A target enrichment approach for enhanced recovery of Synchytrium endobioticum nuclear genome sequences.

Potato wart disease is caused by the obligate fungal pathogen Synchytrium endobioticum. DNA extraction from compost, purified spores and crude wart tissue derived from tuber galls of infected potatoes often results in low S. endobioticum DNA concentration or highly contaminated with DNA coming from other microorganisms and the potato host. Therefore, Illumina sequencing of these samples generally results in suboptimal recovery of the nuclear genome sequences of S. endobioticum. A hybridization-based target enrichment protocol was developed to strongly enhance the recovery of S. endobioticum DNA while off-target organisms DNA remains uncaptured. The design strategy involved creating a set of 180,000 molecular baits targeting both gene and non-gene regions of S. endobioticum. The baits were applied to whole genome amplified DNA samples of various S. endobioticum pathotypes (races) in compost, from purified spores and crude wart tissue samples. This was followed by Illumina sequencing and bioinformatic analyses. Compared to non-enriched samples, target enriched samples: 1) showed a significant increase in the proportion of sequenced bases mapped to the S. endobioticum nuclear genome, especially for crude wart tissue samples; 2) yielded sequencing data with higher and better nuclear genome coverage; 3) biased genome assembly towards S. endobioticum sequences, yielding smaller assembly sizes but higher representation of putative S. endobioticum contigs; 4) showed an increase in the number of S. endobioticum genes detected in the genome assemblies. Our hybridization-based target enrichment protocol offers a valuable tool for enhancing genome sequencing and NGS-based molecular detection of S. endobioticum, especially in difficult samples.

Investigating adverse effects of chronic dietary exposure to herbicide glyphosate on zootechnical characteristics and clinical, biochemical and immunological blood parameters in broiler chickens.

Although the herbicide glyphosate is widely used globally and considered safe, more evidence of its adverse effects on animals and humans is accumulating. The present investigation was aimed at evaluating the impact of different glyphosate concentrations on zootechnical characteristics and clinical, biochemical and immunological blood parameters in Ross 308 broiler chickens. Four groups were employed, including untreated control and three experimental groups fed diets enriched with glyphosate at doses of 10, 20 and 100 ppm that conformed to 0.5, 1 and 5 maximum residue limits, respectively. The results showed that glyphosate is a stress factor triggering a multifaceted effect on important blood parameters (e.g., white blood cell and phagocytic counts), which was shown for the first time in the experiments involving productive meat-type poultry. It was first revealed that glyphosate-induced changes in blood parameters may be related to a negative impact on the zootechnical characteristics including the digestive tract organ development and body weight gain. The study findings suggested that exposure to glyphosate in the feedstuffs can adversely affect the physiological condition and productivity of broilers.

Event rates and risk factors for venous thromboembolism and major bleeding in a population of hospitalized adult patients with acute medical illness receiving enoxaparin thromboprophylaxis.

BACKGROUND: We aimed to describe the event rates and risk-factors for symptomatic venous thromboembolism (VTE) and major bleeding in a population of hospitalized acutely ill medical patients. METHODS: Patients ≥40 years old and hospitalized for acute medical illness who initiated enoxaparin prophylaxis were selected from the US Optum research database. Rates of symptomatic VTE and major bleeding at 90-days were estimated via the Kaplan-Meier (KM) method. Risk factors were identified via the Cox proportional hazards model. RESULTS: A total of 123,022 patients met the selection criteria. The KM rates of VTE and major bleeding at 90-days were 3.5 % and 2.2 %, respectively. Among subgroups, the risk of VTE varied from 3.0 % in patients with ischemic stroke to 6.9 % in patients with a cancer-related hospitalization, and the risk of major bleeding varied from 1.9 % in patients with inflammatory conditions to 3.6 % in patients with ischemic stroke. Key risk factors for VTE were prior VTE (HR=4.15, 95 % confidence interval [CI] 3.80-4.53), cancer-related hospitalization (HR=2.35, 95 % CI 2.10-2.64), and thrombophilia (HR=1.64, 95 % CI 1.29-2.08). Key risk factors for major bleeding were history of major bleeding (HR=2.17, 95 % CI 1.72-2.74), history of non-major bleeding (HR=2.46, 95 % CI 2.24-2.70), and hospitalization for ischemic stroke (2.42, 95 % CI 2.11-2.78). CONCLUSION: There is substantial heterogeneity in the event rates for VTE and major bleeding in acute medically ill patients. History of VTE and cancer related hospitalization represent profiles with a high risk of VTE, where continued VTE prophylaxis may be warranted.

The economic value of insulin glargine 300 U/mL (Gla-300) in people ≥18 years of age with type 2 diabetes mellitus: a value-based economic model from a U.S. payer perspective.

AIMS: This study aimed to evaluate the value and affordability of insulin glargine 300 U/mL (Gla-300) in a budget impact model from a United States (U.S.) payer perspective by leveraging recent real-world evidence (RWE) studies and incorporating the recent insulin price caps where applicable. MATERIALS AND METHODS: An economic model for a hypothetical one million U.S. health-plan population was developed to assess the budgetary impact of therapeutic interchanges in either direction between the two long- and longer-acting basal insulins (BIs) for patients with type 2 diabetes over a three-year model horizon. The utilization of long-acting BIs, longer-acting BIs, biosimilar BIs, and insulin degludec (IDeg-100) were informed by IQVIA data and internal forecasting at Sanofi. The DELIVER-2 and DELIVER-naïve studies provided healthcare resource utilization (HCRU) parameters. In the model base case, 24% of patients switched from long-acting BIs to insulin glargine biosimilars, IDeg-100, and other longer-acting BIs (Gla-300) by projected year 3. RESULTS: The base case total costs were $10,145 per patient per year (PPPY) in year 3 for the cumulative population. When all patients switched to Gla-300, the total costs in year 3 were $8,799, reflecting a net savings of -$660 PPPY compared to the budget increase of $686 PPPY in the base case. However, the longer-acting to long-acting BIs reversal scenario demonstrated a budgetary decrease of $676 PPPY over the model horizon. The reduction in incremental PPPY cost of $93 was observed using net drug costs rather than wholesale acquisition costs (WAC). LIMITATIONS: The market shares for years 1-3 were based on expectations supported by the clinicians' expert opinions and were not obtained from real-world data. CONCLUSIONS: The economic value of increased utilization of Gla-300 was driven by the reduction in HCRU, costs and market shares assumptions. Budgetary reductions were achieved by switching patients from long-acting BIs to Gla-300.

Type 2 Diabetes (T2D) is a chronic and debilitating condition that can lead to severe macro or microvascular complications. To mitigate these complications, it is crucial to effectively manage blood glucose levels. When other treatments prove ineffective in achieving adequate glucose control, insulin-based therapy becomes necessary. However, insulin-based treatments often come with the risk of hypoglycemic episodes, which can lead to increased utilization of healthcare resources (HCRU) and have a negative impact on costs.This study aimed to assess the budgetary impact of higher market shares of longer-acting basal insulins (specifically insulin glargine Gla-300) compared to long-acting basal insulins, insulin glargine biosimilars, and insulin degludec (IDeg) in the treatment of T2D. The perspective taken was that of a U.S. payer, taking into account the recent insulin price caps where applicable.The economic benefit of increased utilization of Gla-300 was driven by reductions in HCRU, costs, and market share assumptions. This resulted in a budgetary increase of $686 per patient per year (PPPY). In an alternative scenario where all patients transitioned to Gla-300, it led to a net savings of $660 PPPY.These findings provide valuable insights for decision-makers and healthcare professionals when making choices related to formulary placement and treatment utilization.

Probiotics as an alternative to antibiotics in modulating the intestinal microbiota and performance of broiler chickens.

AIMS: Gut bacteria play an important role in poultry nutrition and the immune defense system. Changes in the intestinal microbiome affect the physiological state, metabolism, and innate immunity of poultry. The present study aimed to characterize age-related changes in the gastrointestinal tract microflora in broiler chickens, depending on supplementation of the diet with the in-feed antibiotic Stafac® 110 and a Bacillus subtilis strain-based probiotic. METHODS AND RESULTS: In this regard, a comprehensive analysis of the taxonomic structure of the microbial community in the gastrointestinal tract (GIT) of broiler chickens was carried out using a molecular genetic technique of the terminal-restriction fragment length polymorphism analysis and taking into account age dynamics and feeding treatment. A beneficial effect on the microbiological composition and body weight of broilers was observed when using the antibiotic and probiotic in compound feeds. Different bacterial communities were revealed in the duodenum and cecum, and their positive impact on broiler growth was established. The results obtained shed light on the formation of GIT microflora of broiler chickens during the growing period and its changes in response to the use of the antibiotic and the probiotic. CONCLUSIONS: We suggest that the implementation of the tested in-feed antibiotic and probiotic can be beneficial in regulating the intestinal microflora microbiological processes in the GIT and improving the feeding efficiency and productivity of broiler chickens.

Simulation of long-term impact of intravitreal anti-VEGF therapy on patients with severe non-proliferative diabetic retinopathy.

OBJECTIVE: A simulation model was constructed to assess long-term outcomes of proactively treating severe non-proliferative diabetic retinopathy (NPDR) with anti-vascular endothelial growth factor (anti-VEGF) therapy versus delaying treatment until PDR develops. METHODS AND ANALYSIS: Simulated patients were generated using a retrospective real-world cohort of treatment-naive patients identified in an electronic medical records database (IBM Explorys) between 2011 and 2017. Impact of anti-VEGF treatment was derived from clinical trial data for intravitreal aflibercept (PANORAMA) and ranibizumab (RISE/RIDE), averaged by weighted US market share. Real-world risk of PDR progression was modelled using Cox multivariable regression. The Monte Carlo simulation model examined rates of progression to PDR and sustained blindness (visual acuity <20/200) for 2 million patients scaled to US NPDR disease prevalence. Simulated progression rates from severe NPDR to PDR over 5 years and blindness rates over 10 years were compared for delayed versus early-treatment patients. RESULTS: Real-world data from 77 454 patients with mild-to-severe NPDR simulated 2 million NPDR patients, of which 86 680 had severe NPDR. Early treatment of severe NPDR with anti-VEGF therapy led to a 51.7% relative risk reduction in PDR events over 5 years (15 704 early vs 32 488 delayed), with a 19.4% absolute risk reduction (18.1% vs 37.5%). Sustained blindness rates at 10 years were 4.4% for delayed and 1.9% for early treatment of severe NPDR. CONCLUSION: The model suggests treating severe NPDR early with anti-VEGF therapy, rather than delaying treatment until PDR develops, could significantly reduce PDR incidence over 5 years and sustained blindness over 10 years.

Molecular-Induced Chirality Transfer to Plasmonic Lattice Modes.

Molecular chirality plays fundamental roles in biology. The chiral response of a molecule occurs at a specific spectral position, determined by its molecular structure. This fingerprint can be transferred to other spectral regions via the interaction with localized surface plasmon resonances of gold nanoparticles. Here, we demonstrate that molecular chirality transfer occurs also for plasmonic lattice modes, providing a very effective and tunable means to control chirality. We use colloidal self-assembly to fabricate non-close packed, periodic arrays of achiral gold nanoparticles, which are embedded in a polymer film containing chiral molecules. In the presence of the chiral molecules, the surface lattice resonances (SLRs) become optically active, i.e., showing handedness-dependent excitation. Numerical simulations with varying lattice parameters show circular dichroism peaks shifting along with the spectral positions of the lattice modes, corroborating the chirality transfer to these collective modes. A semi-analytical model based on the coupling of single-molecular and plasmonic resonances rationalizes this chirality transfer.

Whole genome sequencing and phylogenomic analysis show support for the splitting of genus Pythium.

The genus Pythium (nom. cons.) sensu lato (s.l.) is composed of many important species of plant pathogens. Early molecular phylogenetic studies suggested paraphyly of Pythium, which led to a formal proposal by Uzuhashi and colleagues in 2010 to split the genus into Pythium sensu stricto (s.s.), Elongisporangium, Globisporangium, Ovatisporangium (= Phytopythium), and Pilasporangium using morphological characters and phylogenies of the mt cytochrome c oxidase subunit 2 (cox2) and D1-D2 domains of nuc 28S rDNA. Although the split was fairly justified by the delineating morphological characters, there were weaknesses in the molecular analyses, which created reluctance in the scientific community to adopt these new genera for the description of new species. In this study, this issue was addressed using phylogenomics. Whole genomes of 109 strains of Pythium and close relatives were sequenced, assembled, and annotated. These data were combined with 10 genomes sequenced in previous studies. Phylogenomic analyses were performed with 148 single-copy genes represented in at least 90% of the taxa in the data set. The results showed support for the division of Pythium s.l. The status of alternative generic names that have been used for species of Pythium in the past (e.g., Artotrogus, Cystosiphon, Eupythium, Nematosporangium, Rheosporangium, Sphaerosporangium) was investigated. Based on our molecular analyses and review of the Pythium generic concepts, we urge the scientific community to adopt the generic names Pythium, Elongisporangium, Globisporangium, and their concepts as proposed by Uzuhashi and colleagues in 2010 in their work going forward. In order to consolidate the taxonomy of these genera, some of the recently described Pythium spp. are transferred to Elongisporangium and Globisporangium.

The fuzzy sphere morphology is responsible for the increase in light scattering during the shrinkage of thermoresponsive microgels.

Thermoresponsive microgels undergo a volume phase transition from a swollen state under good solvent conditions to a collapsed state under poor solvent conditions. The most prominent examples of such responsive systems are based on poly-(N-isopropylacrylamide). When cross-linked with N,N'-methylenebisacrylamide, such microgels typically possess a fuzzy-spherelike morphology with a higher cross-linked core and a loosely cross-linked fuzzy shell. Despite the efforts devoted to understanding the internal structure of microgels and their kinetics during collapse/swelling, the origins of the accompanying changes in light scattering intensity have barely been addressed. In this work, we study core-shell microgels that contain small gold nanoparticle cores with microgel shells of different thicknesses and cross-linker densities. All microgels are small enough to fulfill the Rayleigh-Debye-Gans criterion at all stages of swelling. Due to the high X-ray contrast of the gold cores, we can use absolute intensity small-angle X-ray scattering to determine the number density in the dilute dispersions. This allows us to extract polymer volume fractions of the microgels at different stages of swelling from form factor analysis of small-angle neutron scattering data. We match our findings to results from temperature-dependent absorbance measurements. The increase in absorbance during the shrinkage of the microgels is related to the transition from fuzzy spheres to hard sphere-like scattering objects with a rather homogeneous density profile. We provide a first attempt to model experimental spectra using finite difference time domain simulations that take into account the structural changes during the volume phase transition. Our findings significantly contribute to the understanding of the optical properties of thermoresponsive microgels. Further, we provide polymer volume fractions and microgel refractive indices as a function of the swelling state.

Genome Characterization and Development of Real-Time PCR Assays for Ditylenchus Dipsaci and D. Weischeri.

The stem and bulb nematode Ditylenchus dipsaci is a destructive nematode pest on many crops and is internationally quarantined in many countries, whereas Ditylenchus weischeri, only known to infect a weed plant (Cirsium arvense), is an unregulated nematode species with no known economic importance. In this study, we used comparative genomics to identify multiple gene regions and developed novel real-time PCR assays for the detection of D. dipsaci and D. weischeri. We sequenced the genomes of two mixed-stage nematode populations of D. dipsaci and two mixed-stage nematode populations of D. weischeri. The assembled genomes of D. dipsaci were 228.2 Mb and 239.5 Mb, and the genomes of D. weischeri were 177.0 Mb and 196.3 Mb. Depending on the species, 21,403-27,365 gene models were predicted. Using orthologous group analysis, single-copy and species-specific genes were identified. Primers and probes were designed targeting two species-specific genes in each species. The assays detected as low as 12 pg of DNA from the target species, or as few as five nematodes, with a Cq of 31 cycles or less. Our study provides genome data for two additional D. dipsaci isolates and two D. weischeri isolates, and four new and validated molecular assays to be used for rapid detection and identification of the two species.

Surface Lattice Resonances in Self-Assembled Gold Nanoparticle Arrays: Impact of Lattice Period, Structural Disorder, and Refractive Index on Resonance Quality.

Surface lattice resonances are optical resonances composed of hybridized plasmonic and diffractive modes. These collective resonances occur in periodic arrays of plasmonic nanoparticles with wavelength-scale interparticle distances. The appearance and strength of surface lattice resonances strongly depend on the single particle localized surface plasmon resonance and its spectral overlap with the diffractive modes of the array. Coupling to in-plane orders of diffraction is also strongly affected by the refractive index environment and its symmetry. In this work, we address the impact of the interparticle distance, the symmetry of the refractive index environment, and structural imperfections in self-assembled colloidal monolayers on the plasmonic-diffractive coupling. For this purpose, we prepared hexagonally ordered, nonclose packed monolayers of gold nanoparticles using a fast and efficient, interface-mediated, colloidal self-assembly approach. By tuning the thickness and deformability of the polymer shells, we were able to prepare monolayers with a broad range of interparticle distances. The optical properties of the samples were studied experimentally by UV-Vis spectroscopy and theoretically by finite difference time domain simulations. The measured and simulated spectra allow a comprehensive analysis of the details of electromagnetic coupling in periodic plasmonic arrays. In particular, we identify relevant criteria required for surface lattice resonances in the visible wavelength range with optimized quality factors in self-assembled monolayers.

Ochratoxin A production by Penicillium thymicola.

Ochratoxin A (OTA) is a mycotoxin produced by some Aspergillus and Penicillium species that grow on economically important agricultural crops and food products. OTA is classified as Group 2B carcinogen and is potently nephrotoxic, which is the basis for its regulation in some jurisdictions. Using high resolution mass spectroscopy, OTA and ochratoxin B (OTB) were detected in liquid culture extracts of Penicillium thymicola DAOMC 180753 isolated from Canadian cheddar cheese. The genome of this strain was sequenced, assembled and annotated to probe for putative genes involved in OTA biosynthesis. Known OTA biosynthetic genes from Penicillium verrucosum or Penicillium nordicum, two related Penicillium species that produce OTA, were not found in P. thymicola. However, a gene cluster containing a polyketide synthase (PKS) and PKS-nonribosomal peptide synthase (NRPS) hybrid encoding genes were located in the P. thymicola genome that showed a high degree of similarity to OTA biosynthetic enzymes of Aspergillus carbonarius and Aspergillus ochraceus. This is the first report of ochratoxin from P. thymicola and a new record of the species in Canada.

IMA Genome-F 6: Draft genome sequences of Armillaria fuscipes, Ceratocystiopsis minuta, Ceratocystis adiposa, Endoconidiophora laricicola, E. polonica and Penicillium freii DAOMC 242723.

The genomes of Armillaria fuscipes, Ceratocystiopsis minuta, Ceratocystis adiposa, Endoconidiophora laricicola, E. polonica, and Penicillium freii DAOMC 242723 are presented in this genome announcement. These six genomes are from plant pathogens and otherwise economically important fungal species. The genome sizes range from 21 Mb in the case of Ceratocystiopsis minuta to 58 Mb for the basidiomycete Armillaria fuscipes. These genomes include the first reports of genomes for the genus Endoconidiophora. The availability of these genome data will provide opportunities to resolve longstanding questions regarding the taxonomy of species in these genera. In addition these genome sequences through comparative studies with closely related organisms will increase our understanding of how these pathogens cause disease.

Comparative study of genome divergence in salmonids with various rates of genetic isolation.

The aim of the study is a comparative investigation of changes that certain genome parts undergo during speciation. The research was focused on divergence of coding and noncoding sequences in different groups of salmonid fishes of the Salmonidae (Salmo, Parasalmo, Oncorhynchus, and Salvelinus genera) and the Coregonidae families under different levels of reproductive isolation. Two basic approaches were used: (1) PCR-RAPD with a 20-22 nt primer design with subsequent cloning and sequencing of the products and (2) a modified endonuclease restriction analysis. The restriction fragments were shown with sequencing to represent satellite DNA. Effects of speciation are found in repetitive sequences. The revelation of expressed sequences in the majority of the employed anonymous loci allows for assuming the adaptive selection during allopatric speciation in isolated char forms.

Myasthenia gravis accompanied by thymomas not related to foamy virus genome in Belarusian's patients.

The spectrum and features of neurological disorders have been changed due to the Chernobyl catastrophe in the Republic of Belarus. More recently neurologists in Belarus have noted a significant increase in the frequency of myasthenia gravis (MG) with concomitant rise in the thymomas. There is some evidence suggesting that retroviruses play a key role in the development and pathogenesis of autoimmune diseases. This study analyzed thymomas from 45 MG patients from the Republic of Belarus by using PCR and primers for two regions of FV--gag and bel-2 genes. The results showed that none of the varied thymuses from the 45 MG patients contained FV genome. No relationship can be confirmed between FV and this disease and the results suggest that no pathological link between FV and MG exists.