Conservation of long-range synteny and microsynteny between the genomes of two distantly related nematodes

BACKGROUND: Comparisons between the genomes of the closely related nematodes Caenorhabditis elegans and Caenorhabditis briggsae reveal high rates of rearrangement, with a bias towards within-chromosome events. To assess whether this pattern is true of nematodes in general, we have used genome sequence to compare two nematode species that last shared a common ancestor approximately 300 million years ago: the model C. elegans and the filarial parasite Brugia malayi. RESULTS: An 83 kb region flanking the gene for Bm-mif-1 (macrophage migration inhibitory factor, a B. malayi homolog of a human cytokine) was sequenced. When compared to the complete genome of C. elegans, evidence for conservation of long-range synteny and microsynteny was found. Potential C. elegans orthologs for II of the 12 protein-coding genes predicted in the B. malayi sequence were identified. Ten of these orthologs were located on chromosome I, with eight clustered in a 2.3 Mb region. While several, relatively local, intrachromosomal rearrangements have occurred, the order, composition, and configuration of two gene clusters, each containing three genes, was conserved. Comparison of B. malayi BAC-end genome survey sequence to C. elegans also revealed a bias towards intrachromosome rearrangements. CONCLUSIONS: We suggest that intrachromosomal rearrangement is a major force driving chromosomal organization in nematodes, but is constrained by the interdigitation of functional elements of neighboring genes

Angular sensitivity of blowfly photoreceptors: intracellular measurements and wave-optical predictions

The angular sensitivity of blowfly photoreceptors was measured in detail at wavelengths λ = 355, 494 and 588 nm. The measured curves often showed numerous sidebands, indicating the importance of diffraction by the facet lens. The shape of the angular sensitivity profile is dependent on wavelength. The main peak of the angular sensitivities at the shorter wavelengths was flattened. This phenomenon as well as the overall shape of the main peak can be quantitatively described by a wave-optical theory using realistic values for the optical parameters of the lens-photoreceptor system. At a constant response level of 6 mV (almost dark adapted), the visual acuity of the peripheral cells R1-6 is at longer wavelengths mainly diffraction limited, while at shorter wavelengths the visual acuity is limited by the waveguide properties of the rhabdomere. Closure of the pupil narrows the angular sensitivity profile at the shorter wavelengths. This effect can be fully described by assuming that the intracellular pupil progressively absorbs light from the higher order modes. In light-adapted cells R1-6 the visual acuity is mainly diffraction limited at all wavelengths.

Evaluation of Lateglacial temperatures in the Southern Alps of New Zealand based on glacier modelling at Irishman Stream, Ben Ohau Range

Climate proxy records from the middle to high latitude Southern Hemisphere indicate that a Lateglacial (15,000-11,500 years ago) climate reversal, approximately coeval with the Antarctic Cold Reversal (ACR), interrupted a warming trend during deglaciation. In New Zealand, some palaeoclimate proxy records indicate a cool episode during the ACR (ca 14,500-12,500 years ago), while others do not express a significant change in climate. Recently published moraine maps and ages present an opportunity to improve the palaeoclimate interpretation through numerical modelling of glaciers. We use a coupled energy-balance and ice-flow model to quantify palaeoclimate from past glacier extent constrained by mapped and dated moraines in the headwaters of Irishman Stream, a high-elevation catchment in the Southern Alps. First, a suite of steady-state model runs is used to identify the temperature and precipitation forcing required to fit the modelled glacier to well-dated Lateglacial moraine crests. Second, time dependent glacier simulations forced by a nearby proxy temperature record derived from chironomids are used to assess the fit with the glacial geomorphic record. Steady-state experiments using an optimal parameter set demonstrate that the conditions under which the 13,000 year old moraine formed were 2.3-3.2 *C colder than present with the range in temperature corresponding to a +/- 20% variance in precipitation relative to the present-day. This reconstructed climate change relative to the present-day corresponds to an equilibrium-line altitude of ca 2000 +/- 40 m above sea level (asl), which is ca 400 m lower than present. Time-dependent simulations of glacier length produce ice advance to within 100 m of the 13,000 year old terminal moraine, indicating that the chironomid-based temperature forcing and moraine record provide consistent information about past climate. Our results, together with other climate proxy reconstructions from pollen records and marine sediment cores, support the notion that temperatures during the ACR in New Zealand were ~2-3 *C cooler than today

A Ship-Based Characterization of Coherent Boundary-Layer Structures Over the Lifecycle of a Marine Cold-Air Outbreak

Convective coherent structures shape the atmospheric boundary layer over the lifecycle of marine cold-air outbreaks (CAOs). Aircraft measurements have been used to characterize such structures in past CAOs. Yet, aircraft case studies are limited to snapshots of a few hours and do not capture how coherent structures, and the associated boundary-layer characteristics, change over the CAO time scale, which can be on the order of several days. We present a novel ship-based approach to determine the evolution of the coherent-structure characteristics, based on profiling lidar observations. Over the lifecycle of a multi-day CAO we show how these structures interact with boundary-layer characteristics, simultaneously obtained by a multi-sensor set-up. Observations are taken during the Iceland Greenland Seas Project’s wintertime cruise in February and March 2018. For the evaluated CAO event, we successfully identify cellular coherent structures of varying size in the order of 4 × 102 m to 104 m and velocity amplitudes of up to 0.5 m s−1 in the vertical and 1 m s−1 in the horizontal. The structures’ characteristics are sensitive to the near-surface stability and the Richardson number. We observe the largest coherent structures most frequently for conditions when turbulence generation is weakly buoyancy dominated. Structures of increasing size contribute efficiently to the overturning of the boundary layer and are linked to the growth of the convective boundary-layer depth. The new approach provides robust statistics for organized convection, which would be easy to extend by additional observations during convective events from vessels of opportunity operating in relevant areas

Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis

Background: Streptococcus suis is a zoonotic pathogen that infects pigs and can occasionally cause serious infections in humans. S. suis infections occur sporadically in human Europe and North America, but a recent major outbreak has been described in China with high levels of mortality. The mechanisms of S. suis pathogenesis in humans and pigs are poorly understood. Methodology/Principal Findings: The sequencing of whole genomes of S. suis isolates provides opportunities to investigate the genetic basis of infection. Here we describe whole genome sequences of three S. suis strains from the same lineage: one from European pigs, and two from human cases from China and Vietnam. Comparative genomic analysis was used to investigate the variability of these strains. S. suis is phylogenetically distinct from other Streptococcus species for which genome sequences are currently available. Accordingly, ,40% of the ,2 Mb genome is unique in comparison to other Streptococcus species. Finer genomic comparisons within the species showed a high level of sequence conservation; virtually all of the genome is common to the S. suis strains. The only exceptions are three ,90 kb regions, present in the two isolates from humans, composed of integrative conjugative elements and transposons. Carried in these regions are coding sequences associated with drug resistance. In addition, small-scale sequence variation has generated pseudogenes in putative virulence and colonization factors. Conclusions/Significance: The genomic inventories of genetically related S. suis strains, isolated from distinct hosts and diseases, exhibit high levels of conservation. However, the genomes provide evidence that horizontal gene transfer has contributed to the evolution of drug resistance

Foreign direct investment and institutional reform : evidence and an application to Portugal

We examine the role of geographic, economic, and institutional factors in attracting Foreign Direct Investment (FDI) in Europe, using a cross-section of inward bilateral investments. We estimate and assess the expected benefits, the required reform efforts, and the efficiency of reform options corresponding to a con- vergence of Portuguese institutions to EU standards. We conclude that improving home institutions is likely to have a quantitatively very significant role in attracting FDI. Geographical and market size factors also play a role. Reforms promoting the independence of financial institutions and a leaner bureaucracy, lowering political risk and corruption, and improving the investment code may significantly affect the amount of bilateral inward FDI that is targeted to Portugal.info:eu-repo/semantics/publishedVersio

Quality of Computationally Inferred Gene Ontology Annotations

Gene Ontology (GO) has established itself as the undisputed standard for protein function annotation. Most annotations are inferred electronically, i.e. without individual curator supervision, but they are widely considered unreliable. At the same time, we crucially depend on those automated annotations, as most newly sequenced genomes are non-model organisms. Here, we introduce a methodology to systematically and quantitatively evaluate electronic annotations. By exploiting changes in successive releases of the UniProt Gene Ontology Annotation database, we assessed the quality of electronic annotations in terms of specificity, reliability, and coverage. Overall, we not only found that electronic annotations have significantly improved in recent years, but also that their reliability now rivals that of annotations inferred by curators when they use evidence other than experiments from primary literature. This work provides the means to identify the subset of electronic annotations that can be relied upon—an important outcome given that >98% of all annotations are inferred without direct curation