IL-13 protects from C. difficile Colitis

OBJECTIVES

Clostridioides difficile infection (CDI) is the leading hospital-acquired infection in North America. We have previously discovered that antibiotic disruption of the gut microbiota decreases intestinal IL-33 and IL-25 and increases susceptibility to CDI. We further found that IL-33 promotes protection through type 2 Innate Lymphoid Cells (ILC2s), which produce IL-13. However, the contribution of IL-13 to disease has never been explored.

METHODS

We used a validated model of CDI in mice, in which we neutralized via blocking antibodies, or administered recombinant protein, IL-13 to assess the role of this cytokine during infection using weight and clinical scores. Fluorescent activated cell sorting (FACS) was used to characterize myeloid cell population changes in response to IL-13 manipulation.

RESULTS

We found that administration of IL-13 protected, and anti-IL-13 exacerbated CDI. Additionally, we observe alterations to the monocyte/macrophage cells following neutralization of IL-13 as early as day three post infection. We also observed elevated accumulation of myeloid cells by day four post-infection following IL-13 neutralization. Neutralization of the decoy receptor, IL-13Rα2, resulted in protection from disease, likely through increased available endogenous IL-13.

CONCLUSIONS

Our data highlight the protective role of IL-13 in protecting from more severe CDI and the association of poor responses with a dysregulated monocyte-macrophage compartment. These results increase our understanding of type 2 immunity in CDI and may have implications for treating disease in patients.

High-Energy-Density Material with Magnetically Modulated Ignition

Preparation of a redox-frustrated high-energy-density energetic material is achieved by gentle protolysis of Mn[N(SiMe3)2]2 with the perchlorate salt of the tetrazolamide [H2NtBuMeTz]ClO4 (Tz = tetrazole), yielding the Mn6N6 hexagonal prismatic cluster, Mn6(μ3-NTztBuMe)6(ClO4)6. Quantum mechanics-based molecular dynamics simulations of the decomposition of this molecule predict that magnetic ordering of the d5 Mn2+ ions influences the pathway and rates of decomposition, suggesting that the initiation of decomposition of the bulk material might be significantly retarded by an applied magnetic field. We report here experimental tests of the prediction showing that the presence of a 0.5 T magnetic field modulates the ignition onset temperature by +10.4 ± 3.9 °C (from 414 ± 4 °C), demonstrating the first example of a magnetically modulated explosive.

Heterocycles via SiCl4-Promoted Isocyanide Additions to Oxonitriles

SiCl4 promotes isocyanide additions to oxoalkenenitriles to selectively generate 3-acylpyrroles, 2-aminofurans, or pyrrolidinones. Cyclic oxoalkenenitriles add 2 equiv of an isocyanide that installs the two core atoms of an acylpyrrole and a nitrile substituent, whereas acyclic oxoalkenenitriles add 1 equiv of an isocyanide to afford 2-aminofurans; subsequent air oxidation generates pyrrolidinones via a furan oxygenation-cleavage-cyclization sequence. The syntheses proceed under mild conditions to rapidly access three richly decorated heterocycles.

Ensembl 2022

Ensembl (https://www.ensembl.org) is unique in its flexible infrastructure for access to genomic data and annotation. It has been designed to efficiently deliver annotation at scale for all eukaryotic life, and it also provides deep comprehensive annotation for key species. Genomes representing a greater diversity of species are increasingly being sequenced. In response, we have focussed our recent efforts on expediting the annotation of new assemblies. Here, we report the release of the greatest annual number of newly annotated genomes in the history of Ensembl via our dedicated Ensembl Rapid Release platform (http://rapid.ensembl.org). We have also developed a new method to generate comparative analyses at scale for these assemblies and, for the first time, we have annotated non-vertebrate eukaryotes. Meanwhile, we continually improve, extend and update the annotation for our high-value reference vertebrate genomes and report the details here. We have a range of specific software tools for specific tasks, such as the Ensembl Variant Effect Predictor (VEP) and the newly developed interface for the Variant Recoder. All Ensembl data, software and tools are freely available for download and are accessible programmatically.

Scripting Analyses of Genomes in Ensembl Plants

Ensembl Plants ( http://plants.ensembl.org ) offers genome-scale information for plants, with four releases per year. As of release 47 (April 2020) it features 79 species and includes genome sequence, gene models, and functional annotation. Comparative analyses help reconstruct the evolutionary history of gene families, genomes, and components of polyploid genomes. Some species have gene expression baseline reports or variation across genotypes. While the data can be accessed through the Ensembl genome browser, here we review specifically how our plant genomes can be interrogated programmatically and the data downloaded in bulk. These access routes are generally consistent across Ensembl for other non-plant species, including plant pathogens, pests, and pollinators.

K-mer counting and curated libraries drive efficient annotation of repeats in plant genomes

The annotation of repetitive sequences within plant genomes can help in the interpretation of observed phenotypes. Moreover, repeat masking is required for tasks such as whole-genome alignment, promoter analysis, or pangenome exploration. Although homology-based annotation methods are computationally expensive, k-mer strategies for masking are orders of magnitude faster. Here, we benchmarked a two-step approach, where repeats were first called by k-mer counting and then annotated by comparison to curated libraries. This hybrid protocol was tested on 20 plant genomes from Ensembl, with the k-mer-based Repeat Detector (Red) and two repeat libraries (REdat, last updated in 2013, and nrTEplants, curated for this work). Custom libraries produced by RepeatModeler were also tested. We obtained repeated genome fractions that matched those reported in the literature but with shorter repeated elements than those produced directly by sequence homology. Inspection of the masked regions that overlapped genes revealed no preference for specific protein domains. Most Red-masked sequences could be successfully classified by sequence similarity, with the complete protocol taking less than 2 h on a desktop Linux box. A guide to curating your own repeat libraries and the scripts for masking and annotating plant genomes can be obtained at https://github.com/Ensembl/plant-scripts.

Solitary and periodic waves in collisionless plasmas: The Adlam-Allen model revisited

We consider the Adlam-Allen (AA) system of partial differential equations, which, arguably, is the first model that was introduced to describe solitary waves in the context of propagation of hydrodynamic disturbances in collisionless plasmas. Here, we identify the solitary waves of the model by implementing a dynamical systems approach. The latter suggests that the model also possesses periodic wave solutions-which reduce to the solitary wave in the limiting case of an infinite period-as well as rational solutions that are obtained herein. In addition, employing a long-wave approximation via a relevant multiscale expansion method, we establish the asymptotic reduction of the AA system to the Korteweg-de Vries equation. Such a reduction is not only another justification for the above solitary wave dynamics, but may also offer additional insights for the emergence of other possible plasma waves. Direct numerical simulations are performed for the study of multiple solitary waves and their pairwise interactions. The stability of solitary waves is discussed in terms of potentially relevant criteria, while the robustness of spatially periodic wave solutions is touched upon via numerical experiments.

Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes

BACKGROUND

Tsetse flies (Glossina sp.) are the vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse flies are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood-specific diet by both sexes, and obligate bacterial symbiosis. This work describes the comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans, G. pallidipes, G. austeni), Palpalis (G. palpalis, G. fuscipes), and Fusca (G. brevipalpis) which represent different habitats, host preferences, and vectorial capacity.

RESULTS

Genomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossina relative to Drosophila melanogaster shows reduced structural conservation across the sex-linked X chromosome. Sex-linked scaffolds show increased rates of female-specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse-specific genes are enriched in protease, odorant-binding, and helicase activities. Lactation-associated genes are conserved across all Glossina species while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other insects. Vision-associated Rhodopsin genes show conservation of motion detection/tracking functions and variance in the Rhodopsin detecting colors in the blue wavelength ranges.

CONCLUSIONS

Expanded genomic discoveries reveal the genetics underlying Glossina biology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies.

Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes

BACKGROUND

Tsetse flies (Glossina sp.) are the vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse flies are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood-specific diet by both sexes, and obligate bacterial symbiosis. This work describes the comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans, G. pallidipes, G. austeni), Palpalis (G. palpalis, G. fuscipes), and Fusca (G. brevipalpis) which represent different habitats, host preferences, and vectorial capacity.

RESULTS

Genomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossina relative to Drosophila melanogaster shows reduced structural conservation across the sex-linked X chromosome. Sex-linked scaffolds show increased rates of female-specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse-specific genes are enriched in protease, odorant-binding, and helicase activities. Lactation-associated genes are conserved across all Glossina species while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other insects. Vision-associated Rhodopsin genes show conservation of motion detection/tracking functions and variance in the Rhodopsin detecting colors in the blue wavelength ranges.

CONCLUSIONS

Expanded genomic discoveries reveal the genetics underlying Glossina biology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies.

Enhanced monocyte recruitment and delayed alternative macrophage polarization accompanies impaired repair following myocardial infarction in C57BL/6 compared to BALB/c mice

Activation of the innate immune response following myocardial infarction (MI) is essential for infarct repair. Preclinical models of MI commonly use C57BL/6 mice, which have a type 1‐dominant immune response, whereas other mouse strains such as BALB/c mice have a type 2‐dominant immune response. We compared C57BL/6 and BALB/c mice to investigate whether predisposition towards a proinflammatory phenotype influences the dynamics of the innate immune response to MI and associated infarct healing and the risk of cardiac rupture. MI was induced by permanent coronary artery ligation in 12–15‐week‐old male wild‐type BALB/c and C57BL/6 mice. Prior to MI, C57BL/6 mice had a lower proportion of CD206⁺ anti‐inflammatory macrophages in the heart and an expanded blood pool of proinflammatory Ly6C^high monocytes in comparison to BALB/c mice. The systemic inflammatory response in C57BL/6 mice following MI was more pronounced, with greater peripheral blood Ly6C^high monocytosis, splenic Ly6C^high monocyte mobilization and myeloid cell infiltration of pericardial adipose tissue. This led to an increased and prolonged macrophage accumulation, as well as delayed transition towards anti‐inflammatory macrophage polarization in the infarct zone and surrounding tissues of C57BL/6 mice. These findings accompanied a higher rate of mortality due to cardiac rupture in C57BL/6 mice compared with BALB/c mice. We conclude that lower post‐MI survival of C57BL/6 mice over BALB/c mice is mediated in part by a more pronounced and prolonged inflammatory response. Outcomes in BALB/c mice highlight the therapeutic potential of modulating resolution of the innate immune response following MI for the benefit of successful infarct healing.

Management of Barrett's esophagus with low-grade dysplasia

Barrett's esophagus progresses to esophageal adenocarcinoma in a stepwise histological fashion of no dysplasia, low grade dysplasia, high grade dysplasia and cancer. Hence the progression to cancer from various histological stages is different. Progression to cancer from low grade dysplasia is highly variable in the literature due to high inter-observer variability between pathologists in diagnosing it. Studies have shown the utility of having confirmation of low grade dysplasia by expert pathologists or documenting its persistence on two subsequent endoscopies in order to unify the diagnosis. The treatment of low grade dysplasia is variable. In this article we summarize the diagnosis, evaluation and management of low grade dysplasia in Barrett's Esophagus.

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including genome sequence, gene models, transcript sequence, genetic variation, and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments and expansions. These include the incorporation of almost 20 000 additional genome sequences and over 35 000 tracks of RNA-Seq data, which have been aligned to genomic sequence and made available for visualization. Other advances since 2015 include the release of the database in Resource Description Framework (RDF) format, a large increase in community-derived curation, a new high-performance protein sequence search, additional cross-references, improved annotation of non-protein-coding genes, and the launch of pre-release and archival sites. Collectively, these changes are part of a continuing response to the increasing quantity of publicly-available genome-scale data, and the consequent need to archive, integrate, annotate and disseminate these using automated, scalable methods.

Polyp characterization at colonoscopy: Clinical implications

Although advancements in endoscopic imaging of colorectal mucosa have outstripped the pace of research in the field, the potential clinical applications of these novel technologies are promising. Chief among these is the ability to diagnose colorectal polyps in vivo. This feature appears most applicable to diminuitive polyps, which have very little malignant potential yet represent over 70% of resected polyps. In an ideal application, the capability to predict diminutive hyperplastic polyp histology in vivo precludes the need for excision whereas dimunitive adenomas do require excision, but not necessarily histopathologic analysis if the diagnosis is made in vivo with adequate confidence. However, the vast array of new advanced imaging modalities and polyp classification tools have been difficult to reconcile. We aim to highlight the current status of real-time colorectal polyp diagnosis and identify the barriers that remain to its widespread implementation.

Scheduling terminology for oral and maxillofacial surgery. Are we speaking a universal language?

Use of a universal vocabulary to assist with the scheduling of operations has been shown to considerably reduce delays and improve the use of theatre resources. Within the UK the National Confidential Enquiry into Patient Outcome and Death (NCEPOD) has established a classification to assist with the triage of both emergency and non-emergency operating lists. We completed a survey to assess the uptake and understanding of this classification when scheduling maxillofacial operations. From a list of eight scheduling terms, respondents had to choose one each for 20 different clinical situations (that represented equally) immediate, urgent, expedited, and elective operations as defined by them. A total of 50 surveys were collated. Only 65% of answers selected represented NCPOD terms. 25% of answers represented a term higher and 18% a term lower, on the scale of intervention for the same category of situation. Current NCEPOD terms do not seem to be used universally and are poorly understood. Considerable variation in terminology exists when scheduling maxillofacial operations.

Ensembl Genomes 2016: more genomes, more complexity

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces.

Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes

Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts.

ModelOMatic: fast and automated model selection between RY, nucleotide, amino acid, and codon substitution models

Molecular phylogenetics is a powerful tool for inferring both the process and pattern of evolution from genomic sequence data. Statistical approaches, such as maximum likelihood and Bayesian inference, are now established as the preferred methods of inference. The choice of models that a researcher uses for inference is of critical importance, and there are established methods for model selection conditioned on a particular type of data, such as nucleotides, amino acids, or codons. A major limitation of existing model selection approaches is that they can only compare models acting upon a single type of data. Here, we extend model selection to allow comparisons between models describing different types of data by introducing the idea of adapter functions, which project aggregated models onto the originally observed sequence data. These projections are implemented in the program ModelOMatic and used to perform model selection on 3722 families from the PANDIT database, 68 genes from an arthropod phylogenomic data set, and 248 genes from a vertebrate phylogenomic data set. For the PANDIT and arthropod data, we find that amino acid models are selected for the overwhelming majority of alignments; with progressively smaller numbers of alignments selecting codon and nucleotide models, and no families selecting RY-based models. In contrast, nearly all alignments from the vertebrate data set select codon-based models. The sequence divergence, the number of sequences, and the degree of selection acting upon the protein sequences may contribute to explaining this variation in model selection. Our ModelOMatic program is fast, with most families from PANDIT taking fewer than 150 s to complete, and should therefore be easily incorporated into existing phylogenetic pipelines. ModelOMatic is available at https://code.google.com/p/modelomatic/.

Assessing the state of substitution models describing noncoding RNA evolution

Phylogenetic inference is widely used to investigate the relationships between homologous sequences. RNA molecules have played a key role in these studies because they are present throughout life and tend to evolve slowly. Phylogenetic inference has been shown to be dependent on the substitution model used. A wide range of models have been developed to describe RNA evolution, either with 16 states describing all possible canonical base pairs or with 7 states where the 10 mismatched nucleotides are reduced to a single state. Formal model selection has become a standard practice for choosing an inferential model and works well for comparing models of a specific type, such as comparisons within nucleotide models or within amino acid models. Model selection cannot function across different sized state spaces because the likelihoods are conditioned on different data. Here, we introduce statistical state-space projection methods that allow the direct comparison of likelihoods between nucleotide models and 7-state and 16-state RNA models. To demonstrate the general applicability of our new methods, we extract 287 RNA families from genomic alignments and perform model selection. We find that in 281/287 families, RNA models are selected in preference to nucleotide models, with simple 7-state RNA models selected for more conserved families with shorter stems and more complex 16-state RNA models selected for more divergent families with longer stems. Other factors, such as the function of the RNA molecule or the GC-content, have limited impact on model selection. Our models and model selection methods are freely available in the open-source PHASE 3.0 software.

Residents' willingness-to-pay for attributes of rural health care facilities

CONTEXT

As today's rural hospitals have struggled with financial sustainability for the past 2 decades, it is critical to understand their value relative to alternatives, such as rural health clinics and private practices.

PURPOSE

To estimate the willingness-to-pay for specific attributes of rural health care facilities in rural Kentucky to determine which services and operational characteristics are most valued by rural residents.

METHODOLOGY

We fitted choice experiment data from 769 respondents in 10 rural Kentucky counties to a conditional logit model and used the results to estimate willingness-to-pay for attributes in several categories, including hours open, types of insurance accepted, and availability of health care professionals and specialized care.

FINDINGS

Acceptance of Medicaid/Medicare with use of a sliding fee scale versus acceptance of only private insurance was the most valued attribute. Presence of full diagnostic services, an emergency room, and 24-hour/7-day-per-week access were also highly valued. Conversely, the presence of specialized care, such as physical therapy, cancer care, or dialysis, was not valued. In total, respondents were willing to pay $225 more annually to support a hospital relative to a rural health clinic.

CONCLUSION

Rural Kentuckians value the services, convenience, and security that rural hospitals offer, though they are not willing to pay more for specialized care that may be available in larger medical treatment centers. The results also inform which attributes might be added to existing rural health facilities to make them more valuable to local residents.

Ensembl Genomes 2013: scaling up access to genome-wide data

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future.

Abstract P6-02-01: Elucidating the change of TRAIL sensitivity in basal like TNBC cell lines by lapatinib, and further therapeutic implication

Triple negative breast cancer (TNBC) comprises 15-20% of breast cancer, and carries a poor prognosis. Recently, efforts to understand this heterogeneous group of cancers have led to recognition of different subtypes of TNBC by Dr. Pietenpol et al based on genetic and functional signature. So far, the only targeting agent for TNBC still remains as androgen receptor inhibitor for LAR group. Thus, other strategies in therapeutic development for TNBCs are necessary. TRAIL (Tumor Necrosis Factor-related apoptosis inducing ligand), a member of the TNF-alpha family of death receptor ligands, induces apoptosis by binding death receptors (DR4 and DR5), could be a good strategy in therapeutic development in TNBC. Unfortunately, majority of breast cancer cell lines are resistant to TRAIL targeted therapy especially basal like group of cells, as previously shown in the work of Lipkowitz at the NCI. Lapatinib, a well known as erbB 1 and 2 inhibitor had been found to have off target activity inducing JNK, an important activator of nuclear transcription of death receptor, and mitochondrial mediated intrinsic apoptosis pathway. Interestingly, study of combination therapy with lapatinib and TRAIL not only confirmed baseline poor sensitivity to TRAIL induced apoptosis in “basal like” HCC 1937 and MDA-MB-468 cell lines, but also revealed an unexpected difference in sensitization to TRAIL induced apoptosis by Lapatinib pre-treatment between these two cell lines. When treated with 48hrs Lapatinib high–dose treatment, HCC 1937 showed increased sensitization whereas MDA-MB-468 did not. Both HCC 1937 and MDA-MB-468 are in the same basal like 1(BL1) group by Dr. Pietenpol's analysis, and their baseline sensitivity to TRAIL inducing apoptosis are the same. In terms of apoptosis - there are two big categories of cells. Type I cells are independent of mitochondria for the induction of Fas death receptor mediated apoptosis, where as type II cells are mitochrondria-dependent. Thus we hypothesized that this difference in lapatinib induced TRAIL sensitization between two cell lines is due to difference in one being type I vs the other being type II cell, and this type of apoptosis is not likely equal in same subgroup of TNBC. If this hypothesis is correct, targeting apoptosis pathway in TNBC should incorporate the recognition of apoptosis cell types rather than functional/genetic based subtypes. We will further elucidate our hypothesis by studying JNK, caspase 3 and 9 activity and downstream of both intrinsic, extrinsic apoptosis pathway.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P6-02-01.

Future prospects and challenges of vaccines against filariasis

Filarial infections remain a major public health and socio-economic problem across the tropics, despite considerable effort to reduce disease burden or regionally eliminate the infection with mass drug administration programmes. The sustainability of these programmes is now open to question owing to a range of issues, not least of which is emerging evidence for drug resistance. Vaccination, if developed appropriately, remains the most cost-effective means of long-term disease control. The rationale for the feasibility of vaccination against filarial parasites including onchocerciasis (river blindness, Onchocerca volvulus) and lymphatic filariasis (Wuchereria bancrofti or Brugia malayi) is founded on evidence from both humans and animal models for the development of protective immunity. Nonetheless, enormous challenges need to be faced in terms of overcoming parasite-induced suppression without inducing pathology as well as the need to both recognize and tackle evolutionary and ecological obstacles to successful vaccine development. Nonetheless, new technological advances in addition to systems biology approaches offer hope that optimal immune responses can be induced that will prevent infection, disease and/or transmission.

Floating potential of large dust grains in a collisionless flowing plasma

Dust immersed in plasma quickly charges to a potential where the ion and electron currents to its surface balance; this is the floating potential. In order to accurately determine dust behavior, the floating potential must be known. The charging of dust grains that are small with respect to electron Debye length (λ(D)) may be adequately approximated using the orbital-motion-limited (OML) approach. A modified version of OML is presented for large dust grains in both stationary and flowing plasmas. This modified OML is compared with simulation and found to be in good agreement. The modified OML is applied to large grains charging under tokamak conditions and found to have an appreciable effect on the drag force.

Wakes formed by dust grains in supersonically flowing plasmas

Interesting wake effects are found in simulations of dust grains in supersonically flowing plasma. A Mach cone is formed at an angle to the flow determined by the ratio of flow to Bohm speed. The latter is well approximated by [k(T(e)+γT(i))/m(i)](1/2) with γ=3. For ion temperatures significantly lower than the electron temperature, a second (inner) cone forms due to flow convergence. An "ion vacuum" and stagnation point occur downstream. These latter effects cannot be described by conventional (cold-ion) gas dynamics. Critically, none of the cones observed are shocks but are more akin to weak discontinuities.

Cold machine perfusion versus static cold storage of kidneys donated after cardiac death: a UK multicenter randomized controlled trial

One third of deceased donor kidneys for transplantation in the UK are donated following cardiac death (DCD). Such kidneys have a high rate of delayed graft function (DGF) following transplantation. We conducted a multicenter, randomized controlled trial to determine whether kidney preservation using cold, pulsatile machine perfusion (MP) was superior to simple cold storage (CS) for DCD kidneys. One kidney from each DCD donor was randomly allocated to CS, the other to MP. A sequential trial design was used with the primary endpoint being DGF, defined as the necessity for dialysis within the first 7 days following transplant. The trial was stopped when data were available for 45 pairs of kidneys. There was no difference in the incidence of DGF between kidneys assigned to MP or CS (58% vs. 56%, respectively), in the context of an asystolic period of 15 min and median cold ischemic times of 13.9 h for MP and 14.3 h for CS kidneys. Renal function at 3 and 12 months was similar between groups, as was graft and patient survival. For kidneys from controlled DCD donors (with mean cold ischemic times around 14 h), MP offers no advantage over CS, which is cheaper and more straightforward.

Cocaine and human immunodeficiency virus type 1 gp120 mediate neurotoxicity through overlapping signaling pathways

Although it has been well documented that drugs of abuse such as cocaine cause enhanced progression of human immunodeficiency virus (HIV)-associated neuropathological disorders, the underlying mechanisms mediating these effects remain poorly understood. The present study demonstrated that exposure of rat primary neurons to both cocaine and gp120 resulted in increased cell toxicity compared to cells treated with either factor alone. The combinatorial toxicity of cocaine and gp120 was accompanied by an increase in both caspase-3 activity and expression of the proapoptotic protein Bax. Furthermore, increased neurotoxicity in the presence of both the agents was associated with a concomitant increase in the production of intracellular reactive oxygen species and loss of mitochondrial membrane potential. Increased neurotoxicity mediated by cocaine and gp120 was ameliorated by NADPH oxidase inhibitor apocynin, thus underscoring the role of oxidative stress in this cooperation. Signaling pathways including c-jun N-teminal kinase (JNK), p38, extracellular signal-regulated kinase (ERK)/mitogen-activated protein kinases (MAPK), and nuclear factor (NF)-kappaB were also identified to be critical in the neurotoxicity induced by cocaine and gp120. These findings thus underscore the role of oxidative stress, mitochondrial and MAPK signal pathways in cocaine and HIV gp120-mediated neurotoxicity.

Aspects of the geographical variations of naturally occurring 210Pb/210Po in permanent teeth of juveniles in the UK

PURPOSE

To study geographical variations in the level of naturally occurring 210Pb-supported 210Po in permanent teeth of juveniles in the UK.

MATERIALS AND METHODS

Permanent teeth extracted from 278 juveniles for orthodontic purposes were obtained from 48 counties in the UK. 210Po activity concentration was measured on the outer enamel surface using TASTRAK alpha-particle-sensitive plastic track detectors.

RESULTS

Geometric mean +/- SE activity concentrations in teeth from urban, suburban and rural areas, excluding the high radon area of Devon, were 8.41 + 0.25/-0.24, 7.76 + 0.37/-0.35 and 7.20 +0.49/-0.46 Bq kg(-1), respectively. Overall, there was no significant association between alpha-activity on the outer enamel surface of permanent teeth and proximity to the major UK motorways. However, when the data were considered with respect to the prevailing south-westerly wind on the western side of the UK, a statistically significant association with respect to donors living downwind (on the easterly side) of the motorways was found. This effect was greater for sections of the M5 and M6 motorways that traverse urban areas. 210Po levels in teeth were also associated with domestic radon concentration. This effect was comparable with that from traffic and urban pollution.

CONCLUSIONS

Higher levels of 210Pb-supported 210Po are seen in permanent teeth of juveniles near sources of increased exposure in the UK. Inhalation uptake is an important pathway of exposure, especially with respect to domestic radon exposure. The results might be important in assessing integrated exposure to 210Po in the skeleton and consequent high linear energy transfer dose to bone marrow.

Morphological features of the microdistribution of naturally occurring 210Pb/210Po and 226Ra in the teeth of children and juveniles

PURPOSE

To examine the microdistribution of natural alpha-radioactivity in deciduous teeth of children and the permanent teeth of juveniles extracted for orthodontic purpose from across the UK.

MATERIALS AND METHODS

The microdistribution of 210Pb-supported 210Po and 226Ra in 708 deciduous and permanent teeth and 32 foetal teeth was measured on 1442 TASTRAK alpha-particle track detectors.

RESULTS

Of the various findings, a number are of special interest. Around half of the 210Pb activity in the outer enamel of deciduous teeth appears to have been acquired in utero as a result of transplacental transfer. In deciduous and permanent teeth, 226Ra is concentrated mainly in the circumpulpal region, while the highest levels of 210Po are on the highly calcified outer enamel surface. Furthermore, activity concentrations recorded on this surface were In-normally distributed.

CONCLUSIONS

210Pb-supported 210Po activity on the outer enamel surface of permanent teeth constitutes an assay of cumulative environmental exposure with which to assess exposure in bone, both in utero and in childhood. Such assessment can be used to study geographical variations in the alpha-activity in teeth. More work is also required to determine the concentrations of both 210Po and 210Pb in the foetal skeleton.

Chitinases and chitinase-like proteins: potential therapeutic targets for the treatment of T-helper type 2 allergies

Mammalian chitinase and chitinase-like proteins (CLPs) are a family of mediators increasingly associated with infection, T cell-mediated inflammation, wound healing, allergy and asthma. Although our current knowledge of the function of mammalian chitinases and CLPs is very limited, important information can be deduced from research carried out in lower organisms, and in different immunopathological conditions. Enzymatically active mammalian chitinase proteins may have evolved to degrade the copious amounts of chitin mammals are exposed to on a daily basis, and to form an innate barrier to chitin-containing organisms. CLPs are homologous to chitinases but lack the ability to degrade chitin. It is most striking that both chitinases and CLPs are up-regulated in T-helper type 2 (Th2)-driven conditions, and the first evidence is now emerging that these proteins may accentuate Th2 reactivity, and possibly contribute to the repair process that follows inflammation. Following studies demonstrating that chitinase inhibition leads to an attenuated allergic response, several strategies are being used to develop enzyme inhibitors for therapeutic use in human diseases. In this review, we will summarize recent insights into the effects of chitinases and CLPs in the context of Th2-dominated pathology with particular focus on allergy and asthma, discussing whether chitinase enzyme inhibitors may be of therapeutic value.

Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci

We carried out a meta-analysis of data from three genome-wide association (GWA) studies of type 1 diabetes (T1D), testing 305,090 SNPs in 3,561 T1D cases and 4,646 controls of European ancestry. We obtained further support for 4q27 (IL2-IL21, P = 1.9 x 10(-8)) and, after genotyping an additional 6,225 cases, 6,946 controls and 2,828 families, convincing evidence for four previously unknown and distinct risk loci in chromosome regions 6q15 (BACH2, P = 4.7 x 10(-12)), 10p15 (PRKCQ, P = 3.7 x 10(-9)), 15q24 (CTSH, P = 3.2 x 10(-15)) and 22q13 (C1QTNF6, P = 2.0 x 10(-8)).

Does Litomosoides sigmodontis synthesize dimethylethanolamine from choline?

Juvenile female Litomosoides sigmodontis secrete a protein (Juv-p120) highly modified with dimethylethanolamine (DMAE). In an attempt to establish the source of this decoration worms were pulsed with [3H]-choline and [3H]-ethanolamine and the radio-isotope labelled products analysed. Both isotope labels were successfully taken up by the worms, as demonstrated by labelling of phospholipids with [3H]-choline, being predominantly incorporated into phosphatidylcholine and [3H]-ethanolamine into phosphatidylethanolamine. Isotope labelling of phosphatidylethanolamine was particularly striking with the worms taking up approximately 30 times as much labelled ethanolamine as choline. It was possible to detect faint labelling of Juv-p120 with [3H]-ethanolamine after prolonged exposure periods but, unlike the situation with the phospholipids, it was much more readily labelled with [3H]-choline. When pulsing with [3H]-ethanolamine it was also possible to detect isotope-labelled phosphatidylcholine, which may ultimately account for the low levels of labelling of Juv-p120. Overall our results raise the previously unconsidered but intriguing possibility that in L. sigmodontis, choline may be the precursor of DMAE.

Recovery of consciousness after epileptic seizures in children

OBJECTIVE

To investigate the duration of postictal impairment of consciousness and the factors that affect it.

PATIENTS AND METHODS

90 children aged 1-16 years (37 male, 53 female, median age 6 years), attending the accident and emergency department, and inpatients of Leeds General Infirmary, Leeds, UK, who had experienced seizures involving impairment of consciousness. Interventions-hourly modified paediatric coma scores were determined, until a coma score of 15 was obtained. Linear regression analysis was used to determine the factors influencing recovery time.

RESULTS

49 children were excluded owing to incomplete coma scoring, lost notes and refusal of consent. Median time for full recovery of consciousness was 38 min (0.63 h, range 0.05-17 h). Median recovery time was 18 min (0.3 h, range 0.05-9 h) from febrile seizures, which was significantly shorter than for seizures of other aetiologies (p<0.05), 1.35 h (range 0.07-13.13 h) from idiopathic seizures, 1.25 h (0.07-12.1 h) from remote symptomatic seizures and 4.57 h (0.25-17 h) from acute symptomatic seizures. Median recovery time after the use of benzodiazepines was 3.46 h (range 0.08-14.25 h), and was significantly longer (p<0.05) than for seizures not treated with benzodiazepines (median 0.47 h, range 0.05-17 h). Age, sex, seizure type and duration did not significantly affect recovery time.

CONCLUSIONS

Most children experiencing febrile seizures recover within 30 min. An acute symptomatic aetiology should be considered if recovery takes >1 h.

T1DBase: integration and presentation of complex data for type 1 diabetes research

T1DBase () [Smink et al. (2005) Nucleic Acids Res., 33, D544–D549; Burren et al. (2004) Hum. Genomics, 1, 98–109] is a public website and database that supports the type 1 diabetes (T1D) research community. T1DBase provides a consolidated T1D-oriented view of the complex data world that now confronts medical researchers and enables scientists to navigate from information they know to information that is new to them. Overview pages for genes and markers summarize information for these elements. The Gene Dossier summarizes information for a list of genes. GBrowse [Stein et al. (2002) Genome Res., 10, 1599–1610] displays genes and other features in their genomic context, and Cytoscape [Shannon et al. (2003) Genome Res., 13, 2498–2504] shows genes in the context of interacting proteins and genes. The Beta Cell Gene Atlas shows gene expression in β cells, islets, and related cell types and lines, and the Tissue Expression Viewer shows expression across other tissues. The Microarray Viewer shows expression from more than 20 array experiments. The Beta Cell Gene Expression Bank contains manually curated gene and pathway annotations for genes expressed in β cells. T1DMart is a query tool for markers and genotypes. PosterPages are ‘home pages’ about specific topics or datasets. The key challenge, now and in the future, is to provide powerful informatics capabilities to T1D scientists in a form they can use to enhance their research.

Parasite genetic diversity does not influence TNF-mediated effects on the virulence of primary rodent malaria infections

The pro-inflammatory cytokine tumour necrosis factor alpha (TNF-alpha) is associated with malaria virulence (disease severity) in both rodents and humans. We are interested in whether parasite genetic diversity influences TNF-mediated effects on malaria virulence. Here, primary infections with genetically distinct Plasmodium chabaudi chabaudi (P.c.c.) clones varied in the virulence and cytokine responses induced in female C57BL/6 mice. Even when parasitaemia was controlled for, a greater day 7 TNF-alpha response was induced by infection with more virulent P.c.c. clones. Since many functions of TNF-alpha are exerted through TNF receptor 1 (TNFR1), a TNFR-1 fusion protein (TNFR-Ig) was used to investigate whether TNFR1 blockade eliminated clone virulence differences. We found that TNFR-1 blockade ameliorated the weight loss but not the anaemia induced by malaria infection, regardless of P.c.c. clone. We show that distinct P.c.c. infections induced significantly different plasma interferon gamma (IFN-gamma), interleukin 6 (IL-6) and interleukin 10 (IL-10) levels. Our results demonstrate that regardless of P.c.c. genotype, blocking TNFR1 signalling protected against weight loss, but had negligible effects on both anaemia and asexual parasite kinetics. Thus, during P.c.c. infection, TNF-alpha is a key mediator of weight loss, independent of parasite load and across parasite genotypes.

The transcriptional landscape of the mammalian genome

This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.

Co-infected C57BL/6 mice mount appropriately polarized and compartmentalized cytokine responses to Litomosoides sigmodontis and Leishmania major but disease progression is altered

This study examines the capacity of the mammalian host to fully compartmentalize the response to infection with type 1 vs. type 2 inducing organisms that infect different sites in the body. For this purpose, C57BL/6 mice were infected with the rodent filarial nematode Litomosoides sigmodontis followed by footpad infection with the protozoan parasite Leishmania major. In this host, nematode infection is established in the thoracic cavity but no microfilariae circulate in the bloodstream. We utilized quantitative ELISPOT analysis of IL-4 and IFN-gamma producing cells to assess cytokine bias and response magnitude in the lymph nodes draining the sites of infection as well as more systemic responses in the spleen and serum. Contrary to other systems where co-infection has a major impact on bias, cytokine ratios were unaltered in either local lymph node. The most notable effect of co-infection was an unexpected increase in the magnitude of the IFN-gamma response to L. major in mice previously infected with L. sigmodontis. Further, lesion development was significantly delayed in these mice. Thus, despite the ability of the immune system to appropriately compartmentalize the immune response, interactions between responses at distinct infection sites can alter disease progression.

A Brugia malayi homolog of macrophage migration inhibitory factor reveals an important link between macrophages and eosinophil recruitment during nematode infection

Infections with the helminth parasite Brugia malayi share many key features with Th2-mediated allergic diseases, including recruitment of eosinophils. We have investigated the dynamics of inflammatory cell recruitment under type 2 cytokine conditions in mice infected with B. malayi. Among the cells recruited to the site of infection is a novel population of "alternatively activated" macrophages that ablate cell proliferation and enhance Th2 differentiation. By profiling gene expression in this macrophage population, we found a dramatic up-regulation of a recently described eosinophil chemotactic factor, eosinophil chemotactic factor-L/Ym1, representing over 9% of clones randomly selected from a cDNA library. Because B. malayi is known to secrete homologs (Bm macrophage migration inhibitory factor (MIF)-1 and -2) of the human cytokine MIF, we chose to investigate the role this cytokine mimic may play in the development of the novel macrophage phenotype observed during infection. Strikingly, administration of soluble recombinant Bm-MIF-1 was able to reproduce the effects of live parasites, leading both to the up-regulation of Ym1 by macrophages and a marked recruitment of eosinophils in vivo. Because activity of Bm-MIF-1 is dependent upon an amino-terminal proline, this residue was mutated to glycine; the resultant recombinant (Bm-MIF-1G) was unable to induce Ym1 transcription in macrophages or to mediate the recruitment of eosinophils. These data suggest that macrophages may provide a crucial link between helminth parasites, their active cytokine mimics, and the recruitment of eosinophils in infection.

Divergent roles for macrophages in lymphatic filariasis

Macrophages have long been recognized as important cells associated with filarial infection but their function as effectors and/or suppressors has not been elucidated. Recent advances in our understanding of the role that macrophages may play in lymphatic filariasis have come from in vitro studies and mouse models of filarial infection. Based on these new findings, we hypothesize that while dead or dying worms induce the 'classical' activation of macrophages and a subsequent pro-inflammatory response, live and healthy worms secrete products that induce type 2 cytokines and the differentiation of 'alternatively' activated macrophages that downregulate an inflammatory response. Thus, the balance between the 'classical' and 'alternative' activation pathways of macrophages could be an important factor in inflammatory pathology associated with filariasis.

An in situ study of CD34(+) cells in human fetal bone marrow

The purpose of this study was to characterize the spatial distribution, number and size of CD34(+) cells in fetal bone marrow. Thin sections of normal fetal bone marrow from lumbar vertebrae were stained using CD34 antibody QBend/10. Sections were used under light microscopy with various eyepiece graticules to make measurements of CD34(+) cells in situ. Results showed that at mid- and late gestation, approximately 2% and 0.5% of fetal bone marrow cells were CD34(+) respectively. The mean distance of CD34(+) cells from the nearest trabecular bone surface was 61 +/- 4 and 46 +/- 4 microm, respectively, for mid- and late gestation. The mean distance to the nearest neighbour was 46 +/- 5 and 105 +/- 15 microm, and the mean distance to the nearest blood vessel was 13 +/- 1 and 17 +/- 2 microm respectively. The concentration of CD34(+) cells in the peripheral region was 6.5 times greater than that at the centre of the sections. Overall, the percentage number of CD34(+) cells decreased with gestational age. The cellular and nuclear diameters of CD34(+) cells remained unchanged throughout mid- and late gestation at 5.4 +/- 0.1 and 3.8 +/- 0.1 microm respectively. This information will be used to calculate the natural background alpha-radiation dose to haemopoietic stem cells.

Gongylonema infection of the mouth in a resident of Cambridge, Massachusetts

We report a case of Gongylonema infection of the mouth, which caused a migrating, serpiginous tract in a resident of Massachusetts. This foodborne infection, which is acquired through accidental ingestion of an infected insect, such as a beetle or a roach, represents the 11th such case reported in the United States.