Short-read sequencing for genomic analysis of the brown rot fungus Fibroporia radiculosa

The feasibility of short-read sequencing for genomic analysis was demonstrated for Fibroporia radiculosa, a copper-tolerant fungus that causes brown rot decay of wood. The effect of read quality on genomic assembly was assessed by filtering Illumina GAIIx reads from a single run of a paired-end library (75-nucleotide read length and 300-bp fragment size) at three different stringency levels and then assembling each data set with Velvet. A simple approach was devised to determine which filter stringency was "best." Venn diagrams identified the regions containing reads that were used in an assembly but were of a low-enough quality to be removed by a filter. By plotting base quality histograms of reads in this region, we judged whether a filter was too stringent or not stringent enough. Our best assembly had a genome size of 33.6 Mb, an N50 of 65.8 kb for a k-mer of 51, and a maximum contig length of 347 kb. Using GeneMark, 9,262 genes were predicted. TargetP and SignalP analyses showed that among the 1,213 genes with secreted products, 986 had motifs for signal peptides and 227 had motifs for signal anchors. Blast2GO analysis provided functional annotation for 5,407 genes. We identified 29 genes with putative roles in copper tolerance and 73 genes for lignocellulose degradation. A search for homologs of these 102 genes showed that F. radiculosa exhibited more similarity to Postia placenta than Serpula lacrymans. Notable differences were found, however, and their involvements in copper tolerance and wood decay are discussed.     

Correlates of attendance at community engagement meetings held in advance of bio-behavioral research studies: A longitudinal,sociocentric social network study in rural Uganda

BackgroundCommunity engagement is central to the conduct of health-related research studies as a way to determine priorities, inform study design and implementation, increase recruitment and retention, build relationships, and ensure that research meets the goals of the community. Community sensitization meetings, a form of community engagement, are often held prior to the initiation of research studies to provide information about upcoming study activities and resolve concerns in consultation with potential participants. This study estimated demographic, health, economic, and social network correlates of attendance at community sensitization meetings held in advance of a whole-population, combined behavioral, and biomedical research study in rural Uganda.Methods and findingsResearch assistants collected survey data from 1,630 adults participating in an ongoing sociocentric social network cohort study conducted in a rural region of southwestern Uganda. These community survey data, collected between 2016 and 2018, were linked to attendance logs from community sensitization meetings held in 2018 and 2019 before the subsequent community survey and community health fair. Of all participants, 264 (16%) attended a community sensitization meeting before the community survey, 464 (28%) attended a meeting before the community health fair, 558 (34%) attended a meeting before either study activity (survey or health fair), and 170 (10%) attended a meeting before both study activities (survey and health fair). Using multivariable Poisson regression models, we estimated correlates of attendance at community sensitization meetings. Attendance was more likely among study participants who were women (adjusted relative risk [ARR]_{health fair} = 1.71, 95% confidence interval [CI], 1.32 to 2.21, p < 0.001), older age (ARR_survey = 1.02 per year, 95% CI, 1.01 to 1.02, p < 0.001; ARR_{health fair} = 1.02 per year, 95% CI, 1.01 to 1.02, p < 0.001), married (ARR_survey = 1.74, 95% CI, 1.29 to 2.35, p < 0.001; ARR_{health fair} = 1.41, 95% CI, 1.13 to 1.76, p = 0.002), and members of more community groups (ARR_survey = 1.26 per group, 95% CI, 1.10 to 1.44, p = 0.001; ARR_{health fair} = 1.26 per group, 95% CI, 1.12 to 1.43, p < 0.001). Attendance was less likely among study participants who lived farther from meeting locations (ARR_survey = 0.54 per kilometer, 95% CI, 0.30 to 0.97, p = 0.041; ARR_{health fair} = 0.57 per kilometer, 95% CI, 0.38 to 0.86, p = 0.007). Leveraging the cohort’s sociocentric design, social network analyses suggested that information conveyed during community sensitization meetings could reach a broader group of potential study participants through attendees’ social network and household connections. Study limitations include lack of detailed data on reasons for attendance/nonattendance at community sensitization meetings; achieving a representative sample of community members was not an explicit aim of the study; and generalizability may not extend beyond this study setting.ConclusionsIn this longitudinal, sociocentric social network study conducted in rural Uganda, we observed that older age, female sex, being married, membership in more community groups, and geographical proximity to meeting locations were correlated with attendance at community sensitization meetings held in advance of bio-behavioral research activities. Information conveyed during meetings could have reached a broader portion of the population through attendees’ social network and household connections. To ensure broader input and potentially increase participation in health-related research studies, the dissemination of research-related information through community sensitization meetings may need to target members of underrepresented groups.

In a social network cohort study, Emily Satinsky and colleagues estimate demographic, health, economic and social network factor associated with attendance at community sensitization meetings held in advance of participation in health-related research studies in rural Uganda.     

Bumblebee flight distances in relation to the forage landscape

1. Foraging range is a key aspect of the ecology of 'central place foragers'. Estimating how far bees fly under different circumstances is essential for predicting colony success, and for estimating bee-mediated gene flow between plant populations. It is likely to be strongly influenced by forage distribution, something that is hard to quantify in all but the simplest landscapes; and theories of foraging distance tend to assume a homogeneous forage distribution. 2. We quantified the distribution of bumblebee Bombus terrestris L. foragers away from experimentally positioned colonies, in an agricultural landscape, using two methods. We mass-marked foragers as they left the colony, and analysed pollen from foragers returning to the colonies. The data were set within the context of the 'forage landscape': a map of the spatial distribution of forage as determined from remote-sensed data. To our knowledge, this is the first time that empirical data on foraging distances and forage availability, at this resolution and scale, have been collected and combined for bumblebees. 3. The bees foraged at least 1.5 km from their colonies, and the proportion of foragers flying to one field declined, approximately linearly, with radial distance. In this landscape there was great variation in forage availability within 500 m of colonies but little variation beyond 1 km, regardless of colony location. 4. The scale of B. terrestris foraging was large enough to buffer against effects of forage patch and flowering crop heterogeneity, but bee species with shorter foraging ranges may experience highly variable colony success according to location.     

Like herbivores,parasitic plants are limited by host nitrogen content

Herbivores generally benefit from increased plant nitrogen content, because the nitrogen content of animals is much higher than that of plants. Consequently, high plant nitrogen alleviates the profound stoichiometric imbalance that herbivores face in their diets. Parasitic plants provide the opportunity to test this generalization for consumers across kingdoms. We fertilized two microhabitats in a California salt marsh that were dominated by Salicornia virginica or a mixture of S. virginica and Jaumea carnosa. The nitrogen content of both host plants and of the holoparasite Cuscuta salina (dodder) increased in fertilized plots in both microhabitats. Cuscuta preferred to attack Jaumea, although Jaumea had lower nitrogen content than Salicornia. When host nitrogen content was altered by fertilizing plots, however, the percent cover of the parasite doubled. Although parasitic plants and their hosts have similar tissue nitrogen contents, suggesting no stoichiometric imbalance between host and consumer, parasitic plants do not feed on host tissue, but on host xylem and phloem, which are very low in nitrogen. Consequently, parasitic plants face the same dietary stoichiometric constraints as do herbivores, and both herbivores and holoparasitic plants may respond positively to increases in host nitrogen status.     

Electrophysiological and behavioural responses of the pollen beetle, Meligethes aeneus, to volatiles from a non-host plant, lavender, Lavandula angustifolia (Lamiaceae)

A semiochemical based push-pull strategy for control of oilseed rape pests is being developed at Rothamsted Research. This strategy uses insect and plant derived semiochemicals to manipulate pests and their natural enemies. An important element within this strategy is an understanding of the importance of non-host plant cues for pest insects and how such signals could be used to manipulate their behaviour. Previous studies using a range of non-host plants have shown that, for the pollen beetle Meligethes aeneus (Coleoptera: Nitidulidae), the essential oil of lavender, Lavandula angustifolia (Lamiaceae), was the most repellent. The aim of this study was to identify the active components in L. angustifolia oil, and to investigate the behaviour of M. aeneus to these chemicals, to establish the most effective use of repellent stimuli to disrupt colonisation of oilseed rape crops. Coupled gas chromatography-electroantennography (GC-EAG) and gas chromatography-mass spectrometry (GC-MS) resulted in the identification of seven active compounds which were tested for behavioural activity using a 4-way olfactometer. Repellent responses were observed with (±)-linalool and (±)-linalyl acetate. The use of these chemicals within a push-pull pest control strategy is discussed. Handling Editor: Yvan Rahbe.     

Small molecule, non-peptide p75 ligands inhibit Abeta-induced neurodegeneration and synaptic impairment

The p75 neurotrophin receptor (p75(NTR)) is expressed by neurons particularly vulnerable in Alzheimer's disease (AD). We tested the hypothesis that non-peptide, small molecule p75(NTR) ligands found to promote survival signaling might prevent Abeta-induced degeneration and synaptic dysfunction. These ligands inhibited Abeta-induced neuritic dystrophy, death of cultured neurons and Abeta-induced death of pyramidal neurons in hippocampal slice cultures. Moreover, ligands inhibited Abeta-induced activation of molecules involved in AD pathology including calpain/cdk5, GSK3beta and c-Jun, and tau phosphorylation, and prevented Abeta-induced inactivation of AKT and CREB. Finally, a p75(NTR) ligand blocked Abeta-induced hippocampal LTP impairment. These studies support an extensive intersection between p75(NTR) signaling and Abeta pathogenic mechanisms, and introduce a class of specific small molecule ligands with the unique ability to block multiple fundamental AD-related signaling pathways, reverse synaptic impairment and inhibit Abeta-induced neuronal dystrophy and death.     

Impact of long-term treatment with ivermectin on the prevalence and intensity of soil-transmitted helminth infections

Background

Control of soil-transmitted helminth (STH) infections relies on the periodic and long-term administration of anthelmintic drugs to high-risk groups, particularly school-age children living in endemic areas. There is limited data on the effectiveness of long-term periodic anthelmintic treatment on the prevalence of STHs, particularly from operational programmes. The current study investigated the impact of 15 to 17 years of treatment with the broad-spectrum anthelmintic ivermectin, used for the control of onchocerciasis, on STH prevalence and intensity in school-age and pre-school children.

Methods and Findings

A cross-sectional study was conducted in communities that had received annual or twice-annual ivermectin treatments and geographically adjacent communities that had not received treatment in two districts of Esmeraldas Province in Ecuador. Stool samples were collected from school-age children and examined for STH infection using the Kato-Katz and formol-ether concentration methods. Samples were collected also from pre-school children and examined by the formol-ether concentration method. Data on risk factors for STH infection were collected by parental questionnaire. We sampled a total of 3,705 school-age children (6–16 years) from 31 treated and 27 non-treated communities, and 1,701 pre-school children aged 0–5 years from 18 treated and 18 non-treated communities. Among school-age children, ivermectin treatment had significant effects on the prevalence (adjusted OR =  0.06, 95% CI 0.03–0.14) and intensity of Trichuris trichiura infection (adjusted RR = 0.28, 95% CI 0.11–0.70), but appeared to have no impact on Ascaris lumbricoides or hookworm infection. Reduced prevalence and intensities of T. trichiura infection were observed among children not eligible to receive ivermectina, providing some evidence of reduced transmission of T. trichiura infection in communities receiving mass ivermectin treatments.

Conclusion

Annual and twice-annual treatments with ivermectin over a period of up to 17 years may have had a significant impact on T. trichiura infection. The present data indicate that the long-term control of onchocerciasis with ivermectin may provide additional health benefits by reducing infections with trichuriasis. The addition of a second anthelmintic drug such as albendazole may be useful for a long-term effect on A. lumbricoides infection.     

Random and independent sampling of endogenous tryptic peptides from normal human EDTA plasma by liquid chromatography micro electrospray ionization and tandem mass spectrometry

Background

Normal human EDTA plasma samples were collected on ice, processed ice cold, and stored in a freezer at – 80 °C prior to experiments. Plasma test samples from the – 80 °C freezer were thawed on ice or intentionally warmed to room temperature.

Methods

Protein content was measured by CBBR binding and the release of alcohol soluble amines by the Cd ninhydrin assay. Plasma peptides released over time were collected over C18 for random and independent sampling by liquid chromatography micro electrospray ionization and tandem mass spectrometry (LC–ESI–MS/MS) and correlated with X!TANDEM.

Results

Fully tryptic peptides by X!TANDEM returned a similar set of proteins, but was more computationally efficient, than “no enzyme” correlations. Plasma samples maintained on ice, or ice with a cocktail of protease inhibitors, showed lower background amounts of plasma peptides compared to samples incubated at room temperature. Regression analysis indicated that warming plasma to room temperature, versus ice cold, resulted in a ~ twofold increase in the frequency of peptide identification over hours–days of incubation at room temperature. The type I error rate of the protein identification from the X!TANDEM algorithm combined was estimated to be low compared to a null model of computer generated random MS/MS spectra.

Conclusion

The peptides of human plasma were identified and quantified with low error rates by random and independent sampling that revealed 1000s of peptides from hundreds of human plasma proteins from endogenous tryptic peptides.