Factors Affecting the Quality of Bacterial Genomes Assemblies by Canu after Nanopore Sequencing

Long-read sequencing (LRS), like Oxford Nanopore Technologies, is usually associated with higher error rates compared to previous generations. Factors affecting the assembly quality are the integrity of DNA, the flowcell efficiency, and, not least all, the raw data processing. Among LRS-intended de novo assemblers, Canu is highly flexible, with its dozens of adjustable parameters. Different Canu parameters were compared for assembling reads of Salmonellaenterica ser. Bovismorbificans (genome size of 4.8 Mbp) from three runs on MinION (N50 651, 805, and 5573). Two of them, with low quality and highly fragmented DNA, were not usable alone for assembly, while they were successfully assembled when combining the reads from all experiments. The best results were obtained by modifying Canu parameters related to the error correction, such as corErrorRate (exclusion of overlaps above a set error rate, set up at 0.40), corMhapSensitivity (the coarse sensitivity level, set to “high”), corMinCoverage (set to 0 to correct all reads, regardless the overlaps length), and corOutCoverage (corrects the longest reads up to the imposed coverage, set to 100). This setting produced two contigs corresponding to the complete sequences of the chromosome and a plasmid. The overall results highlight the importance of a tailored bioinformatic analysis

1H-NMR metabolomic profile of healthy and osteoarthritic canine synovial fluid before and after UC-II supplementation

The aim of the study was to compare the metabolomic synovial fluid (SF) profile of dogs affected by spontaneous osteoarthritis (OA) and supplemented with undenatured type II collagen (UC-II), with that of healthy control dogs. Client-owned dogs were enrolled in the study and randomized in two different groups, based on the presence/absence of OA (OA group and OA-free group). All dogs were clinically evaluated and underwent SF sampling for 1H-Nuclear Magnetic Resonance spectroscopy (1H-NMR) analysis at time of presentation. All dogs included in OA group were supplemented with UC-II orally administered for 30 days. After this period, they were reassessed (OA-T30). The differences in the 1H-NMR metabolic SFs profiles between groups (OA-free, OA-T0 and OA-T30) were studied. The multivariate statistical analysis performed on SFs under different conditions (OA-T0 vs OA-T30 SFs; OA-T0 vs OA-free SFs and OA-T30 vs OA-free SFs) gave models with excellent goodness of fit and predictive parameters, revealed by a marked separation between groups. β-Hydroxybutyrate was identified as a characteristic compound of osteoarthritic joints, showing the important role of fat metabolism during OA. The absence of β-hydroxybutyrate after UC-II supplementation suggests the supplement’s effectiveness in rebalancing the metabolism inside the joint. The unexpectedly high level of lactate in the OA-free group suggests that lactate could not be considered a good marker for OA. These results prove that 1H-NMR-based metabolomic analysis is a valid tool to study and monitor OA and that UC-II improves clinical symptoms and the SF metabolic profile in OA dog

Dermanyssus gallinae: the long journey of the poultry red mite to become a vector

: The possibility that Dermanyssus gallinae, the poultry red mite, could act as a vector of infectious disease-causing pathogens has always intrigued researchers and worried commercial chicken farmers, as has its ubiquitous distribution. For decades, studies have been carried out which suggest that there is an association between a wide range of pathogens and D. gallinae, with the transmission of some of these pathogens mediated by D. gallinae as vector. The latter include the avian pathogenic Escherichia coli (APEC), Salmonella enterica serovars Enteritidis and Gallinarum and influenza virus. Several approaches have been adopted to investigate the relationship between D. gallinae and pathogens. In this comprehensive review, we critically describe available strategies and methods currently available for conducting trials, as well as outcomes, analyzing their possible strengths and weaknesses, with the aim to provide researchers with useful tools for correctly approach the study of the vectorial role of D. gallinae

Release of {DNA} from Dermanyssus gallinae during the Biting Process

: Dermanyssus gallinae is a hematophagous ectoparasitic mite that usually infests poultry, but is also known for occasionally attacking other animals and humans. It represents a major problem for poultry systems all over the world, with detrimental effects for both production and animal welfare. Despite the significance of D. gallinae, very little is known about the biting process to date. Therefore, this study has aimed to verify if mite DNA is injected into the host skin during the blood meal. Mite DNA has been detected by seminested PCR from infested chicken skin and quantified by real-time PCR. Furthermore, its localization within the host tissue has been checked by fluorescent in situ hybridization. Results showed that a very little amount of D. gallinae DNA can be released by mites, suggesting that the latter do not introduce whole or partially destroyed cells into the host, but rather it injects traces of nucleic acids, possibly together with merocrine secretions

Release of DNA from Dermanyssus gallinae during the Biting Process

none10noDermanyssus gallinae is a hematophagous ectoparasitic mite that usually infests poultry, but is also known for occasionally attacking other animals and humans. It represents a major problem for poultry systems all over the world, with detrimental effects for both production and animal welfare. Despite the significance of D. gallinae, very little is known about the biting process to date. Therefore, this study has aimed to verify if mite DNA is injected into the host skin during the blood meal. Mite DNA has been detected by seminested PCR from infested chicken skin and quantified by real-time PCR. Furthermore, its localization within the host tissue has been checked by fluorescent in situ hybridization. Results showed that a very little amount of D. gallinae DNA can be released by mites, suggesting that the latter do not introduce whole or partially destroyed cells into the host, but rather it injects traces of nucleic acids, possibly together with merocrine secretions.Pugliese, Nicola; Raele, Donato Antonio; Schiavone, Antonella; Cafiero, Maria Assunta; Potenza, Lucia; Samarelli, Rossella; Circella, Elena; Vasco, Ilaria; Pennuzzi, Germana; Camarda, AntonioPugliese, Nicola; Raele, Donato Antonio; Schiavone, Antonella; Cafiero, Maria Assunta; Potenza, Lucia; Samarelli, Rossella; Circella, Elena; Vasco, Ilaria; Pennuzzi, Germana; Camarda, Antoni

Physiological effects of lung protective ventilation in patients with lung fibrosis and usual interstitial pneumonia pattern versus primary ARDS: a matched-control study.

Background- Although patients with interstitial pneumonia pattern (ILD-UIP) and acute exacerbation (AE) leading to severe acute respiratory failure may require invasive mechanical ventilation (MV), physiological data on lung mechanics during MV are lacking. We aimed at describing the physiological effect of lung protective ventilation in patients with AE-ILD-UIP compared with primary ARDS. Methods- Partitioned lung and chest wall mechanics were assessed in a series of AE-ILD-UIP patients matched 1:1 with primary ARDS as controls (based on BMI and PaO2/FiO2 ratio). Three PEEP levels (zero=ZEEP, 4-8 cmH2O=PEEPLOW, and titrated to achieve positive end-expiratory transpulmonary pressure-PL,EE=PEEPTITRATED) were used for measurements. Results- Ten AE-ILD-UIP patients and 10 matched ARDS were included. In AE-ILD-UIP median PL,EE at ZEEP was - 4.3 [-7.6 – -2.3] cmH2O and lung elastance (EL) 44 [40 – 51] cmH2O/L. At PEEPLOW, PL,EE remained negative and EL did not change (p=0.995) versus ZEEP. At PEEPTITRATED, PL,EE increased to 0.8 [0.3 – 1.5] cmH2O and EL to 49 [43 – 59] (p=0.004 and p<0.001 compared to ZEEP and PEEPLOW, respectively). PL decreased at PEEPLOW (p=0.018) and increased at PEEPTITRATED (p=0.003). In matched ARDS control PEEP titration to obtain a positive PL,EE did not result in significant changes in EL and PL. Conclusions- In mechanically ventilated AE-ILD-UIP patients, differently than in patients with primary ARDS, PEEP titrated to obtain a positive PL,EE significantly worsened lung mechanics

Evaluation of clinical efficacy of undenatured type II collagen supplementation compared to cimicoxib and their association in dogs affected by natural occurring osteoarthritis

The aim of the study was to evaluate the clinical efficacy of 30 days treatment of undenatured type II collagen (UC-II (R)), compared to cimicoxib and to their combination, in osteoarthritic dogs. Client-owned dogs were enrolled in a clinical, randomized, controlled and prospective study. Posture, lameness, pain, range of motion and x-ray of affected joint(s) were evaluated and scored based on severity (CLINICAL score). The Liverpool Osteoarthritis in Dogs survey was used to score the owner evaluation of dog's mobility (LOAD score and MOBILITY score). Osteoarthritis (OA) stage was defined through the Canine Osteoarthritis Staging tool (COAST). After diagnosis (T0), all patients were randomly assigned to different treatment groups: C group = cimicoxib 2 mg/kg/day orally OS, F group = UC-II (R) 1 tablet per day OS; C + F group = cimicoxib-UC-II (R) at the same previous dosages; CTR group = dogs who didn't received any treatment. All treatments were administered for 30 days. Seventy-six dogs completed the study. LOAD score was recorded significant lower after treatment for each group, with a reduction in percentage of 29.5% for C, 31.4% for F, 21.1% for C + F. LOAD score was lower in C(P = 0.04), F(P = 0.001) and C + F(P = 0.009) group at T30 than CTR group. MOBILITY and CLINICAL scores were significantly lower in all groups at T30, when compared to T0. MOBILITY score was lower than CTR in C(P = 0.02) and F(P = 0.01); CLINICAL score was lower in C + F(P = 0.016). The present findings prove that the treatment with UC-II (R), cimicoxib and their combination provide significant reduction in clinical signs associated with OA

Evaluation of the Effects of Undenatured Type II Collagen (UC-II) as Compared to Robenacoxib on the Mobility Impairment Induced by Osteoarthritis in Dogs

Osteoarthritis (OA) is a chronic disease that requires a multimodal therapeutic approach. The aim of this study was to evaluate the effects of undenatured type II collagen (UC-II) as compared to robenacoxib in dogs affected by OA. Our hypothesis was that the two compounds would be similar (non-inferiority) in improving mobility. To test this hypothesis, a complete orthopedic examination, x-ray and the Liverpool Osteoarthritis in Dogs (LOAD) survey were performed in dogs affected by OA before and after the treatments. The study was designed as a clinical, randomized, controlled and prospective study. Sixty client-owned dogs were randomized in the R group (n = 30, robenacoxib 1 mg/kg/day for 30 days) and in the UC-II group (n = 30, UC-II 1 tablet/day for 30 days). Thirty days after the beginning of the treatment (T30), the dogs were reassessed for the LOAD, MOBILITY and CLINICAL scores. Based on the data obtained from the study, a significant reduction in LOAD and MOBILITY scores was recorded between T0 and T30 with a similar magnitude among the two groups (R = 31.5%, p < 0.001; UC-II = 32.7%, p = 0.013). The results of this study showed that UC-II and robenacoxib were able to similarly improve mobility of dogs affected by OA

Vertical Transmission of <i>Salmonella enterica</i> ser. Gallinarum in <i>Dermanyssus gallinae</i> by the Mean of the Baudruche-Based Artificial Feeding Device

The poultry red mite (PRM) Dermanyssus gallinae is well known for its vectorial role for pathogens, such as Salmonella enterica ser. Gallinarum, the causative agent of fowl typhoid. Here, we ascertained the vertical transmission of S. Gallinarum across the PRM life stages, combining the Baudruche-based in vitro feeding system and a PRM-fitting DNA extraction and detection method by qPCR. Small-sized pools (4–5 specimens) of adult mites, eggs, larvae, and protonymphs, as well as single eggs, were tested for S. Gallinarum. The pathogen was detected in 89% of adult mites, 5% of single eggs, 17% of pooled eggs, 9% of larvae, and 43% of protonymphs. Additionally, the feeding rate for infected and uninfected mites was similar, while differences in ovipositing and fecundity rate were observed. The method allowed to confirm the infection of mites through the bloodmeal and to strongly suggest the transmission of S. Gallinarum across the PRM life stages. Furthermore, it allows to avoid in vivo studies and it could be useful for further investigating the vectorial role of D. gallinae or other hematophagous arthropods for infectious agents

Vertical Transmission of Salmonella enterica ser. Gallinarum in Dermanyssus gallinae by the Mean of the Baudruche-Based Artificial Feeding Device

The poultry red mite (PRM) Dermanyssus gallinae is well known for its vectorial role for pathogens, such as Salmonella&nbsp;enterica ser. Gallinarum, the causative agent of fowl typhoid. Here, we ascertained the vertical transmission of S. Gallinarum across the PRM life stages, combining the Baudruche-based in vitro feeding system and a PRM-fitting DNA extraction and detection method by qPCR. Small-sized pools (4&ndash;5 specimens) of adult mites, eggs, larvae, and protonymphs, as well as single eggs, were tested for S. Gallinarum. The pathogen was detected in 89% of adult mites, 5% of single eggs, 17% of pooled eggs, 9% of larvae, and 43% of protonymphs. Additionally, the feeding rate for infected and uninfected mites was similar, while differences in ovipositing and fecundity rate were observed. The method allowed to confirm the infection of mites through the bloodmeal and to strongly suggest the transmission of S. Gallinarum across the PRM life stages. Furthermore, it allows to avoid in vivo studies and it could be useful for further investigating the vectorial role of D. gallinae or other hematophagous arthropods for infectious agents