Miracle-dz/UniFAR-FTUs huggingface dataset:
Impaired Innate and Adaptive Immunity to Streptococcus pneumoniae and Its Effect on Colonization in an Infant Mouse Model

ABSTRACT Streptococcus pneumoniae colonization and invasive disease peak around the third and first birthdays, respectively, and decline thereafter. While these declines are attributable in part to immunity acquired via natural exposure, maturation of innate immune responses may also be involved. A mucosally administered candidate whole-cell pneumococcal vaccine (WCV) containing killed pneumococcal antigen (WCA) plus a cholera toxin adjuvant protects against intranasal carriage of pneumococci by a mechanism that is antibody independent and CD4+ TH17 cell dependent. Because infants and children are a key target population for this vaccine, we sought to evaluate the immune responses of neonatal and infant mice to S. pneumoniae and to assess whether the WCV would be effective in these mice. Like human infants, infant mice showed impaired clearance of nasopharyngeal colonization with S. pneumoniae. Macrophages from neonatal and infant mice stimulated with killed pneumococci in vitro showed significantly reduced cytokine production, including that of KC, granulocyte colony-stimulating factor, granulocyte-macrophage colony-stimulating factor, macrophage chemoattractant protein 1, interleukin-6 (IL-6), IL-1α, tumor necrosis factor alpha, and gamma interferon, whereas IL-10 expression was significantly increased compared to that in macrophages from adult mice. IL-17A production from adult immune CD4+ T cells was significantly delayed when neonatal macrophages instead of adult macrophages were used as antigen-presenting cells. Moreover, whole blood from mice immunized as neonates with WCV produced significantly less IL-17A after stimulation with WCA than did blood from mice immunized as adults. Nonetheless, a single immunization of neonatal mice with WCV significantly reduced colonization density. Overall, our data suggest an impairment of both innate and acquired cellular immune responses in neonatal and infant mice. However, WCV confers a significant reduction in colonization following pneumococcal challenge, suggesting that it may still be effective in the setting of immature immune responses.
The Streptococcuspneumoniae Capsule Inhibits Complement Activity and Neutrophil Phagocytosis by Multiple Mechanisms

ABSTRACT The Streptococcuspneumoniae capsule is vital for virulence and may inhibit complement activity and phagocytosis. However, there are only limited data on the mechanisms by which the capsule affects complement and the consequences for S. pneumoniae interactions with phagocytes. Using unencapsulated serotype 2 and 4 S. pneumoniae mutants, we have confirmed that the capsule has several effects on complement activity. The capsule impaired bacterial opsonization with C3b/iC3b by both the alternative and classical complement pathways and also inhibited conversion of C3b bound to the bacterial surface to iC3b. There was increased binding of the classical pathway mediators immunoglobulin G (IgG) and C-reactive protein (CRP) to unencapsulated S. pneumoniae, indicating that the capsule could inhibit classical pathway complement activity by masking antibody recognition of subcapsular antigens, as well as by inhibiting CRP binding. Cleavage of serum IgG by the enzyme IdeS reduced C3b/iC3b deposition on all of the strains, but there were still marked increases in C3b/iC3b deposition on unencapsulated TIGR4 and D39 strains compared to encapsulated strains, suggesting that the capsule inhibits both IgG-mediated and IgG-independent complement activity against S. pneumoniae. Unencapsulated strains were more susceptible to neutrophil phagocytosis after incubation in normal serum, normal serum treated with IdeS, complement-deficient serum, and complement-deficient serum treated with IdeS or in buffer alone, suggesting that the capsule inhibits phagocytosis mediated by Fcγ receptors, complement receptors, and nonopsonic receptors. Overall, these data show that the S. pneumoniae capsule affects multiple aspects of complement- and neutrophil-mediated immunity, resulting in a profound inhibition of opsonophagocytosis.
Evidence for an Intramacrophage Growth Phase of Mycobacterium ulcerans

ABSTRACT Mycobacterium ulcerans is the etiologic agent of Buruli ulcer (BU), an emerging tropical skin disease. Virulent M. ulcerans secretes mycolactone, a cytotoxic exotoxin with a key pathogenic role. M. ulcerans in biopsy specimens has been described as an extracellular bacillus. In vitro assays have suggested a mycolactone-induced inhibition of M. ulcerans uptake by macrophages in which its proliferation has not been demonstrated. Therefore, and uniquely for a mycobacterium, M. ulcerans has been classified as an extracellular pathogen. In specimens from patients and in mouse footpad lesions, extracellular bacilli were concentrated in central necrotic acellular areas; however, we found bacilli within macrophages in surrounding inflammatory infiltrates. We demonstrated that mycolactone-producing M. ulcerans isolates are efficiently phagocytosed by murine macrophages, indicating that the extracellular location of M. ulcerans is not a result of inhibition of phagocytosis. Additionally, we found that M. ulcerans multiplies inside cultured mouse macrophages when low multiplicities of infection are used to prevent early mycolactone-associated cytotoxicity. Following the proliferation phase within macrophages, M. ulcerans induces the lysis of the infected host cells, becoming extracellular. Our data show that M. ulcerans, like M. tuberculosis, is an intracellular parasite with phases of intramacrophage and extracellular multiplication. The occurrence of an intramacrophage phase is in accordance with the development of cell-mediated and delayed-type hypersensitivity responses in BU patients.
The Yersinia pestis Ail Protein Mediates Binding and Yop Delivery to Host Cells Required for Plague Virulence

ABSTRACT Although adhesion to host cells is a critical step in the delivery of cytotoxic Yop proteins by Yersinia pestis, the mechanism has not been defined. To identify adhesins critical for Yop delivery, we initiated two transposon mutagenesis screens using the mariner transposon. To avoid redundant cell binding activities, we initiated the screen with a strain deleted for two known adhesins, pH 6 antigen and the autotransporter, YapC, as well as the Caf1 capsule, which is known to obscure some adhesins. The mutants that emerged contained insertions within the ail (attachment and invasion locus) gene of Y. pestis. A reconstructed mutant with a single deletion in the ail locus (y1324) was severely defective for delivery of Yops to HEp-2 human epithelial cells and significantly defective for delivery of Yops to THP-1 human monocytes. Specifically, the Yop delivery defect was apparent when cell rounding and translocation of an ELK-tagged YopE derivative into host cells were monitored. Although the ail mutant showed only a modest decrease in cell binding capacity in vitro, the KIM5 Δail mutant exhibited a >3,000-fold-increased 50% lethal dose in mice. Mice infected with the Δail mutant also had 1,000-fold fewer bacteria in their spleens, livers, and lungs 3 days after infection than did those infected with the parental strain, KIM5. Thus, the Ail protein is critical for both Y. pestis type III secretion in vitro and infection in mice.
Toll-Like Receptor 7 Mediates Early Innate Immune Responses to Malaria

ABSTRACT Innate immune recognition of malaria parasites is the critical first step in the development of the host response. At present, Toll-like receptor 9 (TLR9) is thought to play a central role in sensing malaria infection. However, we and others have observed that Tlr9 −/− mice, in contrast to mice deficient in the downstream adaptor, Myeloid differentiation primary response gene 88 (MYD88), exhibit few deficiencies in immune function during early infection with the malaria parasite Plasmodium chabaudi, implying that another MYD88-dependent receptor also contributes to the antimalarial response. Here we use candidate-based screening to identify TLR7 as a key sensor of early P. chabaudi infection. We show that TLR7 mediates a rapid systemic response to infection through induction of cytokines such as type I interferons (IFN-I), interleukin 12, and gamma interferon. TLR7 is also required for induction of IFN-I by other species and strains of Plasmodium, including an etiological agent of human disease, P. falciparum, suggesting that malaria parasites harbor a common pathogen-associated molecular pattern (PAMP) recognized by TLR7. In contrast to the nonredundant requirement for TLR7 in early immune activation, sensing through both TLR7 and TLR9 was required for proinflammatory cytokine production and immune cell activation during the peak of parasitemia. Our findings indicate that TLR7 plays a central role in early immune activation during malaria infection, whereas TLR7 and TLR9 contribute combinatorially to immune responses as infection progresses.
A Comparative Genomic Analysis of Diverse Clonal Types of Enterotoxigenic Escherichia coli Reveals Pathovar-Specific Conservation

ABSTRACT Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrheal illness in children less than 5 years of age in low- and middle-income nations, whereas it is an emerging enteric pathogen in industrialized nations. Despite being an important cause of diarrhea, little is known about the genomic composition of ETEC. To address this, we sequenced the genomes of five ETEC isolates obtained from children in Guinea-Bissau with diarrhea. These five isolates represent distinct and globally dominant ETEC clonal groups. Comparative genomic analyses utilizing a gene-independent whole-genome alignment method demonstrated that sequenced ETEC strains share approximately 2.7 million bases of genomic sequence. Phylogenetic analysis of this “core genome” confirmed the diverse history of the ETEC pathovar and provides a finer resolution of the E. coli relationships than multilocus sequence typing. No identified genomic regions were conserved exclusively in all ETEC genomes; however, we identified more genomic content conserved among ETEC genomes than among non-ETEC E. coli genomes, suggesting that ETEC isolates share a genomic core. Comparisons of known virulence and of surface-exposed and colonization factor genes across all sequenced ETEC genomes not only identified variability but also indicated that some antigens are restricted to the ETEC pathovar. Overall, the generation of these five genome sequences, in addition to the two previously generated ETEC genomes, highlights the genomic diversity of ETEC. These studies increase our understanding of ETEC evolution, as well as provide insight into virulence factors and conserved proteins, which may be targets for vaccine development.
Alveolar Epithelial Cells Are Critical in Protection of the Respiratory Tract by Secretion of Factors Able To Modulate the Activity of Pulmonary Macrophages and Directly Control Bacterial Growth

ABSTRACT The respiratory epithelium is a physical and functional barrier actively involved in the clearance of environmental agents. The alveolar compartment is lined with membranous pneumocytes, known as type I alveolar epithelial cells (AEC I), and granular pneumocytes, type II alveolar epithelial cells (AEC II). AEC II are responsible for epithelial reparation upon injury and ion transport and are very active immunologically, contributing to lung defense by secreting antimicrobial factors. AEC II also secrete a broad variety of factors, such as cytokines and chemokines, involved in activation and differentiation of immune cells and are able to present antigen to specific T cells. Another cell type important in lung defense is the pulmonary macrophage (PuM). Considering the architecture of the alveoli, a good communication between the external and the internal compartments is crucial to mount effective responses. Our hypothesis is that being in the interface, AEC may play an important role in transmitting signals from the external to the internal compartment and in modulating the activity of PuM. For this, we collected supernatants from AEC unstimulated or stimulated in vitro with lipopolysaccharide (LPS). These AEC-conditioned media were used in various setups to test for the effects on a number of macrophage functions: (i) migration, (ii) phagocytosis and intracellular control of bacterial growth, and (iii) phenotypic changes and morphology. Finally, we tested the direct effect of AEC-conditioned media on bacterial growth. We found that AEC-secreted factors had a dual effect, on one hand controlling bacterial growth and on the other hand increasing macrophage activity.
FlashTrie: Beyond 100-Gb/s IP Route Lookup Using Hash-Based Prefix-Compressed Trie

It is becoming apparent that the next-generation IP route lookup architecture needs to achieve speeds of 100 Gb/s and beyond while supporting IPv4 and IPv6 with fast real-time updates to accommodate ever-growing routing tables. Some of the proposed multibit-trie-based schemes, such as TreeBitmap, have been used in today's high-end routers. However, their large data structures often require multiple external memory accesses for each route lookup. A pipelining technique is widely used to achieve high-speed lookup with the cost of using many external memory chips. Pipelining also often leads to poor memory load-balancing. In this paper, we propose a new IP route lookup architecture called FlashTrie that overcomes the shortcomings of the multibit-trie-based approaches. We use a hash-based membership query to limit off-chip memory accesses per lookup and to balance memory utilization among the memory modules. By compacting the data structure size, the lookup depth of each level can be increased. We also develop a new data structure called Prefix-Compressed Trie that reduces the size of a bitmap by more than 80%. Our simulation and implementation results show that FlashTrie can achieve 80-Gb/s worst-case throughput while simultaneously supporting 2 M prefixes for IPv4 and 318 k prefixes for IPv6 with one lookup engine and two Double-Data-Rate (DDR3) SDRAM chips. When implementing five lookup engines on a state-of-the-art field programmable gate array (FPGA) chip and using 10 DDR3 memory chips, we expect FlashTrie to achieve 1-Gpps (packet per second) throughput, equivalent to 400 Gb/s for IPv4 and 600 Gb/s for IPv6. FlashTrie also supports incremental real-time updates.
08 Disruption of hexokinase II-mitochondrial binding affects cardiac oxygen consumption and lactate production in the beating heart

Background The glycolytic enzyme hexokinase (HK) is located either in the cytosol or bound to mitochondria (mitoHK). We recently demonstrated that a decrease in mitoHK increased cardiac ischaemia (I)-reperfusion (R) injury and cardiac remodelling, and prevented ischaemic preconditioning. However, the physiological implication of HK binding to mitochondria is unknown. Hypothesis In the present study we hypothesise that mitoHK affects cardiac oxygen consumption (MVO2) and glycolysis-glucose oxidation coupling (lactate efflux). Methods and Results Isolated Langendorff perfused rat hearts (substrate 10 mM glucose) were treated 20 min with saline (control group 1), 1 μM TAT only (control group 2), 200 nM TAT-HKII or 1 μM TAT- HKII, followed by 15 min I and 30 min R. TAT-HKII peptide contains the binding motif of HKII with mitochondria and was shown to displace HKII from mitochondria. MVO2 and lactate efflux were measured during peptide treatment. Low-dose TAT-HK reduced cardiac MVO2 by approximately 10%. High-dose TAT-HK only transiently reduced MVO2, with increased MVO2 at the end of peptide treatment. Effluent lactate concentration increased dose-dependently with TAT-HK peptide treatment from 0.02 to 0.03 mM (control groups) to 0.06 mM (200 nM TAT-HK) and 0.09 mM (1 μM TAT-HK). No cell necrosis was observed in both control groups following IR. However, TAT-HK treatment dose-dependently increased cell necrosis. Peptide treatment was not associated with changes in MDA or aconitase activity. Conclusions This study shows for the first time that mitoHK affects cardiac MVO2. In addition, our data suggest that mitoHK may also determine glycolysis-glucose oxidation coupling.
Anterior and Posterior Corneal Spherical Aberration Measured With Pentacam in the Korean

Purpose: To evaluate the spherical aberrations of the anterior and posterior surfaces of normal corneas using Pentacam in a Korean sample population and determine their ranges and changes with age. Methods: We used Pentacam (Oculus Inc.,Germany) to measure the anterior and posterior corneal spherical aberrations of 240 eyes in 240 patients with normal corneas who visited our clinic. The means and ranges of spherical aberrations and their changes with age were determined. We examined both eyes of 90 patients to confirm the inter-ocular symmetry in spherical aberration. Results: The mean age of the 240 patients (M:F=103:137) was 49.8 years (range: 20-79), and the mean spherical aberrations of the anterior and posterior surfaces of the cornea were 0.2300. 078 , and -0.040. 021 , respectively. The mean total corneal spherical aberration was 0.190. 087 . There were no differences between males and females, and inter-ocular symmetry was observed in all tested patients. There was a tendency for the values of anterior, posterior and total corneal spherical aberration to increase with age. Ranges of spherical aberrations were from -0.177 to 0.423 in the anterior cornea, from -0.083 to 0.034 in the posterior cornea, and from -0.238 to 0.410 in the total cornea. Conclusions: In a Korean population, the mean total corneal spherical aberration was 0.19 , which was shown to increase with age. Some patients were shown to have an extreme value. Based on these results, a preoperative analysis for corneal spherical aberration may be helpful when selecting aspheric intraocular lenses.
Babesia divergens Apical Membrane Antigen 1 and Its Interaction with the Human Red Blood Cell

ABSTRACT Multiple parasite ligand-erythrocyte receptor interactions must occur for successful Babesia and Plasmodium invasion of the human red cell. One such parasite ligand is the apical membrane antigen 1 (AMA1) which is a conserved apicomplexan protein present in the micronemes and then secreted onto the surface of the merozoite. Much evidence exists for a vital role for AMA1 in host cell invasion; however, its interaction with the host erythrocyte has remained controversial. In this paper, we present a detailed characterization of a Babesia divergens homolog of AMA1 (BdAMA1), and taking advantage of the relatively high amounts of native BdAMA1 available from the parasite culture system, show that proteolytic products of native BdAMA1 bind to a trypsin- and chymotrypsin-sensitive receptor on the red blood cell. Moreover, immuno-electron microscopic images of the B. divergens merozoite captured during invasion offer additional evidence of the presence of BdAMA1 on the red cell membrane. Given the importance of AMA1 in invasion and the central role invasion plays in pathogenesis, these studies have implications both for novel drug design and for the development of new vaccine approaches aimed at interfering with AMA1 function.
Toll-Like Receptor 9 Signaling in Dendritic Cells Regulates Neutrophil Recruitment to Inflammatory Foci following Leishmania infantum Infection

ABSTRACT Leishmania infantum is a protozoan parasite that causes visceral leishmaniasis (VL). This infection triggers dendritic cell (DC) activation through the recognition of microbial products by Toll-like receptors (TLRs). Among the TLRs, TLR9 is required for DC activation by different Leishmania species. We demonstrated that TLR9 is upregulated in vitro and in vivo during infection. We show that C57BL/6 mice deficient in TLR9 expression (TLR9−/− mice) are more susceptible to infection and display higher parasite numbers in the spleen and liver. The increased susceptibility of TLR9−/− mice was due to the impaired recruitment of neutrophils to the infection foci associated with reduced levels of neutrophil chemoattractants released by DCs in the target organs. Moreover, both Th1 and Th17 cells were also committed in TLR9−/− mice. TLR9-dependent neutrophil recruitment is mediated via the MyD88 signaling pathway but is TIR domain-containing adapter-inducing interferon beta (TRIF) independent. Furthermore, L. infantum failed to activate both plasmacytoid and myeloid DCs from TLR9−/− mice, which presented reduced surface costimulatory molecule expression and chemokine release. Interestingly, neutrophil chemotaxis was affected both in vitro and in vivo when DCs were derived from TLR9−/− mice. Our results suggest that TLR9 plays a critical role in neutrophil recruitment during the protective response against L. infantum infection that could be associated with DC activation.
Yersinia enterocolitica Inhibits Salmonella enterica Serovar Typhimurium and Listeria monocytogenes Cellular Uptake

ABSTRACT Yersinia enterocolitica biovar 1B employs two type three secretion systems (T3SS), Ysa and Ysc, which inject effector proteins into macrophages to prevent phagocytosis. Conversely, Salmonella enterica serovar Typhimurium uses a T3SS encoded by Salmonella pathogenicity island 1 (SPI1) to actively invade cells that are normally nonphagocytic and a second T3SS encoded by SPI2 to survive within macrophages. Given the distinctly different outcomes that occur with regard to host cell uptake of S. Typhimurium and Y. enterocolitica, we investigated how each pathogen influences the internalization outcome of the other. Y. enterocolitica reduces S. Typhimurium invasion of HeLa and Caco-2 cells to a level similar to that observed using an S. Typhimurium SPI1 mutant alone. However, Y. enterocolitica had no effect on S. Typhimurium uptake by J774.1 or RAW264.7 macrophage-like cells. Y. enterocolitica was also able to inhibit the invasion of epithelial and macrophage-like cells by Listeria monocytogenes. Y. enterocolitica mutants lacking either the Ysa or Ysc T3SS were partially defective, while double mutants were completely defective, in blocking S. Typhimurium uptake by epithelial cells. S. Typhimurium encodes a LuxR homolog, SdiA, which detects N-acylhomoserine lactones (AHLs) produced by Y. enterocolitica and upregulates the expression of an invasin (Rck) and a putative T3SS effector (SrgE). Two different methods of constitutively activating the S. Typhimurium SdiA regulon failed to reverse the uptake blockade imposed by Y. enterocolitica.
Enhancing Mobile Networks With Software Defined Networking and Cloud Computing

In the past decade, mobile devices and applications have experienced an explosive growth, and users are expecting higher data rates and better quality services every year. In this paper, we propose several ideas to increase the functionality and capacity of wireless networks using software-defined networking (SDN) and cloud computing technologies. Connections between users and services in mobile networks typically have to pass through a required set of middleboxes. The complex routing is one of the major impetus for the SDN paradigm, which enables flexible policy-aware routing in the next generation mobile networks. In addition, the high costs of middleboxes and limited capabilities of mobile devices call for revolutionary virtualization technologies enabled by cloud computing. Based on these, we consider an online routing problem for mobile networks with SDN and cloud computing. In this problem, connection requests are given one at a time (as in a real mobile system), and the objective is to steer traffic flows to maximize the total amount of traffic accepted over time, subject to capacity, budget, policy, and quality of service constraints. A fast log-competitive approximation algorithm is developed based on time-dependent duals.