Direct sequencing of insect symbionts via nanopore adaptive sampling.

Insect symbionts can alter their host phenotype and their effects can range from beneficial to pathogenic. Moreover, many insects exhibit co-infections, making their study more challenging. Less than 1% of insect species have high-quality referenced genomes available and fewer still also have their symbionts sequenced. Two methods are commonly used to sequence symbionts: whole-genome sequencing to concomitantly capture the host and bacterial genomes, or isolation of the symbiont's genome before sequencing. These methods are limited when dealing with rare or poorly characterized symbionts. Long-read technology is an important tool to generate high-quality genomes as they can overcome high levels of heterozygosity, repeat content, and transposable elements that confound short-read methods. Oxford Nanopore (ONT) adaptive sampling allows a sequencing instrument to select or reject sequences in real time. We describe a method based on ONT adaptive sampling (subtractive) approach that readily permitted the sequencing of the complete genomes of mitochondria, Buchnera and its plasmids (pLeu, pTrp), and Wolbachia genomes in two aphid species, Aphis glycines and Pentalonia nigronervosa. Adaptive sampling is able to retrieve organelles such as mitochondria and symbionts that have high representation in their hosts such as Buchnera and Wolbachia, but is less successful at retrieving symbionts in low concentrations.

Colour as a behavioural guide for fish near hydrokinetic turbines.

Hydropower is a traditional and widespread form of renewable energy and vertical axis turbines are an emerging technology suitable for low to medium velocity water bodies such as rivers. Such devices can provide renewable power to remote communities but may also contribute to fragmenting already poorly connected riverine habitats and the impact could be particularly pronounced for migratory diadromous aquatic species such as salmonids by limiting their ability to pass the turbines. Optimising the design of such turbines is therefore essential to mitigate their impact on aquatic fauna. One easily altered property that does not impact turbine performance is blade colour. Here, juvenile rainbow trout (Oncorhynchus mykiss) free swimming within a flume were monitored in the presence of a vertical axis turbine that was either stationary or rotating, and coloured white or orange. The orange colour of the turbine affected behaviour by increasing turbine avoidance and decreasing the number of potentially harmful interactions with the turbine when it was rotating, whilst not affecting passage or mobility of the trout compared to the white turbine. Visibility is therefore a potentially useful tool in mitigating the environmental impact of hydrokinetic turbines.

Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria.

IMPORTANCE: Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, one of the deadliest infectious diseases worldwide. Previous studies have established that synonymous recoding to introduce rare codon pairings can attenuate viral pathogens. We hypothesized that non-optimal codon pairing could be an effective strategy for attenuating gene expression to create a live vaccine for Mtb. We instead discovered that these synonymous changes enabled the transcription of functional mRNA that initiated in the middle of the open reading frame and from which many smaller protein products were expressed. To our knowledge, this is one of the first reports that synonymous recoding of a gene in any organism can create or induce intragenic transcription start sites.

Human interleukin-12α and EBI3 are cytokines with anti-inflammatory functions.

Interleukins are secreted proteins that regulate immune responses. Among these, the interleukin 12 (IL-12) family holds a central position in inflammatory and infectious diseases. Each family member consists of an α and a ß subunit that together form a composite cytokine. Within the IL-12 family, IL-35 remains particularly ill-characterized on a molecular level despite its key role in autoimmune diseases and cancer. Here we show that both IL-35 subunits, IL-12α and EBI3, mutually promote their secretion from cells but are not necessarily secreted as a heterodimer. Our data demonstrate that IL-12α and EBI3 are stable proteins in isolation that act as anti-inflammatory molecules. Both reduce secretion of proinflammatory cytokines and induce the development of regulatory T cells. Together, our study reveals IL-12α and EBI3, the subunits of IL-35, to be functionally active anti-inflammatory immune molecules on their own. This extends our understanding of the human cytokine repertoire as a basis for immunotherapeutic approaches.

Fish response to the presence of hydrokinetic turbines as a sustainable energy solution.

Hydrokinetic turbines such as vertical axis turbines (VATs) may provide decentralised, clean, sustainable energy for remote communities that lack access to the main energy grid or renewable resources. As traditional hydropower adversely alters aquatic ecosystems, it is essential to evaluate the environmental consequences of deploying VATs in riverine ecosystems to meet current and future energy needs. This study explores the implications of VATs on fish movement by observing fish swimming behaviour under two discharges, turbine operation states, and cross-sections confinements using scaled laboratory experiments. Our findings reveal that for cross-sectional confined conditions neither discharge, turbine presence, nor device operation, prevented fish from passing around and through the turbine both in the up- and downstream directions. However, fish spent the least time near the turbine vicinity and within the turbine's turbulent, low-velocity wake, indicating avoidance behaviour. Swimming in a less confined test section further reduced the time spent within the turbine's vicinity and wake, increasing the distance fish kept away from the device. Our results contribute to an understanding of VATs as low-risk hazards for fish swimming behaviour, advancing the potential of deploying VATs in rivers, estuaries or sea as a renewable energy solution for remote communities.

Effect of Antibiotic Compared to Non-Antibiotic Dry Cow Treatment on the Bacteriological Cure of Intramammary Infections during the Dry Period-A Retrospective Cross-Sectional Study.

Antimicrobials are widely used to cure intramammary infections (IMI) in dairy cows during the dry period (DP). Nevertheless, the IMI cure is influenced by many factors and not all quarters benefit from antimicrobial dry cow treatment (DCT). To evaluate the true effect of antibiotic DCT compared to self-cure and the role of causative pathogens on the IMI cure, a retrospective cross-sectional study was performed. The analysis included 2987 quarters infected at dry-off (DO). Information on DCT, causative pathogens, somatic cell count, milk yield, amount of lactation, Body Condition Score, and season and year of DO were combined into categorical variables. A generalized linear mixed model with a random cow, farm and year effect and the binary outcome of bacteriological cure of IMI during the DP was conducted. In the final model, a significant effect (p < 0.05) on DP cure was seen for the DO season and the category of causative pathogens (categories being: Staphylococcus aureus, non-aureus staphylococci, streptococci, coliforms, 'other Gram-negative bacteria', 'other Gram positive bacteria', non-bacterial infections and mixed infections), while antibiotic DCT (vs. non-antibiotic DCT) only showed a significant effect in combination with the pathogen categories streptococci and 'other Gram-positive bacteria'.

Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria.

Each genome encodes some codons more frequently than their synonyms (codon usage bias), but codons are also arranged more frequently into specific pairs (codon pair bias). Recoding viral genomes and yeast or bacterial genes with non-optimal codon pairs has been shown to decrease gene expression. Gene expression is thus importantly regulated not only by the use of particular codons but by their proper juxtaposition. We therefore hypothesized that non-optimal codon pairing could likewise attenuate Mtb genes. We explored the role of codon pair bias by recoding Mtb genes ( rpoB, mmpL3, ndh ) and assessing their expression in the closely related and tractable model organism M. smegmatis . To our surprise, recoding caused the expression of multiple smaller protein isoforms from all three genes. We confirmed that these smaller proteins were not due to protein degradation, but instead issued from new transcription initiation sites positioned within the open reading frame. New transcripts gave rise to intragenic translation initiation sites, which in turn led to the expression of smaller proteins. We next identified the nucleotide changes associated with these new sites of transcription and translation. Our results demonstrated that apparently benign, synonymous changes can drastically alter gene expression in mycobacteria. More generally, our work expands our understanding of the codon-level parameters that control translation and transcription initiation. IMPORTANCE: Mycobacterium tuberculosis ( Mtb ) is the causative agent of tuberculosis, one of the deadliest infectious diseases worldwide. Previous studies have established that synonymous recoding to introduce rare codon pairings can attenuate viral pathogens. We hypothesized that non-optimal codon pairing could be an effective strategy for attenuating gene expression to create a live vaccine for Mtb . We instead discovered that these synonymous changes enabled the transcription of functional mRNA that initiated in the middle of the open reading frame and from which many smaller protein products were expressed. To our knowledge, this is the first report that synonymous recoding of a gene in any organism can create or induce intragenic transcription start sites.

Association of response time and intermittent hypoxemia in extremely preterm infants.

AIM: To determine the relationship between medical staff's response time (RT) to oxygen saturation (SpO2 ) below 80% and the associated time from tactile intervention until SpO2 normalisation (CT). METHODS: Time-lapse video and continuous SpO2 were recorded for six consecutive 24 h periods. Regression analyses of RT and SpO2 in association with postmenstrual age (PMA), weight, infant sex and frequency of intermittent hypoxemia (IH). RESULTS: Five hundred and twelve hypoxemia episodes received tactile intervention in 20 extremely preterm infants (gestational age ≤28 weeks, birthweight <1500 g). Median RT was 20.5 s (IQR 16.63-25.50). RT increased with increased IH frequency (p = 0.023) independently of PMA and weight. SpO2 decreased by 3.7% with every 10 s RT (p = 0.039). Time until SpO2 normalisation was strongly associated with RT (ß = 0.58, p = 0.042). The association was amplified by lower PMA (p = 0.043). Female preterm infants experienced longer RT than males (p = 0.027). Because the total length of an IH is the sum of RT and CT, preterm infants with low PMA can reach a critical hypoxemia duration of >60 s, even with short RT. CONCLUSION: The RT is a critical factor that affects the overall time of IH treatments and the depth of desaturation. The consequences of a prolonged RT are worse for more immature preterm infants.

Pooled Analysis of Rivaroxaban therapy for acute venous thromboembolism in FIRST registry, SWIVTER and DRESDEN NOAC registry.

Background: The direct factor Xa inhibitor rivaroxaban is approved for the treatment of venous thromboembolism (VTE), based on the results of large phase III trials. Objectives: To confirm rivaroxaban's effectiveness and safety in routine clinical care of patients with VTE. Methods: Data were obtained from prospective, noninterventional registries: the FIRST registry (United Kingdom), DRESDEN NOAC registry (Germany), and SWIVTER (Switzerland). Baseline characteristics of these registries and effectiveness and safety outcome rates for the FIRST and DRESDEN NOAC registries were compared. Results: A total of 1841 rivaroxaban-treated patients with acute VTE (57.9% male, 76.6% deep vein thrombosis [DVT]; 23.4% pulmonary embolism ± DVT; median age, 61 years) were included: 1217 from the FIRST registry, 418 from the DRESDEN NOAC registry, and 206 from SWIVTER. Median time between VTE diagnosis and initiation of rivaroxaban was 1.4 ± 1.81 days (25th-75th percentile 1-1; range, 0-15 days). On-treatment outcome rates for the FIRST and DRESDEN NOAC registries were 0.74 per 100 patient-years (95% confidence interval [CI], 0.35-1.54) versus 0.96 per 100 patient-years (95% CI, 0.46-2.01) for VTE recurrence; 1.16 per 100 patient years (95% CI, 0.64-2.09) versus 2.51 per 100 patient-years (95% CI, 1.58-3.98) for ISTH major bleeding and 1.69 per 100 patient-years (95% CI, 1.21-2.35) versus 1.73 per 100 patient-years (95% CI, 1.27-2.36) for all-cause mortality (intention-to-treat analysis), respectively. Conclusion: Overall treatment outcomes were consistent with the results of the phase III rivaroxaban trials in VTE treatment, indicating that the use of rivaroxaban offers acceptable treatment results also in routine care. However, we observed significant differences in patient characteristics and management patterns across Switzerland, the United Kingdom, and Germany, limiting direct comparisons of unadjusted outcome event rates between registries.

Microdosing with psilocybin mushrooms: a double-blind placebo-controlled study.

The use of low sub-perceptual doses of psychedelics ("microdosing") has gained popularity in recent years. Although anecdotal reports claim multiple benefits associated with this practice, the lack of placebo-controlled studies severely limits our knowledge of microdosing and its effects. Moreover, research conducted in standard laboratory settings could fail to capture the motivation of individuals engaged or planning to engage in microdosing protocols, thus underestimating the likelihood of positive effects on creativity and cognitive function. We recruited 34 individuals starting to microdose with psilocybin mushrooms (Psilocybe cubensis), one of the materials most frequently used for this purpose. Following a double-blind placebo-controlled experimental design, we investigated the acute and short-term effects of 0.5 g of dried mushrooms on subjective experience, behavior, creativity (divergent and convergent thinking), perception, cognition, and brain activity. The reported acute effects were significantly more intense for the active dose compared to the placebo, but only for participants who correctly identified their experimental condition. These changes were accompanied by reduced EEG power in the theta band, together with preserved levels of Lempel-Ziv broadband signal complexity. For all other measurements there was no effect of microdosing except for few small changes towards cognitive impairment. According to our findings, low doses of psilocybin mushrooms can result in noticeable subjective effects and altered EEG rhythms, but without evidence to support enhanced well-being, creativity and cognitive function. We conclude that expectation underlies at least some of the anecdotal benefits attributed to microdosing with psilocybin mushrooms.

An inertial mechanism behind dynamic station holding by fish swinging in a vortex street.

Many aquatic and aerial animal species are known to utilise their surrounding flow field and/or the induced flow field of a neighbour to reduce their physical exertion, however, the mechanism by which such benefits are obtained has remained elusive. In this work, we investigate the swimming dynamics of rainbow trout in the wake of a thrust-producing oscillating hydrofoil. Despite the higher flow velocities in the inner region of the vortex street, some fish maintain position in this region, while exhibiting an altered swimming gait. Estimates of energy expenditure indicate a reduction in the propulsive cost when compared to regular swimming. By examining the accelerations of the fish, an explanation of the mechanism by which energy is harvested from the vortices is proposed. Similar to dynamic soaring employed by albatross, the mechanism can be linked to the non-equilibrium hydrodynamic forces produced when fish encounter the cross-flow velocity generated by the vortex street.

Natural language signatures of psilocybin microdosing.

RATIONALE: Serotonergic psychedelics are being studied as novel treatments for mental health disorders and as facilitators of improved well-being, mental function, and creativity. Recent studies have found mixed results concerning the effects of low doses of psychedelics ("microdosing") on these domains. However, microdosing is generally investigated using instruments designed to assess larger doses of psychedelics, which might lack sensitivity and specificity for this purpose. OBJECTIVES: Determine whether unconstrained speech contains signatures capable of identifying the acute effects of psilocybin microdoses. METHODS: Natural speech under psilocybin microdoses (0.5 g of psilocybin mushrooms) was acquired from thirty-four healthy adult volunteers (11 females: 32.09 ± 3.53 years; 23 males: 30.87 ± 4.64 years) following a double-blind and placebo-controlled experimental design with two measurement weeks per participant. On Wednesdays and Fridays of each week, participants consumed either the active dose (psilocybin) or the placebo (edible mushrooms). Features of interest were defined based on variables known to be affected by higher doses: verbosity, semantic variability, and sentiment scores. Machine learning models were used to discriminate between conditions. Classifiers were trained and tested using stratified cross-validation to compute the AUC and p-values. RESULTS: Except for semantic variability, these metrics presented significant differences between a typical active microdose and the inactive placebo condition. Machine learning classifiers were capable of distinguishing between conditions with high accuracy (AUC [Formula: see text] 0.8). CONCLUSIONS: These results constitute first evidence that low doses of serotonergic psychedelics can be identified from unconstrained natural speech, with potential for widely applicable, affordable, and ecologically valid monitoring of microdosing schedules.

Isolation of Bacterial and Fungal Microbiota Associated with Hermetia illucens Larvae Reveals Novel Insights into Entomopathogenicity.

Larvae of the black soldier fly (BSF) Hermetia illucens are polyphagous feeders and show tremendous bioconversion capabilities of organic matter into high-quality insect biomass. However, the digestion of lignocellulose-rich palm oil side streams such as palm kernel meal (PKM) is a particular challenge, as these compounds are exceptionally stable and are mainly degraded by microbes. This study aimed to investigate the suitability of BSF larvae as bioconversion agents of PKM. Since the intestinal microbiota is considered to play a key role in dietary breakdown and in increasing digestibility, the bacterial and fungal communities of BSF larvae were characterized in a culture-dependent approach and screened for their putative entomopathogenicity. The lethality of six putative candidates was investigated using intracoelomal injection. In total, 93 isolates were obtained with a bacterial share of 74% that were assigned to the four phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Members of the genera Klebsiella, Enterococcus, and Sphingobacterium are part of the core microbiome, as they were frequently described in the gut of Hermetia larvae regardless of diet, nutritional composition, or rearing conditions. With 75%, a majority of the fungal isolates belonged to the phylum Ascomycota. We identified several taxa already published to be able to degrade lignocelluloses, including Enterococcus, Cellulomonas, Pichia yeasts, or filamentous Fusarium species. The injection assays revealed pronounced differences in pathogenicity against the larvae. While Alcaligenes faecalis caused no, Diutina rugosa weak (23.3%), Microbacterium thalassium moderate (53.3%), and Pseudomonas aeruginosa and Klebsiella pneumoniae high (≥80%) lethality, Fusarium solani injection resulted in 100% lethality.

Pathways of thymidine hypermodification.

The DNAs of bacterial viruses are known to contain diverse, chemically complex modifications to thymidine that protect them from the endonuclease-based defenses of their cellular hosts, but whose biosynthetic origins are enigmatic. Up to half of thymidines in the Pseudomonas phage M6, the Salmonella phage ViI, and others, contain exotic chemical moieties synthesized through the post-replicative modification of 5-hydroxymethyluridine (5-hmdU). We have determined that these thymidine hypermodifications are derived from free amino acids enzymatically installed on 5-hmdU. These appended amino acids are further sculpted by various enzyme classes such as radical SAM isomerases, PLP-dependent decarboxylases, flavin-dependent lyases and acetyltransferases. The combinatorial permutations of thymidine hypermodification genes found in viral metagenomes from geographically widespread sources suggests an untapped reservoir of chemical diversity in DNA hypermodifications.

Shewanella putrefaciens, a rare human pathogen: A review from a clinical perspective.

Shewanella putrefaciens is a gramnegative, facultatively anaerobic, rod shaped bacterium. It belongs to the class of the Gammaproteobacteria and was first described in 1931. S. putrefaciens is part of the marine microflora and especially present in moderate and warm climates. The bacterium is a rare oppurtonistic human pathogen associated mainly with intra-abdominal as well as skin and soft tissue infections. However, it has also been reported in association with more severe diseases such as pneumonia, intracerebral and ocular infections and endocarditis. In these cases the clinical courses are often associated with underlying, predisposing diseases and risk factors. For successful treatment of S. putrefaciens, a combination of appropriate local therapy, e.g. surgical treatment or drainage, and antibiotic therapy should be performed. Since multiple resistances to antibiotics are described, the results of the antimicrobial susceptibility testing must be considered for effective therapy as well. Furthermore, a main challenge in clinical practice is the accurate microbiological identification, and especially the correct differentiation between S. putrefaciens and S. algae. Under certain circumstances, Shewanella-infections can have severe, sometimes even fatal consequences. Therefore, we decided to present the current state of knowledge as well as further aspects with regard to future diagnostics, therapy and research.

Leaky barriers: leaky enough for fish to pass?

Perceived as environmental-friendly hydraulic structures, leaky barriers used for natural flood management are introduced into rivers, potentially creating migration barriers for fish. Using sustainable, local materials to construct wooden barriers across river channels in upper catchments, these barriers aim to slow down the flow, reduce flood peaks and attenuate the flow reaching downstream communities. Yet little is known about their impact on hydrodynamics and fish passage. Here, we examined two model barrier designs under 100% and 80% bankfull flow conditions in an open channel flume. These barriers included a porous and a non-porous design, with the latter emulating the natural accumulation of brush, sediment and leaf material between logs over time. Flow visualization and velocity measurements recorded with acoustic Doppler velocimetry characterized the flow field upstream and downstream of the barriers. Our fish behavioural studies revealed that juvenile salmon (Salmo salar) movement between downstream and upstream sections of the flume was inhibited by barrier design rather than discharge, influencing upstream fish passage and their spatial preference, indicating the importance of barrier design criteria to facilitate fish movement.

A multi-phenotype genome-wide association study of clades causing tuberculosis in a Ghanaian- and South African cohort.

Despite decades of research and advancements in diagnostics and treatment, tuberculosis remains a major public health concern. New computational methods are needed to interrogate the intersection of host- and bacterial genomes. Paired host genotype datum and infecting bacterial isolate information were analysed for associations using a multinomial logistic regression framework implemented in SNPTest. A cohort of 853 admixed South African participants and a Ghanaian cohort of 1359 participants were included. Two directly genotyped variants, namely rs529920 and rs41472447, were identified in the Ghanaian cohort as being statistically significantly associated with risk for infection with strains of different members of the MTBC. Thus, a multinomial logistic regression using paired host-pathogen data may prove valuable for investigating the complex relationships driving infectious disease.

First-line drug resistance profiling of Mycobacterium tuberculosis: a machine learning approach.

The persistence and emergence of new multi-drug resistant Mycobacterium tuberculosis (M. tb) strains continues to advance the devastating tuberculosis (TB) epidemic. Robust systems are needed to accurately and rapidly perform drug-resistance profiling, and machine learning (ML) methods combined with genomic sequence data may provide novel insights into drug-resistance mechanisms. Using 372 M. tb isolates, the combined utility of ML and bioinformatics to perform drug-resistance profiling is demonstrated. SNPs, InDels, and dinucleotide frequencies are explored as input features for three ML models, namely Decision Trees, Random Forest, and the eXtreme Gradient Boosted model. Using SNPs and InDels, all three models performed equally well yielding a 99% accuracy, 97% recall, and 99% F1-score. Using dinucleotide frequencies, the XGBoost algorithm was superior with a 97% accuracy, 94% recall and 97% F1-score. This study validates the use of variants and presents dinucleotide features as another effective feature encoding method for ML-based phenotype classification.