The complete mitochondrial genome of the rodent intra-arterial nematodes Angiostrongylus cantonensis and Angiostrongylus costaricensis

The two rodent intra-arterial nematodes, Angiostrongylus cantonensis and Angiostrongylus costaricensis, can cause human ill-health. The present study aimed to characterize and compare the mitochondrial (mt) genomes of these two species, and clarify their phylogenetic relationship and the position in the phylum Nematoda. The complete mt genomes of A. cantonensis and A. costaricensis are 13,497 and 13,585bp in length, respectively. Hence, they are the smallest in the class of Chromadorea characterized thus far. Like many nematode species in the class of Chromadorea, they encode 12 proteins, 22 transfer RNAs, and two ribosomal RNAs. All genes are located on the same strand. Nucleotide identity of the two mt genomes is 81.6%, ranging from 77.7% to 87.1% in individual gene pairs. Our mt genome-wide analysis identified three major gene arrangement patterns (II-1, II-2, and II-3) from 48 nematode mt genomes. Both patterns II-1 and II-2 are distinct from pattern II-3, which covers the Spirurida, supporting a closer relationship between Ascaridida and Strongylida rather than Spirurida. Thymine (T) was highly concentrated on coding strands in Chromadorea, but balanced between the two strands in Enoplea, probably due to the gene arrangement pattern. Interestingly, the gene arrangement pattern of mt genomes and phylogenetic analysis based on concatenated amino acids indicated a closer relationship between the order Ascaridida and Rhabditida rather than Spirurida as indicated in previous studies. These discrepancies call for new research, reassessing the position of the order of Ascaridida in the phylogenetic tree. Once consolidated, the findings are important for population genetic studies and target identificatio

Human Angiostrongyliasis Outbreak in Dali, China

Angiostrongyliasis, caused by the rat lungworm Angiostrongylus cantonensis, is a potentially fatal food-borne disease. It is endemic in parts of Southeast Asia, the Pacific Islands, Australia, and the Caribbean. Outbreaks have become increasingly common in China due to the spread of efficient intermediate host snails, most notably Pomacea canaliculata. However, infections are difficult to detect since the disease has a rather long incubation period and few diagnostic clinical symptoms. Reliable diagnostic tests are not widely available. The described angiostrongyliasis epidemic in Dali, China lasted for eight months. Only 11 of a total of 33 suspected patients were clinically confirmed based on a set of diagnostic criteria. Our results demonstrate that the rapid and correct diagnosis of the index patient is crucial to adequately respond to an epidemic, and a set of standardized diagnostic procedures is needed to guide clinicians. Integrated control and management measures including health education, clinical guidelines and a hospital-based surveillance system, should be implemented in areas where snails are a popular food item

Genome-wide signatures of complex introgression and adaptive evolution in the big cats.

The great cats of the genus Panthera comprise a recent radiation whose evolutionary history is poorly understood. Their rapid diversification poses challenges to resolving their phylogeny while offering opportunities to investigate the historical dynamics of adaptive divergence. We report the sequence, de novo assembly, and annotation of the jaguar (Panthera onca) genome, a novel genome sequence for the leopard (Panthera pardus), and comparative analyses encompassing all living Panthera species. Demographic reconstructions indicated that all of these species have experienced variable episodes of population decline during the Pleistocene, ultimately leading to small effective sizes in present-day genomes. We observed pervasive genealogical discordance across Panthera genomes, caused by both incomplete lineage sorting and complex patterns of historical interspecific hybridization. We identified multiple signatures of species-specific positive selection, affecting genes involved in craniofacial and limb development, protein metabolism, hypoxia, reproduction, pigmentation, and sensory perception. There was remarkable concordance in pathways enriched in genomic segments implicated in interspecies introgression and in positive selection, suggesting that these processes were connected. We tested this hypothesis by developing exome capture probes targeting ~19,000 Panthera genes and applying them to 30 wild-caught jaguars. We found at least two genes (DOCK3 and COL4A5, both related to optic nerve development) bearing significant signatures of interspecies introgression and within-species positive selection. These findings indicate that post-speciation admixture has contributed genetic material that facilitated the adaptive evolution of big cat lineages

Impact of protein-polymer interactions in the antimicrobial activity of lysozyme/poly(3,4-ethylenedioxythiophene) biocapacitors

Biocapacitors constructed by combining lysozyme (LYZ) and poly(3,4-ethylenedioxythiophene) (PEDOT) retained the bactericidal activity of the protein when this was encapsulated within the polymeric matrix but lost the antimicrobial behaviour when the LYZ was adsorbed onto the polymer. In this work we use atomistic Molecular Dynamics simulations to examine the influence of protein···polymer interactions in the bactericidal activity of LYZ-containing biocapacitors. Results show that the anisotropic forces exerted by oxidized PEDOT chains on the adsorbed protein induce small structural changes that locally affect at the active centre, breaking the intra-residue interactions associated with the antibacterial mechanism. Conversely, isotropic polymer···protein interactions in biocapacitors with encapsulated LYZ do not affect the stability of the active centre. These observations suggest that the strong repulsive or attractive forces between p-doped polymer chains and the positively or negatively charged LYZ residues, respectively, are the only ones responsible for the protein activity.Peer ReviewedPostprint (author's final draft

Profiling of lung microbiota discloses differences in adenocarcinoma and squamous cell carcinoma

The lung is a complex ecosystem of host cells and microbes often disrupted in pathological conditions. Although bacteria have been hypothesized as agents of carcinogenesis, little is known about microbiota profile of the most prevalent cancer subtypes: adenocarcinoma (ADC) and squamous cell carcinoma (SCC). To characterize lung cancer (LC) microbiota a first a screening was performed through a pooled sequencing approach of 16S ribosomal RNA gene (V3-V6) using a total of 103 bronchoalveaolar lavage fluid samples. Then, identified taxa were used to inspect 1009 cases from The Cancer Genome Atlas and to annotate tumor unmapped RNAseq reads. Microbial diversity was analyzed per cancer subtype, history of cigarette smoking and airflow obstruction, among other clinical data. We show that LC microbiota is enriched in Proteobacteria and more diverse in SCC than ADC, particularly in males and heavier smokers. High frequencies of Proteobacteria were found to discriminate a major cluster, further subdivided into well-defined communities’ associated with either ADC or SCC. Here, a SCC subcluster differing from other cases by a worse survival was correlated with several Enterobacteriaceae. Overall, this study provides first evidence for a correlation between lung microbiota and cancer subtype and for its influence on patient life expectancy.We would like to thank all patients for donating their samples and for collaborating in this study. IPATIMUP integrates the i3S Research Unit, which is partially supported by the Portuguese Foundation for Science and Technology (FCT). This work was supported by the Portuguese Foundation for Science and Technology (FCT), financed by the European Social Funds (COMPETE-FEDER) and National Funds through the FCT (projects PEstC/SAU/LA0003/2013 and POCI-01-0145-FEDER-007274, fellowships SFRH/BPD/77646/2011 and SFRH/BPD/120777/2016 to S.G. and P.I.M., respectively, grant PTDC/BEXGMG/0242/2012 to S.S. and by Programa Operacional Regional do Norte (ON.2 – O Novo Norte and Norte 2020), through FEDER funds under the Quadro de Referência Estratégico Nacional (QREN; projects NORTE-07-0162-FEDER-00018 and NORTE-070162-FEDER-000067, and NORTE-01-0145-FEDER-000029)

The incidence of liver injury in Uyghur patients treated for TB in Xinjiang Uyghur autonomous region, China, and its association with hepatic enzyme polymorphisms nat2, cyp2e1, gstm1 and gstt1.

BACKGROUND AND OBJECTIVE: Of three first-line anti-tuberculosis (anti-TB) drugs, isoniazid is most commonly associated with hepatotoxicity. Differences in INH-induced toxicity have been attributed to genetic variability at several loci, NAT2, CYP2E1, GSTM1and GSTT1, that code for drug-metabolizing enzymes. This study evaluated whether the polymorphisms in these enzymes were associated with an increased risk of anti-TB drug-induced hepatitis in patients and could potentially be used to identify patients at risk of liver injury. METHODS AND DESIGN: In a cross-sectional study, 2244 tuberculosis patients were assessed two months after the start of treatment. Anti-TB drug-induced liver injury (ATLI) was defined as an ALT, AST or bilirubin value more than twice the upper limit of normal. NAT2, CYP2E1, GSTM1 and GSTT1 genotypes were determined using the PCR/ligase detection reaction assays. RESULTS: 2244 patients were evaluated, there were 89 cases of ATLI, a prevalence of 4% 9 patients (0.4%) had ALT levels more than 5 times the upper limit of normal. The prevalence of ATLI was greater among men than women, and there was a weak association with NAT2*5 genotypes, with ATLI more common among patients with the NAT2*5*CT genotype. The sensitivity of the CT genotype for identifying patients with ATLI was 42% and the positive predictive value 5.9%. CT ATLI was more common among slow acetylators (prevalence ratio 2.0 (95% CI 0.95,4.20) )compared to rapid acetylators. There was no evidence that ATLI was associated with CYP2E1 RsaIc1/c1genotype, CYP2E1 RsaIc1/c2 or c2/c2 genotypes, or GSTM1/GSTT1 null genotypes. CONCLUSIONS: In Xinjiang Uyghur TB patients, liver injury was associated with the genetic variant NAT2*5, however the genetic markers studied are unlikely to be useful for screening patients due to the low sensitivity and low positive predictive values for identifying persons at risk of liver injury

Quantitative insights into the fast pyrolysis of extracted cellulose, hemicelluloses and lignin

The transformation of lignocellulosic biomass into bio-based commodity chemicals is technically possible. Among thermochemical processes, fast pyrolysis, a relatively mature technology that has now reached the commercial level, produces a high yield of an organic-rich liquid stream. Despite the recent efforts in elucidating the degradation paths of biomass pyrolysis, the selectivity and recovery rates of bio-compounds remain low. In an attempt to clarify the general degradation scheme of biomass fast pyrolysis and provide a quantitative insight, this study has combined the use of fast pyrolysis micro-reactors, spectrometric techniques and mixtures of unlabelled and Carbon-13 enriched materials. The first stage of the work reported aimed at selecting the type of reactor to ensure control of the pyrolysis regime. The comparison of chemical fragmentation patterns of 'primary' fast pyrolysis volatiles detectable by GC-MS between two small scale micro-reactors has shown the inevitable presence of secondary reactions. In a second stage, liquid fractions also made of 'primary' fast pyrolysis condensables have been analysed by quantitative liquid-state 13C-NMR providing a quantitative distribution of functional groups. The compilation of those results into a map that displays the distribution of functional groups according to the individual and main constituents of biomass confirmed the origin of individual chemicals within fast pyrolysis liquids

Spatial Kramers-Kronig relations and the reflection of waves

Copyright © 2015, Rights Managed by Nature Publishing GroupAuthor version of article. The version of record is available from the publisher via DOI: 10.1038/nphoton.2015.106When a planar dielectric medium has a permittivity profile that is an analytic function in the upper or lower half of the complex position plane x=x'+ix'' then the real and imaginary parts of its permittivity are related by the spatial Kramers-Kronig relations. We find that such a medium will not reflect radiation incident from one side, whatever the angle of incidence. Using the spatial Kramers-Kronig relations, one can derive a real part of a permittivity profile from some given imaginary part (or vice versa) such that the reflection is guaranteed to be zero. This result is valid for both scalar and vector wave theories and may have relevance for designing materials that efficiently absorb radiation or for the creation of a new type of anti-reflection surface.Engineering and Physical Sciences Research Council (EPSRC

Interaction Between Convection and Pulsation

This article reviews our current understanding of modelling convection dynamics in stars. Several semi-analytical time-dependent convection models have been proposed for pulsating one-dimensional stellar structures with different formulations for how the convective turbulent velocity field couples with the global stellar oscillations. In this review we put emphasis on two, widely used, time-dependent convection formulations for estimating pulsation properties in one-dimensional stellar models. Applications to pulsating stars are presented with results for oscillation properties, such as the effects of convection dynamics on the oscillation frequencies, or the stability of pulsation modes, in classical pulsators and in stars supporting solar-type oscillations.Comment: Invited review article for Living Reviews in Solar Physics. 88 pages, 14 figure