Organic farming enhances parasitoid diversity at the local and landscape scales

1. The magnitude of the benefits derived from organic farming within contrasting managed landscapes remains unclear and, in particular, the potential scale-dependent response of insect parasitoids is relatively unexplored. Identifying the scale at which parasitoids are affected by organic farming will be an important step to enhance their conservation. 2. We sampled tachinid parasitoids at the centre and margin of arable and grassland fields on paired organic and conventional farms located in landscapes with different proportions of organic land. A total of 192 fields were sampled in two biogeographical regions of the UK. 3. We found that the positive effect of organic farming on tachinid parasitoid diversity can be observed at multiple spatial scales. At the local scale, we found higher abundance and species richness of tachinid parasitoids on organic than on conventional farms and on field margins than on field centres. At the landscape scale, the diversity of tachinids was higher in landscapes with higher proportions of organic land. At both scales, the positive effect of organic farming was clear for arable fields, while it was almost neutral for grasslands. 4. Synthesis and applications. Any attempt to enhance parasitoid diversity in agricultural landscapes needs to consider the local management in relation to the habitat type, location within the field and agricultural management in the surrounding landscape. To restore parasitoid diversity, the promotion of organic agriculture should aim to increase both the total extent of organic farming and the connectivity of individual farms. As the benefits of organic farming to biodiversity clearly spread beyond individual farm boundaries, any assessment of organic farming should consider these positive externalities

Vaccinium dwarf shrubs responses to experimental warming and herbivory resistance treatment are species- and context dependent

Climate change impacts on species and ecosystem functioning may depend on climatic context and study systems. Climate warming and intensified herbivory are two stressors to plants that often appear in combination and are predicted to increase in cold environments. Effects of multiple drivers on plant performance are difficult to predict and warrant studies that use experimental manipulations along climatic gradients to produce more realistic knowledge. Our three study sites by the Sognefjord in Norway, that differed mainly in climatic conditions (ca. 5°C growing season difference), ranged from hemi-boreal lowland (100 masl, Low), via boreal mid-montane (500 masl) to alpine timberline (900 masl, High) bioclimates. At each site, in a randomized block design, we simulated growing-season warming using open-top chambers (OTCs) and experimentally induced herbivory resistance using the plant hormone methyl jasmonate (MeJA). We recorded growth, mortality, flower and fruit numbers, and insect herbivory on tagged ramets in permanent plots across three years (2016-2018) in three open woodland populations of two functionally important plant species with contrasting traits, Vaccinium myrtillus (bilberry) and V. vitis-idaea (lingonberry). Growth of both dwarf shrubs decreased with warming in the warm lowland populations (Low) but increased in the alpine populations (High). Shoot mortality increased most with warming at Low but was reduced at High. Reproduction, both flowering and fruiting, decreased with induced resistance treatment, but the effect was larger when warmed for bilberry and increased with elevation for both species. Leaf herbivory in bilberry increased with warming at Low but decreased at High. The combined warming and resistance treatment had only synergistic negative interaction effects on fruit numbers in bilberry. The clear context- and species-dependent effects of climate warming and increased resistance in this study may predict a potential decline in performance, as well as abundance and distribution, of these functionally important Vaccinium species at our lowest site. Bilberry reproduction appeared to be particularly susceptible to both climate warming and induced resistance in the manipulated populations. Such combined negative effects on plant performance are likely to have considerable knock-on effects via altered species’ interactions and ecosystem functioning

Absolute quantification of transcription factors in human erythropoiesis using selected reaction monitoring mass spectrometry.

Quantitative changes in transcription factor (TF) abundance regulate dynamic cellular processes, including cell fate decisions. Protein copy number provides information about the relative stoichiometry of TFs that can be used to determine how quantitative changes in TF abundance influence gene regulatory networks. In this protocol, we describe a targeted selected reaction monitoring (SRM)-based mass-spectrometry method to systematically measure the absolute protein concentration of nuclear TFs as human hematopoietic stem and progenitor cells differentiate along the erythropoietic lineage. For complete details on the use and execution of this protocol, please refer to Gillespie et al. (2020)

Circulating exosomal microRNA expression patterns distinguish cardiac sarcoidosis from myocardial ischemia.

OBJECTIVE: Cardiac sarcoidosis is difficult to diagnose, often requiring expensive and inconvenient advanced imaging techniques. Circulating exosomes contain genetic material, such as microRNA (miRNA), that are derived from diseased tissues and may serve as potential disease-specific biomarkers. We thus sought to determine whether circulating exosome-derived miRNA expression patterns would distinguish cardiac sarcoidosis (CS) from acute myocardial infarction (AMI). METHODS: Plasma and serum samples conforming to CS, AMI or disease-free controls were procured from the Biologic Specimen and Data Repository Information Coordinating Center repository and National Jewish Health. Next generation sequencing (NGS) was performed on exosome-derived total RNA (n = 10 for each group), and miRNA expression levels were compared after normalization using housekeeping miRNA. Quality assurance measures excluded poor quality RNA samples. Differentially expressed (DE) miRNA patterns, based upon \u3e2-fold change (p \u3c 0.01), were established in CS compared to controls, and in CS compared to AMI. Relative expression of several DE-miRNA were validated by qRT-PCR. RESULTS: Despite the advanced age of the stored samples (~5-30 years), the quality of the exosome-derived miRNA was intact in ~88% of samples. Comparing plasma exosomal miRNA in CS versus controls, NGS yielded 18 DE transcripts (12 up-regulated, 6 down-regulated), including miRNA previously implicated in mechanisms of myocardial injury (miR-92, miR-21) and immune responses (miR-618, miR-27a). NGS further yielded 52 DE miRNA in serum exosomes from CS versus AMI: 5 up-regulated in CS; 47 up-regulated in AMI, including transcripts previously detected in AMI patients (miR-1-1, miR-133a, miR-208b, miR-423, miR-499). Five miRNAs with increased DE in CS included two isoforms of miR-624 and miR-144, previously reported as markers of cardiomyopathy. CONCLUSIONS: MiRNA patterns of exosomes derived from CS and AMI patients are distinct, suggesting that circulating exosomal miRNA patterns could serve as disease biomarkers. Further studies are required to establish their specificity relative to other cardiac disorders

Epidemic Enhancement in Partially Immune Populations

We observe that a pathogen introduce/pmcdata/journal/plosone/2-2007/1/ingest/pmcmod/sgml/pone.0000165.xmld into a population containing individuals with acquired immunity can result in an epidemic longer in duration and/or larger in size than if the pathogen were introduced into a naive population. We call this phenomenon “epidemic enhancement,” and use simple dynamical models to show that it is a realistic scenario within the parameter ranges of many common infectious diseases. This finding implies that repeated pathogen introduction or intermediate levels of vaccine coverage can lead to pathogen persistence in populations where extinction would otherwise be expected

Wholly Rickettsia! Reconstructed Metabolic Profile of the Quintessential Bacterial Parasite of Eukaryotic Cells

Reductive genome evolution has purged many metabolic pathways from obligate intracellular Rickettsia (Alphaproteobacteria; Rickettsiaceae). While some aspects of host-dependent rickettsial metabolism have been characterized, the array of host-acquired metabolites and their cognate transporters remains unknown. This dearth of information has thwarted efforts to obtain an axenic Rickettsia culture, a major impediment to conventional genetic approaches. Using phylogenomics and computational pathway analysis, we reconstructed the Rickettsia metabolic and transport network, identifying 51 host-acquired metabolites (only 21 previously characterized) needed to compensate for degraded biosynthesis pathways. In the absence of glycolysis and the pentose phosphate pathway, cell envelope glycocon- jugates are synthesized from three imported host sugars, with a range of additional host-acquired metabolites fueling the tricarboxylic acid cycle. Fatty acid and glycero- phospholipid pathways also initiate from host precursors, and import of both iso- prenes and terpenoids is required for the synthesis of ubiquinone and the lipid car- rier of lipid I and O-antigen. Unlike metabolite-provisioning bacterial symbionts of arthropods, rickettsiae cannot synthesize B vitamins or most other cofactors, accen- tuating their parasitic nature. Six biosynthesis pathways contain holes (missing en- zymes); similar patterns in taxonomically diverse bacteria suggest alternative en- zymes that await discovery. A paucity of characterized and predicted transporters emphasizes the knowledge gap concerning how rickettsiae import host metabolites, some of which are large and not known to be transported by bacteria. Collectively, our reconstructed metabolic network offers clues to how rickettsiae hijack host met- abolic pathways. This blueprint for growth determinants is an important step toward the design of axenic media to rescue rickettsiae from the eukaryotic cell

Study protocol: azithromycin therapy for chronic lung disease of prematurity (AZTEC) - a randomised, placebo-controlled trial of azithromycin for the prevention of chronic lung disease of prematurity in preterm infants

Introduction Chronic lung disease of prematurity (CLD), also known as bronchopulmonary dysplasia (BPD), is a cause of significant respiratory morbidity in childhood and beyond. Coupled with lung immaturity, infections (especially by Ureaplasma spp) are implicated in the pathogenesis of CLD through promotion of pulmonary inflammation. Azithromycin, which is a highly effective against Ureaplasma spp also has potent anti-inflammatory properties. Thus, azithromycin therapy may improve respiratory outcomes by targeting infective and inflammatory pathways. Previous trials using macrolides have not been sufficiently powered to definitively assess CLD rates. To address this, the azithromycin therapy for chronic lung disease of prematurity (AZTEC) trial aims to determine if a 10-day early course of intravenous azithromycin improves rates of survival without CLD when compared with placebo with an appropriately powered study. Methods and analysis 796 infants born at less than 30 weeks’ gestational age who require at least 2 hours of continuous respiratory support within the first 72 hours following birth are being enrolled by neonatal units in the UK. They are being randomised to receive a double-blind, once daily dose of intravenous azithromycin (20 mg/kg for 3 days, followed by 10 mg/kg for a further 7 days), or placebo. CLD is being assessed at 36 weeks’ PMA. Whether colonisation with Ureaplasma spp prior to randomisation modifies the treatment effect of azithromycin compared with placebo will also be investigated. Secondary outcomes include necrotising enterocolitis, intraventricular/cerebral haemorrhage, retinopathy of prematurity and nosocomial infections, development of antibiotic resistance and adverse reactions will be monitored. Ethics and dissemination Ethics permission has been granted by Wales Research Ethics Committee 2 (Ref 18/WA/0199), and regulatory permission by the Medicines and Healthcare Products Regulatory Agency (Clinical Trials Authorisation reference 21323/0050/001–0001). The study is registered on ISRCTN (ISRCTN11650227). The study is overseen by an independent Data Monitoring Committee and an independent Trial Steering Committee. We shall disseminate our findings via national and international peer-reviewed journals, and conferences. A summary of the findings will also be posted on the trial website