Generalized Martingale and stopping time techniques in Banach spaces.

Probability theory plays a crucial role in the study of the geometry of Banach spaces. In the literature, notions from probability theory have been formulated and studied in the measure free setting of vector lattices. However, there is little evidence of these vector lattice techniques being used in the study of geometry of Banach spaces. In this thesis, we fill this niche. Using the l-tensor product of Chaney-Shaefer, we are able to extend the available vector lattice techniques and apply them to the Lebesgue-Bochner spaces. As a consequence, we obtain new characterizations of the Radon Nikod´ym property and the UMD property

Coherent risk measures and arbitrage

A dissertation submitted to the Faculty of Science, University of the Witwatersrand, in fulfillment of the requirements for the degree of Master of Science, April 2013.No abstract provide

Compositional and functional differences in the human gut microbiome correlate with clinical outcome following infection with wild-type Salmonella enterica serovar Typhi.

Insights into disease susceptibility as well as the efficacy of vaccines against typhoid and other enteric pathogens may be informed by better understanding the relationship between the effector immune response and the gut microbiota. In the present study, we characterized the composition (16S rRNA gene profiling) and function (RNA sequencing [RNA-seq]) of the gut microbiota following immunization and subsequent exposure to wild-type Salmonella enterica serovar Typhi in a human challenge model to further investigate the central hypothesis that clinical outcomes may be linked to the gut microbiota. Metatranscriptome analysis of longitudinal stool samples collected from study subjects revealed two stable patterns of gene expression for the human gut microbiota, dominated by transcripts from either Methanobrevibacter or a diverse representation of genera in the Firmicutes phylum. Immunization with one of two live oral attenuated vaccines against S. Typhi had minimal effects on the composition or function of the gut microbiota. It was observed that subjects harboring the methanogen-dominated transcriptome community at baseline displayed a lower risk of developing symptoms of typhoid following challenge with wild-type S. Typhi. Furthermore, genes encoding antioxidant proteins, metal homeostasis and transport proteins, and heat shock proteins were expressed at a higher level at baseline or after challenge with S. Typhi in subjects who did not develop symptoms of typhoid. These data suggest that functional differences relating to redox potential and ion homeostasis in the gut microbiota may impact clinical outcomes following exposure to wild-type S. Typhi.IMPORTANCES. Typhi is a significant cause of systemic febrile morbidity in settings with poor sanitation and limited access to clean water. It has been demonstrated that the human gut microbiota can influence mucosal immune responses, but there is little information available on the impact of the human gut microbiota on clinical outcomes following exposure to enteric pathogens. Here, we describe differences in the composition and function of the gut microbiota in healthy adult volunteers enrolled in a typhoid vaccine trial and report that these differences are associated with host susceptibility to or protection from typhoid after challenge with wild-type S Typhi. Our observations have important implications in interpreting the efficacy of oral attenuated vaccines against enteric pathogens in diverse populations

Independent evolution of shape and motility allows evolutionary flexibility in Firmicutes bacteria

Functional morphological adaptation is an implicit assumption across many ecological studies. However, despite a few pioneering attempts to link bacterial form and function, functional morphology is largely unstudied in prokaryotes. One intriguing candidate for analysis is bacterial shape, as multiple lines of theory indicate that cell shape and motility should be strongly correlated. Here we present a large-scale use of modern phylogenetic comparative methods to explore this relationship across 325 species of the phylum Firmicutes. In contrast to clear predictions from theory, we show that cell shape and motility are not coupled, and that transitions to and from flagellar motility are common and strongly associated with lifestyle (free-living or host-associated). We find no association between shape and lifestyle, and contrary to recent evidence, no indication that shape is associated with pathogenicity. Our results suggest that the independent evolution of shape and motility in this group might allow a greater evolutionary flexibility

How can the MHC mediate social odor via the microbiota community? A deep dive into mechanisms

Genes of the major histocompatibility complex (MHC) have long been linked to odor signaling and recently researchers’ attention has focused on MHC structuring of microbial communities and how this may in turn impact odor. However, understanding of the mechanisms through which the MHC could affect the microbiota to produce a chemical signal that is both reliable and strong enough to ensure unambiguous transmission of behaviorally important information remains poor. This is largely because empirical studies are rare, predictions are unclear, and the underlying immunological mechanisms governing MHC-microbiota interactions are often neglected. Here we review the immunological processes involving MHC class II (MHC-II) that could affect the commensal community. Focusing on immunological and medical research, we provide background knowledge for non-immunologists by describing key players within the vertebrate immune system relating to MHC-II molecules (which present extracellular-derived peptides, and thus interact with extracellular commensal microbes). We then systematically review the literature investigating MHC-odor-microbiota interactions in animals and identify areas for future research. These insights will help to design studies that are able to explore the role of MHC-II and the microbiota in the behavior of wild populations in their natural environment and consequently propel this research area forward

Bacterial Flagella: Twist and Stick, or Dodge across the Kingdoms

The flagellum organelle is an intricate multiprotein assembly best known for its rotational propulsion of bacteria. However, recent studies have expanded our knowledge of other functions in pathogenic contexts, particularly adherence and immune modulation, e.g., for Salmonella enterica, Campylobacter jejuni, Pseudomonas aeruginosa, and Escherichia coli. Flagella-mediated adherence is important in host colonisation for several plant and animal pathogens, but the specific interactions that promote flagella binding to such diverse host tissues has remained elusive. Recent work has shown that the organelles act like probes that find favourable surface topologies to initiate binding. An emerging theme is that more general properties, such as ionic charge of repetitive binding epitopes and rotational force, allow interactions with plasma membrane components. At the same time, flagellin monomers are important inducers of plant and animal innate immunity: variation in their recognition impacts the course and outcome of infections in hosts from both kingdoms. Bacteria have evolved different strategies to evade or even promote this specific recognition, with some important differences shown for phytopathogens. These studies have provided a wider appreciation of the functions of bacterial flagella in the context of both plant and animal reservoirs

Anti-flagellin antibodies inhibit motility in Roseburia intestinalis and Clostridium ramosum

Here we show that antibodies with specificity to the flagellin protein of Roseburia hominis (Fla2) and Escherichia coli (FliC) are capable of inhibiting motility of cultured Roseburia intestinalis and Clostridium ramosum within 30 minutes of application. Anti-mouse antibodies are included as a specificity control.Video 1. Clostridiumramosumanti-mouse30min. This is Clostridium ramosum 30 minutes after the addition of anti-mouse antibody. Motility is not noticeably altered.Video 2. Clostridiumramosumcontrol30min. This is Clostridium ramosum without the addition of antibody. Motility is not noticeably altered.Video 3. ClostridiumramosumFla230min. This is Clostridium ramosum 30 minutes after the addition of anti-Fla2 antibody. Motility is noticeably inhibited.Video 4. ClostridiumramosumFliC30min. This is Clostridium ramosum 30 minutes after the addition of anti-FliC antibody. Motility is noticeably inhibited.Video 5. Roseburiaintestinalisanti-mouse30min. This is Roseburia intestinalis 30 minutes after the addition of anti-mouse antibody. Motility is not noticeably altered.Video 6. Roseburiaintestinaliscontrol30min. This is Roseburia intestinalis without the addition of antibody. Motility is not noticeably altered.Video 7. RoseburiaintestinalisFla230min. This is Roseburia intestinalis 30 minutes after the addition of anti-Fla2 antibody. Motility is noticeably inhibited.Video 8. RoseburiaintestinalisFliC30min. This is Roseburia intestinalis 30 minutes after the addition of anti-FliC antibody. Motility is noticeably inhibited

The gut microbiome of TLR5-/- mice displays increased motility, which can be inhibited by anti-flagellin antibodies

TLR5-/- mice have an innate immune deficiency in recognizing bacterial flagellin, which results in increased flagellin expression by the microbiota and decreased anti-flagellin antibodies produced by the host. Here we show that the gut microbiome of TLR5-/- mice displays increased motility compared to wild-type controls (WT). The addition of antibodies with specificity to the flagellin protein of Roseburia hominis (Fla2) and Escherichia coli (FliC) decreased motility in bacteria from both mouse types within one hour