Comparative genomics of fungal allergens and epitopes shows widespread distribution of closely related allergen and epitope orthologues

BACKGROUND: Allergy is a common debilitating and occasionally life threatening condition. The fungal kingdom contains a number of species that produce a wide range of well defined protein allergens although the vast majority of fungal species have unknown allergenic potential. The recent genome sequencing of a variety of fungi provides the opportunity to assess the occurrence of allergen orthologues across the fungal kingdom. Here we use comparative genomics to survey the occurrence of allergen orthologues in fungi. RESULTS: A database of 82 allergen sequences was compiled and used to search 22 fungal genomes. Additionally we were able to model allergen structure for representative members of several highly homologous allergen orthologue classes. We found that some allergen orthologue classes that had predicted structural congruence to allergens and allergen epitopes were ubiquitous in all fungi. Other allergen orthologues classes were less well conserved and may not possess conserved allergen epitope orthologues in all fungi. A final group of allergen orthologues, including the major allergens Asp f 1 and Alt a 1, appear to be present in only a limited number of species. CONCLUSION: These results imply that most fungi may possess proteins that have potential to be allergens or to cross react with allergens. This, together with the observation that important allergens such as Asp f 1 are limited to genera or species, has significant implications for understating fungal sensitization, and interpreting diagnosis and management of fungal allergy

Aspergillus fumigatus allergen expression is coordinately regulated in response to hydrogen peroxide and cyclic AMP

<p>Abstract</p> <p>Background</p> <p><it>A. fumigatus </it>has been associated with a wide spectrum of allergic disorders such as ABPA or SAFS. It is poorly understood what allergens in particular are being expressed during fungal invasion and which are responsible for stimulation of immune responses. Study of the dynamics of allergen production by fungi may lead to insights into how allergens are presented to the immune system.</p> <p>Methods</p> <p>Expression of 17 <it>A. fumigatus </it>allergen genes was examined in response to various culture conditions and stimuli as well as in the presence of macrophages in order to mimic conditions encountered in the lung.</p> <p>Results</p> <p>Expression of 14/17 allergen genes was strongly induced by oxidative stress caused by hydrogen peroxide (Asp f 1, -2, -4, -5, -6, -7, -8, -10, -13, -17 and -18, all >10-fold and Asp f 11, -12, and -22, 5-10-fold) and 16/17 allergen genes were repressed in the presence of cAMP. The 4 protease allergen genes (Asp f -5, -10, -13 and -18) were expressed at very low levels compared to the comparator (<it>β</it>-tubulin) under all other conditions examined. Mild heat shock, anoxia, lipid and presence of macrophages did not result in coordinated changes in allergen gene expression. Growth on lipid as sole carbon source contributed to the moderate induction of most of the allergen genes. Heat shock (37°C > 42°C) caused moderate repression in 11/17 genes (Asp f 1, -2, -4, -5, -6, -9, -10, -13, -17, -18 and -23) (2- to 9-fold), which was mostly evident for Asp f 1 and -9 (~9-fold). Anaerobic stress led to moderate induction of 13/17 genes (1.1 to 4-fold) with one, Asp f 8 induced over 10-fold when grown under mineral oil. Complex changes were seen in gene expression during co-culture of <it>A. fumigatus </it>with macrophages.</p> <p>Conclusions</p> <p>Remarkable coordination of allergen gene expression in response to a specific condition (oxidative stress or the presence of cAMP) has been observed, implying that a single biological stimulus may play a role in allergen gene regulation. Interdiction of a putative allergen expression induction signalling pathway might provide a novel therapy for treatment of fungal allergy.</p

Calculation of Minimum-Detectable-Concentration Levels of Radioxenon Isotopes Using the PNNL ARSA System

Measurement of xenon fission product isotopes is a key element in the global network being established to monitor the Comprehensive Nuclear-Test-Ban Treaty. The automated Radio-xenon Analyzer/Sampler (ARSA), built by Pacific Northwest National Laboratory, can detect 131mXe, 133mXe, 133Xe, and 135Xe via a beta-gamma counting system. Due to the variable background and sources of these four radio-xenon isotopes, it is important to have as sensitive a detection system as possible and to quantify the Minimum-Detectable-Concentrations (MDC) that such a system will be able to detect to preclude false negative and false positive results. From data obtained from IAR in Germany MDC values for 133Xe were well below the 1 mBq/SCMA as required by the PTS for the Comprehensive Test BAn Treaty [WGB TL-11,1999]

Monte Carlo studies of two-dimensional polymer–solvent systems

<div><p>Allergic bronchopulmonary aspergillosis (ABPA) in asthma is a severe, life-affecting disease that potentially affects over 4.8 million people globally. In the UK, ABPA is predominantly caused by the fungus <i>Aspergillus fumigatus</i>. Phagocytosis is important in clearance of this fungus, and Early Endosome Antigen 1 (<i>EEA1</i>) has been demonstrated to be involved in phagocytosis of fungi. We sought to investigate the role of <i>EEA1</i> mutations and phagocytosis in ABPA. We used exome sequencing to identify variants in <i>EEA1</i> associated with ABPA. We then cultured monocyte-derived macrophages (MDMs) from 17 ABPA subjects with <i>A</i>. <i>fumigatus</i> conidia, and analyzed phagocytosis and phagolysosome acidification in relation to the presence of these variants. We found that variants in <i>EEA1</i> were associated with ABPA and with the rate of phagocytosis of <i>A</i>. <i>fumigatus</i> conidia and the acidification of phagolysosomes. MDMs from ABPA subjects carrying the disease associated genotype showed increased acidification and phagocytosis compared to those from ABPA subjects carrying the non-associated genotypes or healthy controls.The identification of ABPA-associated variants in EEA that have functional effects on MDM phagocytosis and phagolysosome acidification of <i>A</i>. <i>fumigatus</i> conidia revolutionizes our understanding of susceptibility to this disease, which may in future benefit patients by earlier identification or improved treatments. We suggest that the increased phagocytosis and acidification observed demonstrates an over-active MDM profile in these patients, resulting in an exaggerated cellular response to the presence of <i>A</i>. <i>fumigatus</i> in the airways.</p></div

Bradyzoite pseudokinase 1 is crucial for efficient oral infectivity of the Toxoplasma gondii tissue cyst.

The tissue cyst formed by the bradyzoite stage of Toxoplasma gondii is essential for persistent infection of the host and oral transmission. Bradyzoite pseudokinase 1 (BPK1) is a component of the cyst wall, but nothing has previously been known about its function. Here, we show that immunoprecipitation of BPK1 from in vitro bradyzoite cultures, 4 days postinfection, identifies at least four associating proteins: MAG1, MCP4, GRA8, and GRA9. To determine the role of BPK1, a strain of Toxoplasma was generated with the bpk1 locus deleted. This BPK1 knockout strain (Δbpk1) was investigated in vitro and in vivo. No defect was found in terms of in vitro cyst formation and no difference in pathogenesis or cyst burden 4 weeks postinfection (wpi) was detected after intraperitoneal (i.p.) infection with Δbpk1 tachyzoites, although the Δbpk1 cysts were significantly smaller than parental or BPK1-complemented strains at 8 wpi. Pepsin-acid treatment of 4 wpi in vivo cysts revealed that Δbpk1 parasites are significantly more sensitive to this treatment than the parental and complemented strains. Consistent with this, 4 wpi Δbpk1 cysts showed reduced ability to cause oral infection compared to the parental and complemented strains. Together, these data reveal that BPK1 plays a crucial role in the in vivo development and infectivity of Toxoplasma cysts

A Theorem on Matroid Homomorphism

This note generalizes a result contained in a previous paper [ J. Sanders, Circuit preserving edge maps II, J. Combin. Theory Ser. B 42 (1987), 146-155].Comment: 5 pages, 0 figure

Molecules incorporating a benzothiazole core scaffold inhibit the N-myristoyltransferase of Plasmodium falciparum.

Recombinant N-myristoyltransferase of Plasmodium falciparum (termed PfNMT) has been used in the development of a SPA (scintillation proximity assay) suitable for automation and high-throughput screening of inhibitors against this enzyme. The ability to use the SPA has been facilitated by development of an expression and purification system which yields considerably improved quantities of soluble active recombinant PfNMT compared with previous studies. Specifically, yields of pure protein have been increased from 12 microg x l(-1) to >400 microg x l(-1) by use of a synthetic gene with codon usage optimized for expression in an Escherichia coli host. Preliminary small-scale 'piggyback' inhibitor studies using the SPA have identified a family of related molecules containing a core benzothiazole scaffold with IC50 values 80% at a concentration of 10 microM

Dynamic redox and nutrient cycling response to climate forcing in the Mesoproterozoic ocean

Controls on Mesoproterozoic ocean redox heterogeneity, and links to nutrient cycling and oxygenation feedbacks, remain poorly resolved. Here, we report ocean redox and phosphorus cycling across two high-resolution sections from the ~1.4 Ga Xiamaling Formation, North China Craton. In the lower section, fluctuations in trade wind intensity regulated the spatial extent of a ferruginous oxygen minimum zone, promoting phosphorus drawdown and persistent oligotrophic conditions. In the upper section, high but variable continental chemical weathering rates led to periodic fluctuations between highly and weakly euxinic conditions, promoting phosphorus recycling and persistent eutrophication. Biogeochemical modeling demonstrates how changes in geographical location relative to global atmospheric circulation cells could have driven these temporal changes in regional ocean biogeochemistry. Our approach suggests that much of the ocean redox heterogeneity apparent in the Mesoproterozoic record can be explained by climate forcing at individual locations, rather than specific events or step-changes in global oceanic redox conditions

Aspergillus Genomes and the Aspergillus Cloud

Aspergillus Genomes is a public resource for viewing annotated genes predicted by various Aspergillus sequencing projects. It has arisen from the union of two significant resources: the Aspergillus/Aspergillosis website and the Central Aspergillus Data REpository (CADRE). The former has primarily served the medical community, providing information about Aspergillus and associated diseases to medics, patients and scientists; the latter has focused on the fungal genomic community, providing a central repository for sequences and annotation extracted from Aspergillus Genomes. By merging these databases, genomes benefit from extensive cross-linking with medical information to create a unique resource, spanning genomics and clinical aspects of the genus. Aspergillus Genomes is accessible from http://www.aspergillus-genomes.org.uk

Characterisation of Aspergillus fumigatus Endocytic Trafficking within Airway Epithelial Cells Using High-Resolution Automated Quantitative Confocal Microscopy

From MDPI via Jisc Publications RouterHistory: accepted 2021-06-02, pub-electronic 2021-06-07Publication status: PublishedFunder: National Centre for the Replacement, Refinement and Reduction of Animals in Research; Grant(s): NC/P002390/1Funder: German Science Fundation; Grant(s): DFG, SE2405/1-1Funder: Libyan Ministry of Higher Education and Scientific Research; Grant(s): NAFunder: Consejo Nacional de Ciencia y Tecnología; Grant(s): 359173Funder: NIHR Manchester Biomedical Research Centre; Grant(s): NAFunder: FP7 Ideas: European Research Council; Grant(s): PITN-GA-520 2013-607963The precise characterization of the mechanisms modulating Aspergillus fumigatus survival within airway epithelial cells has been impaired by the lack of live-cell imaging technologies and user-friendly quantification approaches. Here we described the use of an automated image analysis pipeline to estimate the proportion of A. fumigatus spores taken up by airway epithelial cells, those contained within phagolysosomes or acidified phagosomes, along with the fungal factors contributing to these processes. Coupling the use of fluorescent A. fumigatus strains and fluorescent epithelial probes targeting lysosomes, acidified compartments and cell membrane, we found that both the efficacy of lysosome recruitment to phagosomes and phagosome acidification determines the capacity of airway epithelial cells to contain A. fumigatus growth. Overall, the capability of the airway epithelium to prevent A. fumigatus survival was higher in bronchial epithelial than alveolar epithelial cells. Certain A. fumigatus cell wall mutants influenced phagosome maturation in airway epithelial cells. Taken together, this live-cell 4D imaging approach allows observation and measurement of the very early processes of A. fumigatus interaction within live airway epithelial monolayers