Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints

The question of how local adaptation takes place remains a fundamental question in evolutionary biology. The variation of allele frequencies in genes under selection over environmental gradients remains mainly theoretical and its empirical assessment would help understanding how adaptation happens over environmental clines. To bring new insights to this issue we set up a broad framework which aimed to compare the adaptive trajectories over environmental clines in two domesticated mammal species co-distributed in diversified landscapes. We sequenced the genomes of 160 sheep and 161 goats extensively managed along environmental gradients, including temperature, rainfall, seasonality and altitude, to identify genes and biological processes shaping local adaptation. Allele frequencies at putatively adaptive loci were rarely found to vary gradually along environmental gradients, but rather displayed a discontinuous shift at the extremities of environmental clines. Of the 430 candidate adaptive genes identified, only 6 were orthologous between sheep and goats and those responded differently to environmental pressures, suggesting different putative mechanisms involved in local adaptation in these two closely related species. Interestingly, the genomes of the 2 species were impacted differently by the environment, genes related to signatures of selection were most related to altitude, slope and rainfall seasonality for sheep, and summer temperature and spring rainfall for goats. The diversity of candidate adaptive pathways may result from a high number of biological functions involved in the adaptations to multiple eco-climatic gradients, and a differential role of climatic drivers on the two species, despite their co-distribution along the same environmental gradients. This study describes empirical examples of clinal variation in putatively adaptive alleles with different patterns in allele frequency distributions over continuous environmental gradients, thus showing the diversity of genetic responses in adaptive landscapes and opening new horizons for understanding genomics of adaptation in mammalian species and beyond.

Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.

Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding

BACKGROUND

The sequencing of the wheat (Triticum aestivum) genome has been a methodological challenge for many years owing to its large size (15.5 Gb), repeat content, and hexaploidy. Many initiatives aiming at obtaining a reference genome of cultivar Chinese Spring have been launched in the past years and it was achieved in 2018 as the result of a huge effort to combine short-read sequencing with many other resources. Reference-quality genome assemblies were then produced for other accessions, but the rapid evolution of sequencing technologies offers opportunities to reach high-quality standards at lower cost.

RESULTS

Here, we report on an optimized procedure based on long reads produced on the Oxford Nanopore Technology PromethION device to assemble the genome of the French bread wheat cultivar Renan.

CONCLUSIONS

We provide the most contiguous chromosome-scale assembly of a bread wheat genome to date. Coupled with an annotation based on RNA-sequencing data, this resource will be valuable for the crop community and will facilitate the rapid selection of agronomically important traits. We also provide a framework to generate high-quality assemblies of complex genomes using ONT.

Real-time SARS-CoV-2 diagnostic and variants tracking over multiple candidates using nanopore DNA sequencing

Since December 2019, a novel coronavirus responsible for a severe acute respiratory syndrome (SARS-CoV-2) is accountable for a major pandemic situation. The emergence of the B.1.1.7 strain, as a highly transmissible variant has accelerated the world-wide interest in tracking SARS-CoV-2 variants' occurrence. Similarly, other extremely infectious variants, were described and further others are expected to be discovered due to the long period of time on which the pandemic situation is lasting. All described SARS-CoV-2 variants present several mutations within the gene encoding the Spike protein, involved in host receptor recognition and entry into the cell. Hence, instead of sequencing the whole viral genome for variants' tracking, herein we propose to focus on the SPIKE region to increase the number of candidate samples to screen at once; an essential aspect to accelerate diagnostics, but also variants' emergence/progression surveillance. This proof of concept study accomplishes both at once, population-scale diagnostics and variants' tracking. This strategy relies on (1) the use of the portable MinION DNA sequencer; (2) a DNA barcoding and a SPIKE gene-centered variant's tracking, increasing the number of candidates per assay; and (3) a real-time diagnostics and variant's tracking monitoring thanks to our software RETIVAD. This strategy represents an optimal solution for addressing the current needs on SARS-CoV-2 progression surveillance, notably due to its affordable implementation, allowing its implantation even in remote places over the world.

Long-read assembly of the Brassica napus reference genome Darmor-bzh

BACKGROUND

The combination of long reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allows access to the gene catalogue of a given species but also reveals the architecture and organization of chromosomes, including complex regions such as telomeres and centromeres. The Brassica genus is not exempt, and many assemblies based on long reads are now available. The reference genome for Brassica napus, Darmor-bzh, which was published in 2014, was produced using short reads and its contiguity was extremely low compared with current assemblies of the Brassica genus.

FINDINGS

Herein, we report the new long-read assembly of Darmor-bzh genome (Brassica napus) generated by combining long-read sequencing data and optical and genetic maps. Using the PromethION device and 6 flowcells, we generated ∼16 million long reads representing 93× coverage and, more importantly, 6× with reads longer than 100 kb. This ultralong-read dataset allows us to generate one of the most contiguous and complete assemblies of a Brassica genome to date (contig N50 > 10 Mb). In addition, we exploited all the advantages of the nanopore technology to detect modified bases and sequence transcriptomic data using direct RNA to annotate the genome and focus on resistance genes.

CONCLUSION

Using these cutting-edge technologies, and in particular by relying on all the advantages of the nanopore technology, we provide the most contiguous Brassica napus assembly, a resource that will be valuable to the Brassica community for crop improvement and will facilitate the rapid selection of agronomically important traits.

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms.

Video Abstract

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A catalog of 47 million genes was generated from 370 globally distributed metagenomes

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Meta-omics data integration disentangled the mechanisms of changes in transcript pools

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Transcript pool changes of metabolic marker genes show distinct mechanistic patterns

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Community turnover as a response to ocean warming may be strongest in polar regions

FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing

Genome replication mapping methods profile cell populations, masking cell-to-cell heterogeneity. Here, we describe FORK-seq, a nanopore sequencing method to map replication of single DNA molecules at 200-nucleotide resolution. By quantifying BrdU incorporation along pulse-chased replication intermediates from Saccharomyces cerevisiae, we orient 58,651 replication tracks reproducing population-based replication directionality profiles and map 4964 and 4485 individual initiation and termination events, respectively. Although most events cluster at known origins and fork merging zones, 9% and 18% of initiation and termination events, respectively, occur at many locations previously missed. Thus, FORK-seq reveals the full extent of cell-to-cell heterogeneity in DNA replication.

An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity

Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low-coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high-density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low-density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes.

Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps

Plant genomes are often characterized by a high level of repetitiveness and polyploid nature. Consequently, creating genome assemblies for plant genomes is challenging. The introduction of short-read technologies 10 years ago substantially increased the number of available plant genomes. Generally, these assemblies are incomplete and fragmented, and only a few are at the chromosome scale. Recently, Pacific Biosciences and Oxford Nanopore sequencing technologies were commercialized that can sequence long DNA fragments (kilobases to megabase) and, using efficient algorithms, provide high-quality assemblies in terms of contiguity and completeness of repetitive regions^1-4. However, even though genome assemblies based on long reads exhibit high contig N50s (>1 Mb), these methods are still insufficient to decipher genome organization at the chromosome level. Here, we describe a strategy based on long reads (MinION or PromethION sequencers) and optical maps (Saphyr system) that can produce chromosome-level assemblies and demonstrate applicability by generating high-quality genome sequences for two new dicotyledon morphotypes, Brassica rapa Z1 (yellow sarson) and Brassica oleracea HDEM (broccoli), and one new monocotyledon, Musa schizocarpa (banana). All three assemblies show contig N50s of >5 Mb and contain scaffolds that represent entire chromosomes or chromosome arms.

The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes

African rice (Oryza glaberrima) was domesticated independently from Asian rice. The geographical origin of its domestication remains elusive. Using 246 new whole-genome sequences, we inferred the cradle of its domestication to be in the Inner Niger Delta. Domestication was preceded by a sharp decline of most wild populations that started more than 10,000 years ago. The wild population collapse occurred during the drying of the Sahara. This finding supports the hypothesis that depletion of wild resources in the Sahara triggered African rice domestication. African rice cultivation strongly expanded 2,000 years ago. During the last 5 centuries, a sharp decline of its cultivation coincided with the introduction of Asian rice in Africa. A gene, PROG1, associated with an erect plant architecture phenotype, showed convergent selection in two rice cultivated species, Oryza glaberrima from Africa and Oryza sativa from Asia. In contrast, a shattering gene, SH5, showed selection signature during African rice domestication, but not during Asian rice domestication. Overall, our genomic data revealed a complex history of African rice domestication influenced by important climatic changes in the Saharan area, by the expansion of African agricultural society, and by recent replacement by another domesticated species.

Genome evolution across 1,011 Saccharomyces cerevisiae isolates

Large-scale population genomic surveys are essential to explore the phenotypic diversity of natural populations. Here we report the whole-genome sequencing and phenotyping of 1,011 Saccharomyces cerevisiae isolates, which together provide an accurate evolutionary picture of the genomic variants that shape the species-wide phenotypic landscape of this yeast. Genomic analyses support a single 'out-of-China' origin for this species, followed by several independent domestication events. Although domesticated isolates exhibit high variation in ploidy, aneuploidy and genome content, genome evolution in wild isolates is mainly driven by the accumulation of single nucleotide polymorphisms. A common feature is the extensive loss of heterozygosity, which represents an essential source of inter-individual variation in this mainly asexual species. Most of the single nucleotide polymorphisms, including experimentally identified functional polymorphisms, are present at very low frequencies. The largest numbers of variants identified by genome-wide association are copy-number changes, which have a greater phenotypic effect than do single nucleotide polymorphisms. This resource will guide future population genomics and genotype-phenotype studies in this classic model system.

Effect of late prophylaxis in hemophilia on joint status: a randomized trial

Essentials High-quality data are lacking on use of prophylaxis in adults with hemophilia and arthropathy. SPINART was a 3-year randomized clinical trial of late/tertiary prophylaxis vs on-demand therapy. Prophylaxis improved function, quality of life, activity and pain but not joint structure by MRI. Prophylaxis improves function but must start before joint bleeding onset to prevent arthropathy.

SUMMARY

Background Limited data exist on the impact of prophylaxis on adults with severe hemophilia A and pre-existing joint disease. Objectives To describe 3-year bleeding, joint health and structure, health-related quality-of-life (HRQoL) and other outcomes from the open-label, randomized, multinational SPINART study. Patients/Methods Males aged 12-50 years with severe hemophilia A, ≥ 150 factor VIII exposure days, no inhibitors and no prophylaxis for > 12 consecutive months in the past 5 years were randomized to sucrose-formulated recombinant FVIII prophylaxis or on-demand therapy (OD). Data collected included total and joint bleeding events (BEs), joint structure (magnetic resonance imaging [MRI]), joint health (Colorado Adult Joint Assessment Scale [CAJAS]), HRQoL, pain, healthcare resource utilization (HRU), activity, and treatment satisfaction. Results Following 3 years of prophylaxis, adults maintained excellent adherence, with a 94% reduction in BEs despite severe pre-existing arthropathy; 35.7% and 76.2% of prophylaxis participants were bleed-free or had fewer than two BEs per year, respectively. As compared with OD, prophylaxis was associated with improved CAJAS scores (least squares [LS] mean, - 0.31 [n = 42] versus + 0.63 [n = 42]) and HAEMO-QoL-A scores (LS mean, + 3.98 [n = 41] versus - 6.00 [n = 42]), less chronic pain (50% decrease), and approximately two-fold less HRU; activity, Euro QoL-5D-3L (EQ-5D-3L) scores and satisfaction scores also favored prophylaxis. However, MRI score changes were not different for prophylaxis versus OD (LS mean, + 0.79 [n = 41] versus + 0.96 [n = 38]). Conclusions Over a period of 3 years, prophylaxis versus OD in adults with severe hemophilia A and arthropathy led to decreased bleeding, pain, and HRU, better joint health, activity, satisfaction, and HRQoL, but no reduction in structural arthropathy progression, suggesting that pre-existing joint arthropathy may be irreversible.

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009–2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world’s planktonic ecosystems.

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer

Background: Oxford Nanopore Technologies Ltd (Oxford, UK) have recently commercialized MinION, a small single-molecule nanopore sequencer, that offers the possibility of sequencing long DNA fragments from small genomes in a matter of seconds. The Oxford Nanopore technology is truly disruptive; it has the potential to revolutionize genomic applications due to its portability, low cost, and ease of use compared with existing long reads sequencing technologies. The MinION sequencer enables the rapid sequencing of small eukaryotic genomes, such as the yeast genome. Combined with existing assembler algorithms, near complete genome assemblies can be generated and comprehensive population genomic analyses can be performed. Results: Here, we resequenced the genome of the Saccharomyces cerevisiae S288C strain to evaluate the performance of nanopore-only assemblers. Then we de novo sequenced and assembled the genomes of 21 isolates representative of the S. cerevisiae genetic diversity using the MinION platform. The contiguity of our assemblies was 14 times higher than the Illumina-only assemblies and we obtained one or two long contigs for 65 % of the chromosomes. This high contiguity allowed us to accurately detect large structural variations across the 21 studied genomes. Conclusion: Because of the high completeness of the nanopore assemblies, we were able to produce a complete cartography of transposable elements insertions and inspect structural variants that are generally missed using a short-read sequencing strategy. Our analyses show that the Oxford Nanopore technology is already usable for de novo sequencing and assembly; however, non-random errors in homopolymers require polishing the consensus using an alternate sequencing technology.

A double-blind randomized controlled trial comparing dexamethasone and clonidine as adjuvants to a ropivacaine sciatic popliteal block for foot surgery

Background and aims

A popliteal block is effective in managing postoperative pain for foot surgery, but since the duration of analgesia is limited following a single-shot popliteal fossa block technique, methods to prolong effective postoperative analgesia are mandatory. The aim of this study was to assess the effect of adjuvants to ropivacaine on the duration of sensory and motor block.

Methods

In this double-blind randomized placebo-controlled study, we evaluated the analgesic effect of clonidine or dexamethasone (DXM) when added to ropivacaine for hallux valgus surgery. After obtaining institutional ethics research board approval and written informed consent, a total of 72 patients were randomly allocated. Fifty-seven of these patients were statistically analyzed. All patients received an ultrasound-guided single-shot popliteal fossa block with 30 mL of ropivacaine 0.75%, supplemented with saline, clonidine 100 µg, or DXM 5 mg. The primary end point was time to first pain sensation. Secondary end points were time to complete sensory and motor block regression.

Results

Compared to saline, duration to first pain sensation was prolonged by 9 hours (mean ± standard deviation: 31±9 hours) (42%) in the DXM group (P=0.024) and by 6 hours (28±10 hours) (27%) in the clonidine group (P=0.024). Compared to saline, DXM prolonged both complete sensory and motor blockade by 12 hours (25±7 hours) (46%) and 13 hours (36±6 hours) (55%), respectively, while clonidine prolonged complete sensory and motor blockade by 7 hours (30±7 hours) (27%) and 2 hours (22±5 hours) (10%), respectively. DXM prolonged sensory block regression time by 6 hours (21±7 hours) (41%) and clonidine by 2 hours (17±6 hours) (13%) compared to the control group (P=0.006). Similarly, DXM prolonged motor block regression by 7 hours (25±7 hours) (46%) and clonidine by 4 hours (21±4 hours) (19%) (P<0.0001).

Conclusion

Addition of DXM and clonidine to ropivacaine significantly prolonged the duration of postoperative sensory and motor block.

A Comparison of Three Procedures for Robust PCA in High Dimensions

In this paper we compare three procedures for robust Principal Components Analysis (PCA). The first method is called ROBPCA (see Hubert et al., 2005). It combines projection pursuit ideas with robust covariance estimation. The original algorithm for its computation is designed to construct an optimal PCA subspace of a fixed dimension k. If instead the optimal PCA subspace is searched within a whole range of dimensions k, this algorithm is not computationally efficient. Hence we present an adjusted algorithm that yields several PCA models in one single run. A different approach is the LTS-subspace estimator (see Wolbers, 2002; Maronna, 2005). It seeks for the subspace that minimizes an objective function based on the squared orthogonal distances of the observations to this subspace. It can be computed in analogy with the computation of the LTS regression estimator (see Rousseeuw and Van Driessen, 2000). The three approaches are compared by means of a simulation study.

Remifentanil PCIA during labor and delivery: can we improve maternal monitoring?

BACKGROUND

Remifentanil patient controlled intravenous analgesia (PCIA) during labor has rapidly gained popularity. Its pharmacological profile makes it suitable for this indication. However, remifentanil is a potent respiratory depressant that might cause serious maternal hypoventilation, respiratory arrest and desaturation.

METHODS

In the present study we compared standard monitoring of parturients (saturation measurements and visual respiratory rate measurements at set times) with continuous monitoring. Data of patients in the standard monitoring group were collected from handwritten charts containing oxygen saturation and respiratory rate. The patients in the continuous monitoring group were connected to a device that measures the oxygen saturation and respiratory rate every two seconds and automatically saves the data. These data were analyzed retrospectively.

RESULTS

In the standard monitoring group 1 patient (1%) had severe desaturation SpO₂ < 80%, 22 patients (25%) had SpO₂ < 94% and in no patient a respiratory rate (RR) < 8/min was recorded. In the continuous monitoring group 20 patients (33%) showed SpO₂ < 80%, 58 patients (97%) SpO₂ < 94% and 38 patients (63%) had bradypnea (RR < 8/min). The analysis of the data of the continuous monitoring group showed severe desaturations and serious respiratory depression.

CONCLUSION

The standard intermittent monitoring strategy dramatically underestimated the incidence of both bradypnea and oxygen desaturations with undetected hypoxemia and possible complications as a consequence. During use of remifentanil PCIA one-to-one midwifery care is advised. When obstetric caregivers are not present in the immediate vicinity of the parturient, high quality continuous monitoring, remote alarm notification and readiness for immediate corrective intervention are essential for safe use of this analgesic strategy.

Ocean plankton. Structure and function of the global ocean microbiome

Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.

Genome assembly using Nanopore-guided long and error-free DNA reads

Background

Long-read sequencing technologies were launched a few years ago, and in contrast with short-read sequencing technologies, they offered a promise of solving assembly problems for large and complex genomes. Moreover by providing long-range information, it could also solve haplotype phasing. However, existing long-read technologies still have several limitations that complicate their use for most research laboratories, as well as in large and/or complex genome projects. In 2014, Oxford Nanopore released the MinION® device, a small and low-cost single-molecule nanopore sequencer, which offers the possibility of sequencing long DNA fragments.

Results

The assembly of long reads generated using the Oxford Nanopore MinION® instrument is challenging as existing assemblers were not implemented to deal with long reads exhibiting close to 30% of errors. Here, we presented a hybrid approach developed to take advantage of data generated using MinION® device. We sequenced a well-known bacterium, Acinetobacter baylyi ADP1 and applied our method to obtain a highly contiguous (one single contig) and accurate genome assembly even in repetitive regions, in contrast to an Illumina-only assembly. Our hybrid strategy was able to generate NaS (Nanopore Synthetic-long) reads up to 60 kb that aligned entirely and with no error to the reference genome and that spanned highly conserved repetitive regions. The average accuracy of NaS reads reached 99.99% without losing the initial size of the input MinION® reads.

Conclusions

We described NaS tool, a hybrid approach allowing the sequencing of microbial genomes using the MinION® device. Our method, based ideally on 20x and 50x of NaS and Illumina reads respectively, provides an efficient and cost-effective way of sequencing microbial or small eukaryotic genomes in a very short time even in small facilities. Moreover, we demonstrated that although the Oxford Nanopore technology is a relatively new sequencing technology, currently with a high error rate, it is already useful in the generation of high-quality genome assemblies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1519-z) contains supplementary material, which is available to authorized users.

Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data

Since the time of their domestication, goats (Capra hircus) have evolved in a large variety of locally adapted populations in response to different human and environmental pressures. In the present era, many indigenous populations are threatened with extinction due to their substitution by cosmopolitan breeds, while they might represent highly valuable genomic resources. It is thus crucial to characterize the neutral and adaptive genetic diversity of indigenous populations. A fine characterization of whole genome variation in farm animals is now possible by using new sequencing technologies. We sequenced the complete genome at 12× coverage of 44 goats geographically representative of the three phenotypically distinct indigenous populations in Morocco. The study of mitochondrial genomes showed a high diversity exclusively restricted to the haplogroup A. The 44 nuclear genomes showed a very high diversity (24 million variants) associated with low linkage disequilibrium. The overall genetic diversity was weakly structured according to geography and phenotypes. When looking for signals of positive selection in each population we identified many candidate genes, several of which gave insights into the metabolic pathways or biological processes involved in the adaptation to local conditions (e.g., panting in warm/desert conditions). This study highlights the interest of WGS data to characterize livestock genomic diversity. It illustrates the valuable genetic richness present in indigenous populations that have to be sustainably managed and may represent valuable genetic resources for the long-term preservation of the species.

TE-Tracker: systematic identification of transposition events through whole-genome resequencing

Background

Transposable elements (TEs) are DNA sequences that are able to move from their location in the genome by cutting or copying themselves to another locus. As such, they are increasingly recognized as impacting all aspects of genome function. With the dramatic reduction in cost of DNA sequencing, it is now possible to resequence whole genomes in order to systematically characterize novel TE mobilization in a particular individual. However, this task is made difficult by the inherently repetitive nature of TE sequences, which in some eukaryotes compose over half of the genome sequence. Currently, only a few software tools dedicated to the detection of TE mobilization using next-generation-sequencing are described in the literature. They often target specific TEs for which annotation is available, and are only able to identify families of closely related TEs, rather than individual elements.

Results

We present TE-Tracker, a general and accurate computational method for the de-novo detection of germ line TE mobilization from re-sequenced genomes, as well as the identification of both their source and destination sequences. We compare our method with the two classes of existing software: specialized TE-detection tools and generic structural variant (SV) detection tools. We show that TE-Tracker, while working independently of any prior annotation, bridges the gap between these two approaches in terms of detection power. Indeed, its positive predictive value (PPV) is comparable to that of dedicated TE software while its sensitivity is typical of a generic SV detection tool. TE-Tracker demonstrates the benefit of adopting an annotation-independent, de novo approach for the detection of TE mobilization events. We use TE-Tracker to provide a comprehensive view of transposition events induced by loss of DNA methylation in Arabidopsis. TE-Tracker is freely available at http://www.genoscope.cns.fr/TE-Tracker.

Conclusions

We show that TE-Tracker accurately detects both the source and destination of novel transposition events in re-sequenced genomes. Moreover, TE-Tracker is able to detect all potential donor sequences for a given insertion, and can identify the correct one among them. Furthermore, TE-Tracker produces significantly fewer false positives than common SV detection programs, thus greatly facilitating the detection and analysis of TE mobilization events.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0377-z) contains supplementary material, which is available to authorized users.

MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

MicroScope is an integrated platform dedicated to both the methodical updating of microbial genome annotation and to comparative analysis. The resource provides data from completed and ongoing genome projects (automatic and expert annotations), together with data sources from post-genomic experiments (i.e. transcriptomics, mutant collections) allowing users to perfect and improve the understanding of gene functions. MicroScope (http://www.genoscope.cns.fr/agc/microscope) combines tools and graphical interfaces to analyse genomes and to perform the manual curation of gene annotations in a comparative context. Since its first publication in January 2006, the system (previously named MaGe for Magnifying Genomes) has been continuously extended both in terms of data content and analysis tools. The last update of MicroScope was published in 2009 in the Database journal. Today, the resource contains data for >1600 microbial genomes, of which ∼300 are manually curated and maintained by biologists (1200 personal accounts today). Expert annotations are continuously gathered in the MicroScope database (∼50 000 a year), contributing to the improvement of the quality of microbial genomes annotations. Improved data browsing and searching tools have been added, original tools useful in the context of expert annotation have been developed and integrated and the website has been significantly redesigned to be more user-friendly. Furthermore, in the context of the European project Microme (Framework Program 7 Collaborative Project), MicroScope is becoming a resource providing for the curation and analysis of both genomic and metabolic data. An increasing number of projects are related to the study of environmental bacterial (meta)genomes that are able to metabolize a large variety of chemical compounds that may be of high industrial interest.

Supraclavicular brachial plexus blocks: review and current practice

This article reviews the possible revival of the supraclavicular brachial plexus blockade due to the use of ultrasound guidance. The brachial plexus is a complex network of nerves, extending from the neck to the axilla, which supplies motor and sensory fibers to the upper extremity. Understanding the complexities of the formation and structure of the brachial plexus remains a cornerstone for effective regional anaesthesia. On the level of the supraclavicular fossa, the plexus is most compactly arranged. The supraclavicular approach of the brachial plexus has a high success rate including blockade of the ulnar and musculocutaneous nerve, which can be missed respectively with the interscalene and axillary approach. However, because of the proximity of the pleura, most anaesthesiologists have been reluctant to perform this supraclavicular approach. The introduction of ultrasound guidance techniques not only reduces the possible risk of pneumothorax but also allows a faster onset time of the block with a reduction of the local anaesthetic dose. This makes the supraclavicular approach a valuable alternative to the axillary, interscalene and infraclavicular approach for upper limb surgery.

Antiplatelet therapy in the perioperative period

Antiplatelet drugs are the cornerstone treatment in the secondary prevention of arterial thrombosis. Until recently, their intake was interrupted in the perioperative period because of fear for bleeding, but new insights have challenged this old habit: In patients at high risk for atherothrombotic events who need to undergo surgery or an invasive procedure, the risk for bleeding complications because of a treatment with low-dose acetylsalicylic acid (LD ASA) needs to be balanced against the risk of atherothrombotic events after treatment discontinuation. For patients at high risk of atherothrombotic complications recent guidelines do no longer advocate to interrupt LD ASA routinely. However, the likelihood of bleeding versus atherothrombotic complications should be considered on a case-by-case basis. When continued perioperatively, the bleeding risk associated with thienopyridines (ticlopidine, clopidogrel and prasugrel) is higher than that of LD ASA. It is recommended to stop their intake 1 week before the surgical intervention, except in patients with (recent) coronary stenting.

MicroScope: a platform for microbial genome annotation and comparative genomics

The initial outcome of genome sequencing is the creation of long text strings written in a four letter alphabet. The role of in silico sequence analysis is to assist biologists in the act of associating biological knowledge with these sequences, allowing investigators to make inferences and predictions that can be tested experimentally. A wide variety of software is available to the scientific community, and can be used to identify genomic objects, before predicting their biological functions. However, only a limited number of biologically interesting features can be revealed from an isolated sequence. Comparative genomics tools, on the other hand, by bringing together the information contained in numerous genomes simultaneously, allow annotators to make inferences based on the idea that evolution and natural selection are central to the definition of all biological processes. We have developed the MicroScope platform in order to offer a web-based framework for the systematic and efficient revision of microbial genome annotation and comparative analysis (http://www.genoscope.cns.fr/agc/microscope). Starting with the description of the flow chart of the annotation processes implemented in the MicroScope pipeline, and the development of traditional and novel microbial annotation and comparative analysis tools, this article emphasizes the essential role of expert annotation as a complement of automatic annotation. Several examples illustrate the use of implemented tools for the review and curation of annotations of both new and publicly available microbial genomes within MicroScope's rich integrated genome framework. The platform is used as a viewer in order to browse updated annotation information of available microbial genomes (more than 440 organisms to date), and in the context of new annotation projects (117 bacterial genomes). The human expertise gathered in the MicroScope database (about 280,000 independent annotations) contributes to improve the quality of microbial genome annotation, especially for genomes initially analyzed by automatic procedures alone.Database URLs: http://www.genoscope.cns.fr/agc/mage and http://www.genoscope.cns.fr/agc/microcyc.

Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling

The Joint Evolutionary Trees (JET) method detects protein interfaces, the core residues involved in the folding process, and residues susceptible to site-directed mutagenesis and relevant to molecular recognition. The approach, based on the Evolutionary Trace (ET) method, introduces a novel way to treat evolutionary information. Families of homologous sequences are analyzed through a Gibbs-like sampling of distance trees to reduce effects of erroneous multiple alignment and impacts of weakly homologous sequences on distance tree construction. The sampling method makes sequence analysis more sensitive to functional and structural importance of individual residues by avoiding effects of the overrepresentation of highly homologous sequences and improves computational efficiency. A carefully designed clustering method is parametrized on the target structure to detect and extend patches on protein surfaces into predicted interaction sites. Clustering takes into account residues' physical-chemical properties as well as conservation. Large-scale application of JET requires the system to be adjustable for different datasets and to guarantee predictions even if the signal is low. Flexibility was achieved by a careful treatment of the number of retrieved sequences, the amino acid distance between sequences, and the selective thresholds for cluster identification. An iterative version of JET (iJET) that guarantees finding the most likely interface residues is proposed as the appropriate tool for large-scale predictions. Tests are carried out on the Huang database of 62 heterodimer, homodimer, and transient complexes and on 265 interfaces belonging to signal transduction proteins, enzymes, inhibitors, antibodies, antigens, and others. A specific set of proteins chosen for their special functional and structural properties illustrate JET behavior on a large variety of interactions covering proteins, ligands, DNA, and RNA. JET is compared at a large scale to ET and to Consurf, Rate4Site, siteFiNDER|3D, and SCORECONS on specific structures. A significant improvement in performance and computational efficiency is shown.

Information obtained on the structure of macromolecular complexes is important for identifying functionally important partners but also for determining how such interactions will be perturbed by natural or engineered site mutations. Hence, to fully understand or control biological processes we need to predict in the most accurate manner protein interfaces for a protein structure, possibly without knowing its partners. Joint Evolutionary Trees (JET) is a method designed to detect very different types of interactions of a protein with another protein, ligands, DNA, and RNA. It uses a carefully designed sampling method, making sequence analysis more sensitive to the functional and structural importance of individual residues, and a clustering method parametrized on the target structure for the detection of patches on protein surfaces and their extension into predicted interaction sites. JET is a large-scale method, highly accurate and potentially applicable to search for protein partners.

Resistive heating during off-pump coronary bypass surgery

BACKGROUND

Maintaining normothermia during off-pump coronary artery bypass (OPCAB) surgery is difficult. The purpose of the present study is to determine the effect of the Inditherm Patient Warming System (IPWS) with standard institutional care during OPCAB surgery.

METHODS

A control cohort of 10 patients undergoing OPCAB surgery received standard conventional therapy. A study cohort of another 10 patients then underwent similar procedures with the additional use of the IPWS. The nasopharyngeal and rectal temperatures of the two groups were compared during the 4-hour study period.

RESULTS

During the 4-hour study period after induction, the Inditherm patients demonstrated significantly improved core body temperatures compared to the control group: lowest rectal temperature: 35.8 +/- 0.4 degrees C vs. 34.8 +/- 0.6 degrees C (p < 0.01) and lowest nasopharyngeal temperature : 35.5 +/- 0.4 degrees C vs. 34.7 +/- 0.5 degrees C (p < 0.01), respectively. The between-group rectal and nasopharyngeal temperature differences reached statistical significance after 70 minutes, 36.2 +/- 0.5 degrees C vs. 35.7 +/- 0.2 degrees C (p < 0.01) and after 60 minutes 35.8 +/- 0.4 degrees C vs. 35.4 +/- 0.1 degrees C (p < 0.01), respectively. At the end, the rectal core temperatures were 36.1 +/- 0.6 degrees C vs. 34.9 +/- 0.6 degrees C (p < 0.01) and the nasopharyngeal temperatures were 35.8 +/- 0.6 degrees C vs. 34.8 +/- 0.5 degrees C (p < 0.01) in the study and the control groups, respectively.

CONCLUSION

The combination of the IPWS with standard thermal care provides higher core temperatures during OPCAB surgery.

Tibolone relieves climacteric symptoms in highly symptomatic women with at least seven hot flushes and sweats per day

OBJECTIVE

To establish the potency of four dose levels of tibolone, a tissue selective estrogenic activity regulator (STEAR), to relieve climacteric symptoms in a subgroup of highly symptomatic women experiencing a minimum of seven hot flushes and sweats per day.

METHODS

In a group of 770 women receiving tibolone 0.625, 1.25, 2.5 or 5.0 mg or placebo for 12 weeks, a total of 317 women experienced at least seven hot flushes and sweats per day. Frequency and intensity of climacteric symptoms were assessed at baseline and after 4, 8 and 12 weeks of treatment. Vaginal bleeding/spotting was studied using diary cards. Occurrence of adverse events was determined by active questioning.

RESULTS

Tibolone induced a decrease in the frequency and intensity of climacteric symptoms, leading to statistically significant differences compared to placebo for dose levels of 1.25 mg and higher. The incidence of vaginal bleeding/spotting and of drug-related adverse events was similar in all tibolone dose groups, except for the 5.0 mg group, where the incidence was about twice as high. Dropout rate due to insufficient therapeutic effect is substantially higher in the 0.625 and 1.25 mg group (about 10%) compared to the 2.5 and 5.0 mg group (about 1%). These results are consistent with what occurred in the total study population published previously.

CONCLUSION

The effects of tibolone in highly symptomatic women experiencing at least seven hot flushes and sweats per day do not differ much from that in the total study population. A daily dose of 2.5 mg is the optimal dose for both the total study population and the subgroup of highly symptomatic women. However, in order to optimise individual treatment, the 1.25 mg dose might also be taken into consideration.

Molecular markers for cold tolerance and early vigour in maize (Zea mays L.)

Planting maize earlier than the current guidelines recommend, would give great contributions to ecological and sustainable agriculture. In order to plant maize earlier, maize varieties with good cold tolerance and strong early vigour are required. Therefore cold tolerance and early vigour should be important goals in modern maize breeding programmes. Both traits however have a complex, quantitative genetic background and are therefore not easily introduced into modern maize varieties. Marker assisted selection (MAS) can improve the efficiency of breeding activities. In this research project we aim to identify the molecular markers for cold tolerance and early vigour in one of our breeding populations through a QTL analysis. So far nine QTLs for cold tolerance and six QTLs for early vigour could be identified and there is even one QTL in common for the two traits under investigation. The analysis of more populations should reveal whether or not these QTLs might be useful in maize breeding programmes over the world.

Dose-response analysis of effects of tibolone on climacteric symptoms

OBJECTIVE

To assess the clinically optimal tibolone dose for the relief of climacteric complaints.

DESIGN

A randomised, double blind, placebo-controlled trial.

SETTING

Twenty-eight centres in Norway, The Netherlands, Sweden and Finland.

POPULATION

Seven hundred and seventy-five healthy postmenopausal women were randomised to tibolone in a daily dose of 0.625, 1.25, 2.5 or 5.0 mg or placebo for 12 weeks.

METHODS

At baseline, and after 4, 8 and 12 weeks, hot flushes, sweating, vaginal bleeding and adverse experiences were recorded.

MAIN OUTCOME MEASURES

Change in frequency and intensity of hot flushes and sweating over 12 weeks.

RESULTS

From week four onwards, 2.5 and 5.0 mg tibolone were significantly more effective than placebo, regarding the frequency of hot flushes and sweating (P < 0.001), whereas the 0.625 mg dose was not significantly different from placebo during the study. The frequency of hot flushes with the 1.25 mg dose was statistically significantly different from placebo, only from week eight onwards. The incidence of dropouts due to insufficient therapeutic effect was much higher in the tibolone 1.25 mg group (9.5%) than in the 2.5 (1.9%) and 5.0 mg (1.3%) groups. A dose-related increase in incidence of vaginal bleeding or spotting was observed (P < 0.0001). Bleeding incidence in the 5.0 mg dose group was about twice as high as in the 2.5 mg dose group. There was no difference in incidence of adverse experiences between the 2.5- and the 1.25 mg dose group.

CONCLUSION

A daily dose of 2.5 mg tibolone is the clinically optimal dose for the treatment of climacteric complaints in postmenopausal women.

Hormone replacement therapy and endothelial function. Results of a randomized controlled trial in healthy postmenopausal women

OBJECTIVE

To compare the effects of 3 months treatment with tibolone (a single entity synthetic steroid hormone with estrogenic, progestanic and androgenic activities), or continuous combined conjugated equine estrogens (CEE) plus medroxyprogesterone acetate (MPA), with placebo, on endothelial function.

DESIGN

A single center, randomized, double-blind, placebo-controlled study.

SETTING

Research center as part of the University Medical Center Utrecht.

SUBJECTS

One hundred and five healthy postmenopausal women, sampled from the general population.

INTERVENTIONS

Three months treatment with tibolone or CEE+MPA or placebo.

MAIN OUTCOME MEASURE

At baseline and after 3 months, endothelial function was assessed non-invasively by measuring percent lumen diameter change in the brachial artery after reactive hyperemia and sublingual nitroglycerine spray.

RESULTS

Results are presented as mean differences between treatment groups of endothelium dependent flow mediated dilatation (fmd) and endothelium independent nitroglycerine induced dilatation with 95% confidence intervals (95% CI). After treatment, there was a significant difference in mean fmd between the CEE+MPA group and the placebo group of 2.5% (95% CI: 0.3-4.6) while the tibolone group and the placebo group did not differ significantly (0.6%; 95% CI: 1.6-2.8). Nitroglycerine induced dilatation did not differ significantly between the groups.

CONCLUSIONS

Hormone replacement therapy with CEE+MPA for 3 months increases endothelium dependent fmd of the brachial artery in healthy postmenopausal women. Tibolone did not alter fmd. The clinical significance of this improvement in fmd for cardiovascular disease risk needs to be established.

Lipoprotein (a) is associated with endothelial function in healthy postmenopausal women

BACKGROUND

Lipoprotein (a) (Lp(a)) is an independent risk factor for atherosclerotic cardiovascular disease. The atherogenic potential of Lp(a) may be by impairment of endothelial function. Objectives. We investigated the relation of Lp(a) plasma levels to endothelium dependent and independent dilatation of the brachial artery in healthy postmenopausal women.

METHODS

One hundred and five healthy postmenopausal women aged 52-67 years were included in the study. Endothelial function was assessed non-invasively by measuring percent lumen diameter change in the brachial artery after reactive hyperemia and sublingual nitroglycerine spray.

RESULTS

Flow mediated dilatation was inversely related to the plasma logLp(a) level. Mean change per unit logLp(a) increase:-2.83% (95% CI: -5.22--0.43). Elevated Lp(a) (>239 mg/l) (upper quartile) was associated with an impaired flow mediated vasodilatation (2.4%+/-1. 2) compared to Lp(a) < or =239 mg/l (5.2%+/-0.7). Adjustment for other cardiovascular risk factors did not change the magnitude of the association. Nitroglycerine-induced vasodilatation was not significantly lower in the high Lp(a) level group, compared to the group with normal levels of Lp(a) (< or =239 mg/l) (8.0+/-1.2 vs. 11.4%+/-0.8).

CONCLUSION

Elevated lipoprotein (a) levels are associated with an impaired endothelial function in healthy postmenopausal women, independent of conventional risk factors for cardiovascular disease. Since Lp(a) may be pathogenetically important for early vascular damage, elevated Lp(a) levels might contribute to the increased cardiovascular risk seen in postmenopausal women.

Gasterophilus intestinalis infections in horses in Belgium

Over a period of one year, from December 1995 to November 1996, larvae of Gasterophilus intestinalis were found in 193 horse stomachs (58%) of 330 that were examined in two Belgian slaughter houses. When August is excluded, 62% of the stomachs had bot larvae. No other Gasterophilus species were identified. The monthly prevalence ranged from 9% in August to 75% in November and December. The mean intensity of bot larvae varied from 8 in August to 29 in March, and the majority of the horses (67%) harboured less than 50 larvae. Prevalences and intensities were not affected by age, but mares were more frequently infected than stallions and geldings (P < 0.014). The mean size of the lesions increased from 1 cm2 to 17 cm2. The majority of the larvae were localised near the margo plicatus.

Computer-based prediction of psychotropic drug classes based on a discriminant analysis of drug effects on rat sleep

The goal of the present study was to classify psychotropic drugs on the basis of EEG-defined rat sleep-waking behaviour. Using an automated sleep classification system it was found that some of the drug-induced changes in sleep-waking behaviour were specific for the pharmacotherapeutic treatment class to which the drug belonged. In several preliminary experiments we further found that drugs may have effects on rat EEG independent of their effects on rat sleep-waking behaviour and that these pharmaco-EEG effects may be different for the various sleep and waking stages. By analysing sleep class-independent EEG-spectral parameters a single drug effect score can, moreover, be obtained giving information on drug pharmacodynamics. The drug-induced changes in sleep-waking behaviour were used to classify a large number of drugs into several therapy classes by means of a discriminant analysis procedure. Antidepressants, antipsychotics and stimulants were discriminated successfully from each other and from placebo by this system, whereas nootropics classified as placebo. Anxiolytics, hypnotics and anticonvulsants classified poorly. Their classification is hampered by the lack of specific compounds. Assigned drug class and assignment probability were dose dependent. In the discussion of the present study it is suggested that animal pharmaco-sleep and pharmaco-EEG studies are not mutually exclusive approaches, but that they may complement each other.