Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea)

Complete mitochondrial genomes have been shown to be reliable markers for phylogeny reconstruction among diverse animal groups. However, the relative difficulty and high cost associated with obtaining de novo full mitogenomes have frequently led to conspicuously low taxon sampling in ensuing studies. Here, we report the successful use of an economical and accessible method for assembling complete or near-complete mitogenomes through shot-gun next-generation sequencing of a single library made from pooled total DNA extracts of numerous target species. To avoid the use of separate indexed libraries for each specimen, and an associated increase in cost, we incorporate standard polymerase chain reaction-based “bait” sequences to identify the assembled mitogenomes. The method was applied to study the higher level phylogenetic relationships in the weevils (Coleoptera: Curculionoidea), producing 92 newly assembled mitogenomes obtained in a single Illumina MiSeq run. The analysis supported a separate origin of wood-boring behavior by the subfamilies Scolytinae, Platypodinae, and Cossoninae. This finding contradicts morphological hypotheses proposing a close relationship between the first two of these but is congruent with previous molecular studies, reinforcing the utility of mitogenomes in phylogeny reconstruction. Our methodology provides a technically simple procedure for generating densely sampled trees from whole mitogenomes and is widely applicable to groups of animals for which bait sequences are the only required prior genome knowledge

Intraspecific genetic variation in complex assemblages from mitochondrial metagenomics: comparison with DNA barcodes

Metagenomic shotgun sequencing, using Illumina technology, and de novo genome assembly of mixed field-collected amples of invertebrates readily produce mitochondrial genome sequences, allowing rapid identification and quantification of species diversity. However, intraspecific genetic variability present in the specimen pools is lost during mitogenome assembly, which limits the utility of ‘mitochondrial metagenomics’ for studies of population diversity. 2. Using 10 natural communities (>2600 individuals) of leaf beetles (Chrysomelidae), DNA variation in the mitochondrial cox1-5’ ‘barcode’ was compared for Sanger sequenced individuals and Illumina shotgun sequenced specimen pools. 3. Generally, only a single mitochondrial contig was assembled per species, even in the presence of intraspecific variation. Ignoring ambiguity from the use of two different assemblers, the cox1 barcode regions from these assemblies were exact nucleotide matches of a Sanger sequenced barcode in 90.7% of cases, which dropped to 76.0% in assemblies from samples with large intra and interspecific variability. Nucleotide differences between barcodes from both data types were almost exclusively in synonymous 3rd codon position, although the number of affected sites was very low, and the greatest discrepancies were correlated with poor quality of Sanger sequences. 4. Unassembled shotgun reads were also used to score single nucleotide polymorphisms and to calculate intraspecific nucleotide diversity (pi) for all available populations at each site. These values correlated with Sanger sequenced cox1 variation but were significantly higher. 5. Overall, the assemblage-focused shotgun sequencing of pooled samples produced nucleotide variation data comparable to the well-established specimen-focused Sanger approach. The findings thus extend the application of mitochondrial metagenomics of complex biodiversity samples to the estimation of diversity below the species level

N -butyldeoxynojirimycin reduces growth and ganglioside content of experimental mouse brain tumours

Abnormalities in glycosphingolipid (GSL) biosynthesis have been implicated in the oncogenesis and malignancy of brain tumours. GSLs comprise the gangliosides and the neutral GSLs and are major components of the cell surface glycocalyx. N -butyldeoxynojirimycin (N B-DNJ) is an imino sugar that inhibits the glucosyltransferase catalysing the first step in GSL biosynthesis. The influence of N B-DNJ was studied on the growth and ganglioside composition of two 20-methylcholanthrene-induced experimental mouse brain tumours, EPEN and CT-2A, which were grown in vitro and in vivo. N B-DNJ (200 μM) inhibited the proliferation of the EPEN and CT-2A cells by 50%, but did not reduce cell viability. The drug, administered in the diet (2400 mg kg−1) to adult syngeneic C57BL/6 mice, reduced the growth and ganglioside content of subcutaneous and intracerebral EPEN and CT-2A tumours by at least 50% compared to the untreated controls. N B-DNJ treatment also shifted the relative distribution of tumour gangliosides in accordance with the depletion of metabolic substrates. Side effects of N B-DNJ treatment were generally mild and included reductions in body and spleen weights and intestinal distension. We conclude that N B-DNJ may inhibit tumour growth through an effect on ganglioside biosynthesis and may be useful as a new chemotherapy for brain tumours. © 2001 Cancer Research Campaign http://www.bjcancer.co

Analysis of non-pharmaceutical interventions and their impacts on COVID-19 in Kerala

In the absence of an effective vaccine or drug therapy, non-pharmaceutical interventions are the only option for control of the outbreak of the coronavirus disease 2019, a pandemic with global implications. Each of the over 200 countries affected has followed its own path in dealing with the crisis, making it difficult to evaluate the effectiveness of measures implemented, either individually, or collectively. In this paper we analyse the case of the south Indian state of Kerala, which received much attention in the international media for its actions in containing the spread of the disease in the early months of the pandemic, but later succumbed to a second wave. We use a model to study the trajectory of the disease in the state during the first four months of the outbreak. We then use the model for a retrospective analysis of measures taken to combat the spread of the disease, to evaluate their impact. Because of the differences in the trajectory of the outbreak in Kerala, we argue that it is a model worthy of a place in the discussion on how the world might best handle this and other, future, pandemics

Critical exponents in zero dimensions

In the vicinity of the onset of an instability, we investigate the effect of colored multiplicative noise on the scaling of the moments of the unstable mode amplitude. We introduce a family of zero dimensional models for which we can calculate the exact value of the critical exponents $\beta_m$ for all the moments. The results are obtained through asymptotic expansions that use the distance to onset as a small parameter. The examined family displays a variety of behaviors of the critical exponents that includes anomalous exponents: exponents that differ from the deterministic (mean-field) prediction, and multiscaling: non-linear dependence of the exponents on the order of the moment

Decoding the neural substrates of reward-related decision making with functional MRI

Although previous studies have implicated a diverse set of brain regions in reward-related decision making, it is not yet known which of these regions contain information that directly reflects a decision. Here, we measured brain activity using functional MRI in a group of subjects while they performed a simple reward-based decision-making task: probabilistic reversal-learning. We recorded brain activity from nine distinct regions of interest previously implicated in decision making and separated out local spatially distributed signals in each region from global differences in signal. Using a multivariate analysis approach, we determined the extent to which global and local signals could be used to decode subjects' subsequent behavioral choice, based on their brain activity on the preceding trial. We found that subjects' decisions could be decoded to a high level of accuracy on the basis of both local and global signals even before they were required to make a choice, and even before they knew which physical action would be required. Furthermore, the combined signals from three specific brain areas (anterior cingulate cortex, medial prefrontal cortex, and ventral striatum) were found to provide all of the information sufficient to decode subjects' decisions out of all of the regions we studied. These findings implicate a specific network of regions in encoding information relevant to subsequent behavioral choice

Universal Scaling Properties in Large Assemblies of Simple Dynamical Units Driven by Long-Wave Random Forcing

Large assemblies of nonlinear dynamical units driven by a long-wave fluctuating external field are found to generate strong turbulence with scaling properties. This type of turbulence is so robust that it persists over a finite parameter range with parameter-dependent exponents of singularity, and is insensitive to the specific nature of the dynamical units involved. Whether or not the units are coupled with their neighborhood is also unimportant. It is discovered numerically that the derivative of the field exhibits strong spatial intermittency with multifractal structure.Comment: 10 pages, 7 figures, submitted to PR

On the magnetic fields generated by experimental dynamos

We review the results obtained by three successful fluid dynamo experiments and discuss what has been learnt from them about the effect of turbulence on the dynamo threshold and saturation. We then discuss several questions that are still open and propose experiments that could be performed to answer some of them.Comment: 40 pages, 13 figure

The North Atlantic Oscillation controls air pollution transport to the Arctic

This paper studies the interannual variability of pollution pathways from northern hemisphere (NH) continents into the Arctic. Using a 15-year model simulation of the dispersion of passive tracers representative of anthropogenic emissions from NH continents, we show that the North Atlantic Oscillation (NAO) exerts a strong control on the pollution transport into the Arctic, particularly in winter and spring. For tracer lifetimes of 5 (30) days, surface concentrations in the Arctic winter are enhanced by about 70% (30%) during high phases of the NAO (in the following referred to as NAO⁺) compared to its low phases (NAO^-). This is mainly due to great differences in the pathways of European pollution during NAO⁺ and NAO^- phases, respectively, but reinforced by North American pollution, which is also enhanced in the Arctic during NAO⁺phases. In contrast, Asian pollution in the Arctic does not significantly depend on the NAO phase. The model results are confirmed using remotely-sensed NO₂ vertical atmospheric columns obtained from seven years of satellite measurements, which show enhanced northward NO₂ transport and reduced NO₂ outflow into the North Atlantic from Central Europe during NAO⁺ phases. Surface measurements of carbon monoxide (CO) and black carbon at high-latitude stations further corroborate the overall picture of enhanced Arctic pollution levels during NAO⁺ phase