Crop pests and predators exhibit inconsistent responses to surrounding landscape composition

The idea that noncrop habitat enhances pest control and represents a win–win opportunity to conserve biodiversity and bolster yields has emerged as an agroecological paradigm. However, while noncrop habitat in landscapes surrounding farms sometimes benefits pest predators, natural enemy responses remain heterogeneous across studies and effects on pests are inconclusive. The observed heterogeneity in species responses to noncrop habitat may be biological in origin or could result from variation in how habitat and biocontrol are measured. Here, we use a pest-control database encompassing 132 studies and 6,759 sites worldwide to model natural enemy and pest abundances, predation rates, and crop damage as a function of landscape composition. Our results showed that although landscape composition explained significant variation within studies, pest and enemy abundances, predation rates, crop damage, and yields each exhibited different responses across studies, sometimes increasing and sometimes decreasing in landscapes with more noncrop habitat but overall showing no consistent trend. Thus, models that used landscape-composition variables to predict pest-control dynamics demonstrated little potential to explain variation across studies, though prediction did improve when comparing studies with similar crop and landscape features. Overall, our work shows that surrounding noncrop habitat does not consistently improve pest management, meaning habitat conservation may bolster production in some systems and depress yields in others. Future efforts to develop tools that inform farmers when habitat conservation truly represents a win–win would benefit from increased understanding of how landscape effects are modulated by local farm management and the biology of pests and their enemies

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues

Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Abstracts from the 8th International Conference on cGMP Generators, Effectors and Therapeutic Implications

This work was supported by a restricted research grant of Bayer AG

A first update on mapping the human genetic architecture of COVID-19

peer reviewe

Influence of siderophore-iron complexation on the growth of the diatom Skeletonema costatum: a mass spectroscopy approach

The growth of the diatom Skeletonema costatum was monitored using in vivo fluorescence under concentration gradients of desferrioxamine B (DFB) and enterobactin to test the siderophores effect on iron bioavailability. Changes in the composition of dissolved organic matter, including the added siderophores, were then identified using HPLC-MS. Samples for organic matter analysis were taken once when the diatom reached exponential growth in all siderophore conditions. Previous research into the effect of siderophores on algal growth has indicated positive or negative growth of the diatom depends on both the diatom species and the type of siderophore. In this project, DFB inhibited growth at first, but eventually the diatom entered exponential phase growth even at the highest concentration of added DFB, 10 μM. Enterobactin showed less concentration dependent limitation of iron bioavailability and in lower concentrations showed an increase in growth compared to the control. The findings suggest that its ability to act as an iron scavenger in seawater is inhibited by its hydrophobicity. From compound ions found using MS, a range of potential iron chelators was detected. The siderophores were successfully identified along with DFB s complex with iron, ferrioxamine. Potential DFB metabolites matched predicted mass to charge ratios and chemical formulas but could not be confirmed structurally by the MS databases used. Saccharides, potential iron chelators released by algae, were also discovered. In the DFB series, the abundances of compound ions were significantly different based on the concentration of siderophore in the sample. The results of this project represent a snapshot of the dissolved organic matter present in samples. Further experiments tracking siderophores along with a few known chelators throughout diatom growth would enhance understanding of the role of chelators in diatom iron uptake. HPLC-MS is a promising technique to uncover the relationship between iron chelators and diatoms

Effect of hydroxamate and catecholate siderophores on iron availability in the diatom Skeletonema costatum: Implications of siderophore degradation by associated bacteria

The bioavailability of iron (Fe) across marine ecosystems, mainly determined by Fe speciation and species-specific requirements of phytoplankton, remains largely unresolved. Siderophores are relevant within the pool of organic ligands that control organic Fe speciation. The effect on growth and physiology of the diatom Skeletonema costatum following addition over time of the uncomplexed siderophores (apo-form) desferrioxamine B and enterobactin were studied in the laboratory. The diatom was grown in batch culture in concentration gradients up to 50 and 10,000 nM for enterobactin and desferrioxamine B respectively. The potential effect of siderophore degradation was analyzed by electrospray ionization mass spectroscopy (HPLC-ESI-MS). Growth of S. costatum was negatively correlated to desferrioxamine concentration. In treatments where >500 nM was added, growth was negligible until day 9 after which significant growth started. Fe uptake at day 9 was highest at 10,000 nM, while the Fe quota was the lowest. The addition of enterobactin had a negative effect on the abundance, the in-vivo fluorescence and the Fe quota in S. costatum only at the highest concentration of 50 nM, while the in-vivo fluorescence was enhanced at the lowest concentration. The bacterial abundance over time was also negatively correlated to the concentration for both siderophores, but at day 9 the bacterial uptake showed an increase proportional to the siderophore concentration. HPLC-ESI-MS analysis revealed the presence of tentative metabolites of desferrioxamine in 500 and 10,000 nM indicating changes in concentration of the apo-siderophore. In the presence of cathecolate and hydroxamate siderophores, S. costatum exhibited the capacity for different Fe uptake strategies. The late growth exhibited and the high Fe uptake after prolonged Fe-limited growth, suggests that Fe reduction at cell's membrane may be facilitated by possible degradation of desferrioxamine by the associated bacteria. The results emphasize the need for studying Fe bioavailability of algae together with the interacting bacterial community

A genome-wide investigation of the worldwide invader Sargassum muticum shows high success albeit (almost) no genetic diversity

Twenty years of genetic studies of marine invaders have shown that successful invaders are often characterized by native and introduced populations displaying similar levels of genetic diversity. This pattern is presumably due to high propagule pressure and repeated introductions. The opposite pattern is reported in this study of the brown seaweed, Sargassum muticum, an emblematic species for circumglobal invasions. Albeit demonstrating polymorphism in the native range, microsatellites failed to detect any genetic variation over 1,269 individuals sampled from 46 locations over the Pacific-Atlantic introduction range. Single-nucleotide polymorphisms (SNPs) obtained from ddRAD sequencing revealed some genetic variation, but confirmed severe founder events in both the Pacific and Atlantic introduction ranges. Our study thus exemplifies the need for extreme caution in interpreting neutral genetic diversity as a proxy for invasive potential. Our results confirm a previously hypothesized transoceanic secondary introduction from NE Pacific to Europe. However, the SNP panel unexpectedly revealed two additional distinct genetic origins of introductions. Also, conversely to scenarios based on historical records, southern rather than northern NE Pacific populations could have seeded most of the European populations. Finally, the most recently introduced populations showed the lowest selfing rates, suggesting higher levels of recombination might be beneficial at the early stage of the introduction process (i.e., facilitating evolutionary novelties), whereas uniparental reproduction might be favored later in sustainably established populations (i.e., sustaining local adaptation).Agence Nationale de la Recherche - ANR-10-BTBR-04; European Regional Development Fund; Fundacao para a Ciencia e a Tecnologia - SFRH/BPD/107878/2015, UID/Multi/04326/2016, UID/Multi/04326/2019; Brittany Region;info:eu-repo/semantics/publishedVersio

Crop pests and predators exhibit inconsistent responses to surrounding landscape composition

The idea that noncrop habitat enhances pest control and represents a win–win opportunity to conserve biodiversity and bolster yields has emerged as an agroecological paradigm. However, while noncrop habitat in landscapes surrounding farms sometimes benefits pest predators, natural enemy responses remain heterogeneous across studies and effects on pests are inconclusive. The observed heterogeneity in species responses to noncrop habitat may be biological in origin or could result from variation in how habitat and biocontrol are measured. Here, we use a pest-control database encompassing 132 studies and 6,759 sites worldwide to model natural enemy and pest abundances, predation rates, and crop damage as a function of landscape composition. Our results showed that although landscape composition explained significant variation within studies, pest and enemy abundances, predation rates, crop damage, and yields each exhibited different responses across studies, sometimes increasing and sometimes decreasing in landscapes with more noncrop habitat but overall showing no consistent trend. Thus, models that used landscape-composition variables to predict pest-control dynamics demonstrated little potential to explain variation across studies, though prediction did improve when comparing studies with similar crop and landscape features. Overall, our work shows that surrounding noncrop habitat does not consistently improve pest management, meaning habitat conservation may bolster production in some systems and depress yields in others. Future efforts to develop tools that inform farmers when habitat conservation truly represents a win–win would benefit from increased understanding of how landscape effects are modulated by local farm management and the biology of pests and their enemies