vita.Includes bibliographical references (leaves 152-165).This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.T cells are activated by the engagement of their surface T cell receptors (TCR) by antigenic peptide bound to major histocompatibility complex (MHC). The success or failure of this TCR to MHC-peptide interaction determines the specificity of T cell action, and thus plays a central role in proper immune function. In this thesis, soluble oligomers of MHC-peptide complex were used to investigate several aspects of the T cell immune response. Soluble fluorescent oligomers of human class II MHC were produced and used to detect CD4+ T cells of particular specificities. The critical parameters of this interaction were determined, and differing behaviors of various T cell clones were observed. The implications of these results are discussed, and MHC oligomers are suggested as powerful tools for the investigation T cell avidity modulation. Using a novel methodology for the analysis of the antigen-specific TCR repertoire which includes identification by MHC oligomers, T cells specific for a peptide derived from influenza were isolated, cloned and sequenced. This pool of sequences was observed to be extremely diverse in both VP usage and CDR3 sequence. These results are discussed with regard to the TCR repertoire, structural aspects of TCR/MHC-peptide interaction, and future studies of TCR repertoire analysis. Other studies investigating the triggering mechanism of TCR are summarized and implications of these results for various models of transmembrane activation are discussed. A novel mechanism is proposed involving the reorganization of a receptor oligomer from a specific inhibited state into an uninhibited state. Future directions of research based on the work presented in this thesis are suggested.by Thomas O. Cameron.Ph.D

Enrichment of Chemical Libraries Docked to Protein Conformational Ensembles and Application to Aldehyde Dehydrogenase 2

Molecular recognition is a complex process that involves a large ensemble of structures of the receptor and ligand. Yet, most structure-based virtual screening is carried out on a single structure typically from X-ray crystallography. Explicit-solvent molecular dynamics (MD) simulations offer an opportunity to sample multiple conformational states of a protein. Here we evaluate our recently developed scoring method SVMSP in its ability to enrich chemical libraries docked to MD structures of seven proteins from the Directory of Useful Decoys (DUD). SVMSP is a target-specific rescoring method that combines machine learning with statistical potentials. We find that enrichment power as measured by the area under the ROC curve (ROC-AUC) is not affected by increasing the number of MD structures. Among individual MD snapshots, many exhibited enrichment that was significantly better than the crystal structure, but no correlation between enrichment and structural deviation from crystal structure was found. We followed an innovative approach by training SVMSP scoring models using MD structures (SVMSPMD). The resulting models were applied to two difficult cases (p38 and CDK2) for which enrichment was not better than random. We found remarkable increase in enrichment power, particularly for p38, where the ROC-AUC increased by 0.30 to 0.85. Finally, we explored approaches for a priori identification of MD snapshots with high enrichment power from an MD simulation in the absence of active compounds. We found that the use of randomly selected compounds docked to the target of interest using SVMSP led to notable enrichment for EGFR and Src MD snapshots. SVMSP rescoring of protein–compound MD structures was applied for the search of small-molecule inhibitors of the mitochondrial enzyme aldehyde dehydrogenase 2 (ALDH2). Rank-ordering of a commercial library of 50 000 compounds docked to MD structures of ALDH2 led to five small-molecule inhibitors. Four compounds had IC50s below 5 μM. These compounds serve as leads for the design and synthesis of more potent and selective ALDH2 inhibitors

Enhancer control of MicroRNA miR-155 expression in EpsteinBarr virus-infected B cells

The oncogenic microRNA miR-155 is the most frequently upregulated miRNA in Epstein-Barr virus (EBV)-positive B cell malignancies and is upregulated in other non-viral lymphomas. Both the EBV nuclear antigen 2 (EBNA2), and B cell transcription factor, interferon regulatory factor 4 (IRF4) are known to activate transcription of the host cell gene from which miR-155 is processed (miR-155HG, BIC). EBNA2 also activates IRF4 transcription indicating that EBV may upregulate miR-155 through direct and indirect mechanisms. The mechanism of transcriptional regulation of IRF4 and miR-155HG by EBNA2 however has not been defined. We demonstrate that EBNA2 can activate IRF4 and miR-155HG expression through specific upstream enhancers that are dependent on the Notch signaling transcription factor RBPJ, a known binding partner of EBNA2. We demonstrate that in addition to activation of the miR-155HG promoter, IRF4 can also activate miR-155HG via the upstream enhancer also targeted by EBNA2. Gene editing to remove the EBNA2- and IRF4-responsive miR-155HG enhancer located 60 kb upstream of miR-155HG led to reduced miR155HG expression in EBV-infected cells. Our data therefore demonstrate that specific RBPJ-dependent enhancers regulate the IRF4-miR-155 expression network and play a key role in the maintenance of miR-155 expression in EBV-infected B cells. These findings provide important insights that will improve our understanding of miR-155 control in B cell malignancies

Travel history and malaria infection risk in a low-transmission setting in Ethiopia: a case control study

BACKGROUND: Malaria remains the leading communicable disease in Ethiopia, with around one million clinical cases of malaria reported annually. The country currently has plans for elimination for specific geographic areas of the country. Human movement may lead to the maintenance of reservoirs of infection, complicating attempts to eliminate malaria. METHODS: An unmatched case–control study was conducted with 560 adult patients at a Health Centre in central Ethiopia. Patients who received a malaria test were interviewed regarding their recent travel histories. Bivariate and multivariate analyses were conducted to determine if reported travel outside of the home village within the last month was related to malaria infection status. RESULTS: After adjusting for several known confounding factors, travel away from the home village in the last 30 days was a statistically significant risk factor for infection with Plasmodium falciparum (AOR 1.76; p=0.03) but not for infection with Plasmodium vivax (AOR 1.17; p=0.62). Male sex was strongly associated with any malaria infection (AOR 2.00; p=0.001). CONCLUSIONS: Given the importance of identifying reservoir infections, consideration of human movement patterns should factor into decisions regarding elimination and disease prevention, especially when targeted areas are limited to regions within a country

Identification of Novel Fibrosis Modifiers by In Vivo siRNA Silencing.

Fibrotic diseases contribute to 45% of deaths in the industrialized world, and therefore a better understanding of the pathophysiological mechanisms underlying tissue fibrosis is sorely needed. We aimed to identify novel modifiers of tissue fibrosis expressed by myofibroblasts and their progenitors in their disease microenvironment through RNA silencing in vivo. We leveraged novel biology, targeting genes upregulated during liver and kidney fibrosis in this cell lineage, and employed small interfering RNA (siRNA)-formulated lipid nanoparticles technology to silence these genes in carbon-tetrachloride-induced liver fibrosis in mice. We identified five genes, Egr2, Atp1a2, Fkbp10, Fstl1, and Has2, which modified fibrogenesis based on their silencing, resulting in reduced Col1a1 mRNA levels and collagen accumulation in the liver. These genes fell into different groups based on the effects of their silencing on a transcriptional mini-array and histological outcomes. Silencing of Egr2 had the broadest effects in vivo and also reduced fibrogenic gene expression in a human fibroblast cell line. Prior to our study, Egr2, Atp1a2, and Fkbp10 had not been functionally validated in fibrosis in vivo. Thus, our results provide a major advance over the existing knowledge of fibrogenic pathways. Our study is the first example of a targeted siRNA assay to identify novel fibrosis modifiers in vivo

Homeostatic competition drives tumor growth and metastasis nucleation

We propose a mechanism for tumor growth emphasizing the role of homeostatic regulation and tissue stability. We show that competition between surface and bulk effects leads to the existence of a critical size that must be overcome by metastases to reach macroscopic sizes. This property can qualitatively explain the observed size distributions of metastases, while size-independent growth rates cannot account for clinical and experimental data. In addition, it potentially explains the observed preferential growth of metastases on tissue surfaces and membranes such as the pleural and peritoneal layers, suggests a mechanism underlying the seed and soil hypothesis introduced by Stephen Paget in 1889 and yields realistic values for metastatic inefficiency. We propose a number of key experiments to test these concepts. The homeostatic pressure as introduced in this work could constitute a quantitative, experimentally accessible measure for the metastatic potential of early malignant growths.Comment: 13 pages, 11 figures, to be published in the HFSP Journa

Applying artificial intelligence to big data in hepatopancreatic and biliary surgery: a scoping review

Aim: Artificial Intelligence (AI) and its applications in healthcare are rapidly developing. The healthcare industry generates ever-increasing volumes of data that should be used to improve patient care. This review aims to examine the use of AI and its applications in hepatopancreatic and biliary (HPB) surgery, highlighting studies leveraging large datasets.Methods: A PRISMA-ScR compliant scoping review using Medline and Google Scholar databases was performed (5th August 2022). Studies focusing on the development and application of AI to HPB surgery were eligible for inclusion. We undertook a conceptual mapping exercise to identify key areas where AI is under active development for use in HPB surgery. We considered studies and concepts in the context of patient pathways - before surgery (including diagnostics), around the time of surgery (supporting interventions) and after surgery (including prognostication).Results: 98 studies were included. Most studies were performed in China or the USA (n = 45). Liver surgery was the most common area studied (n = 51). Research into AI in HPB surgery has increased rapidly in recent years, with almost two-thirds published since 2019 (61/98). Of these studies, 11 have focused on using “big data” to develop and apply AI models. Nine of these studies came from the USA and nearly all focused on the application of Natural Language Processing. We identified several critical conceptual areas where AI is under active development, including improving preoperative optimization, image guidance and sensor fusion-assisted surgery, surgical planning and simulation, natural language processing of clinical reports for deep phenotyping and prediction, and image-based machine learning.Conclusion: Applications of AI in HPB surgery primarily focus on image analysis and computer vision to address diagnostic and prognostic uncertainties. Virtual 3D and augmented reality models to support complex HPB interventions are also under active development and likely to be used in surgical planning and education. In addition, natural language processing may be helpful in the annotation and phenotyping of disease, leading to new scientific insights