Genomic delineation and description of species and within-species lineages in the genus Pantoea.

As the name of the genus Pantoea ("of all sorts and sources") suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils, components of the water cycle, and humans. Some members of the genus are pathogenic to plants, and some are suspected to be opportunistic human pathogens; while others are used as microbial pesticides or show promise in biotechnological applications. During its taxonomic history, the genus and its species have seen many revisions. However, evolutionary and comparative genomics studies have started to provide a solid foundation for a more stable taxonomy. To move further toward this goal, we have built a 2,509-gene core genome tree of 437 public genome sequences representing the currently known diversity of the genus Pantoea. Clades were evaluated for being evolutionarily and ecologically significant by determining bootstrap support, gene content differences, and recent recombination events. These results were then integrated with genome metadata, published literature, descriptions of named species with standing in nomenclature, and circumscriptions of yet-unnamed species clusters, 15 of which we assigned names under the nascent SeqCode. Finally, genome-based circumscriptions and descriptions of each species and each significant genetic lineage within species were uploaded to the LINbase Web server so that newly sequenced genomes of isolates belonging to any of these groups could be precisely and accurately identified.

Investigating plant disease outbreaks with long-read metagenomics: sensitive detection and highly resolved phylogenetic reconstruction applied to Xylella fastidiosa.

Early disease detection is a prerequisite for enacting effective interventions for disease control. Strains of the bacterial plant pathogen Xylella fastidiosa have recurrently spread to new crops in new countries causing devastating outbreaks. So far, investigation of outbreak strains and highly resolved phylogenetic reconstruction have required whole-genome sequencing of pure bacterial cultures, which are challenging to obtain due to the fastidious nature of X. fastidiosa. Here, we show that culture-independent metagenomic sequencing, using the Oxford Nanopore Technologies MinION long-read sequencer, can sensitively and specifically detect the causative agent of Pierce's disease of grapevine, X. fastidiosa subspecies fastidiosa. Using a DNA sample from a grapevine in Virginia, USA, it was possible to obtain a metagenome-assembled genome (MAG) of sufficient quality for phylogenetic reconstruction with SNP resolution. The analysis placed the MAG in a clade with isolates from Georgia, USA, suggesting introduction of X. fastidiosa subspecies fastidiosa to Virginia from the south-eastern USA. This proof of concept study, thus, revealed that metagenomic sequencing can replace culture-dependent genome sequencing for reconstructing transmission routes of bacterial plant pathogens.

High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing.

BACKGROUND: The lower Dipteran fungus fly, Sciara coprophila, has many unique biological features that challenge the rule of genome DNA constancy. For example, Sciara undergoes paternal chromosome elimination and maternal X chromosome nondisjunction during spermatogenesis, paternal X elimination during embryogenesis, intrachromosomal DNA amplification of DNA puff loci during larval development, and germline-limited chromosome elimination from all somatic cells. Paternal chromosome elimination in Sciara was the first observation of imprinting, though the mechanism remains a mystery. Here, we present the first draft genome sequence for Sciara coprophila to take a large step forward in addressing these features. RESULTS: We assembled the Sciara genome using PacBio, Nanopore, and Illumina sequencing. To find an optimal assembly using these datasets, we generated 44 short-read and 50 long-read assemblies. We ranked assemblies using 27 metrics assessing contiguity, gene content, and dataset concordance. The highest-ranking assemblies were scaffolded using BioNano optical maps. RNA-seq datasets from multiple life stages and both sexes facilitated genome annotation. A set of 66 metrics was used to select the first draft assembly for Sciara. Nearly half of the Sciara genome sequence was anchored into chromosomes, and all scaffolds were classified as X-linked or autosomal by coverage. CONCLUSIONS: We determined that X-linked genes in Sciara males undergo dosage compensation. An entire bacterial genome from the Rickettsia genus, a group known to be endosymbionts in insects, was co-assembled with the Sciara genome, opening the possibility that Rickettsia may function in sex determination in Sciara. Finally, the signal level of the PacBio and Nanopore data support the presence of cytosine and adenine modifications in the Sciara genome, consistent with a possible role in imprinting.

Zn-based physiometacomposite nanoparticles: distribution, tolerance, imaging, and antiviral and anticancer activity.

The aim of this study was to investigate the distribution, tolerance, and anticancer and antiviral activity of Zn-based physiometacomposites (PMCs). Manganese, iron, nickel and cobalt-doped ZnO, ZnS or ZnSe were synthesized. Cell uptake, distribution into 3D culture and mice, and biochemical and chemotherapeutic activity were studied by fluorescence/bioluminescence, confocal microscopy, flow cytometry, viability, antitumor and virus titer assays. Luminescence and inductively coupled plasma mass spectrometry analysis showed that nanoparticle distribution was liver >spleen >kidney >lung >brain, without tissue or blood pathology. Photophysical characterization as ex vivo tissue probes and LL37 peptide, antisense oligomer or aptamer delivery targeting RAS/Ras binding domain (RBD) was investigated. Treatment at 25 µg/ml for 48 h showed ≥98-99% cell viability, 3D organoid uptake, 3-log inhibition of ß-Galactosidase and porcine reproductive respiratory virus infection. Data support the preclinical development of PMCs for imaging and delivery targeting cancer and infectious disease.

A field trial comparing four oral nonsteroidal anti-inflammatory drugs on controlling cautery dehorning pain and stress in calves.

The purpose of this study was to compare the analgesic effect of four nonsteroidal anti-inflammatory drugs (NSAIDs) administered as a single, standardized, oral dose in dairy calves at the time of cautery dehorning. The NSAIDs investigated have pharmacokinetic properties in cattle that produce persistent plasma concentrations that may provide prolonged analgesia with the added practicality of a simple administration regimen. One hundred and eighty-five Holstein calves aged approximately 50 d old were either sham dehorned (n = 31) or cautery dehorned following oral administration of carprofen (n = 31), firocoxib (n = 31), flunixin meglumine (n = 30), meloxicam (n = 31) or placebo (n = 31) in a randomized, controlled trial. A standard dose of 2.0 mg/kg was administered to all calves receiving an oral NSAID. All calves received local anesthesia prior to actual or sham dehorning. Cortisol concentrations, heart rate, mechanical nociception thresholds, ocular and dehorning area temperatures, and average daily gains were evaluated. A linear mixed-effects model with repeated measures was used for statistical analysis. Administration of oral meloxicam, flunixin meglumine, and firocoxib at 2.0 mg/kg resulted in decreased cortisol concentrations compared to placebo-treated controls for the first 24 h postdehorning (AUEC0-24) (P = 0.03). Moreover, firocoxib, flunixin meglumine, and meloxicam attenuated the maximum cortisol concentrations compared to placebo-treated calves (P = 0.04, P= 0.02). In calves treated with flunixin meglumine, cortisol concentrations was reduced at 4 h (P = 0.04) and 8 h (P = 0.02). In addition, analgesic administration was associated with changes in ocular and dehorning area temperature differences (P = 0.09). Carprofen and meloxicam reduced heart rates during the entire study period (P = 0.003). Although a treatment effect (P < 0.0001) was observed in the determination of mechanical nociception threshold among all treatment groups, meloxicam expressed marginally significant effects (P = 0.09) among NSAID treated groups dehorned. A single dose of oral meloxicam, flunixin meglumine, or firocoxib administered at 2.0 mg/kg reduced the acute stress response associated with cautery dehorning. However, carprofen administration was associated with increased cortisol concentrations and dehorning area temperatures for the initial 24 h. Given the changes in pain and stress outcome variables assessed in this study, NSAIDs should be administered at the time of dehorning.

LINflow: a computational pipeline that combines an alignment-free with an alignment-based method to accelerate generation of similarity matrices for prokaryotic genomes.

BACKGROUND: Computing genomic similarity between strains is a prerequisite for genome-based prokaryotic classification and identification. Genomic similarity was first computed as Average Nucleotide Identity (ANI) values based on the alignment of genomic fragments. Since this is computationally expensive, faster and computationally cheaper alignment-free methods have been developed to estimate ANI. However, these methods do not reach the level of accuracy of alignment-based methods. METHODS: Here we introduce LINflow, a computational pipeline that infers pairwise genomic similarity in a set of genomes. LINflow takes advantage of the speed of the alignment-free sourmash tool to identify the genome in a dataset that is most similar to a query genome and the precision of the alignment-based pyani software to precisely compute ANI between the query genome and the most similar genome identified by sourmash. This is repeated for each new genome that is added to a dataset. The sequentially computed ANI values are stored as Life Identification Numbers (LINs), which are then used to infer all other pairwise ANI values in the set. We tested LINflow on four sets, 484 genomes in total, and compared the needed time and the generated similarity matrices with other tools. RESULTS: LINflow is up to 150 times faster than pyani and pairwise ANI values generated by LINflow are highly correlated with those computed by pyani. However, because LINflow infers most pairwise ANI values instead of computing them directly, ANI values occasionally depart from the ANI values computed by pyani. In conclusion, LINflow is a fast and memory-efficient pipeline to infer similarity among a large set of prokaryotic genomes. Its ability to quickly add new genome sequences to an already computed similarity matrix makes LINflow particularly useful for projects when new genome sequences need to be regularly added to an existing dataset.

Genome Resource: Ralstonia solanacearum Phylotype II Sequevar 1 (Race 3 Biovar 2) Strain UW848 From the 2020 U.S. Geranium Introduction.

Ralstonia solanacearum phylotype II sequevar 1 (RsII-1, formerly race 3 biovar 2) causes tomato bacterial wilt, potato brown rot, and Southern wilt of geranium. Strains in RsII-1 cause wilting in potato and tomato at cooler temperatures than tropical lowland R. solanacearum strains. Although periodically introduced, RsII-1 has not established in the United States. This pathogen is of quarantine concern and listed as a Federal Select Agent. We report a rapidly sequenced (<2 days) draft genome of UW848, a RsII-1 isolate introduced to the United States in geranium cuttings in spring 2020. UW848 belongs to the near-clonal cluster of RsII-1 global pandemic strains.

LINbase: a web server for genome-based identification of prokaryotes as members of crowdsourced taxa.

High throughput DNA sequencing in combination with efficient algorithms could provide the basis for a highly resolved, genome phylogeny-based and digital prokaryotic taxonomy. However, current taxonomic practice continues to rely on cumbersome journal publications for the description of new species, which still constitute the smallest taxonomic units. In response, we introduce LINbase, a web server that allows users to genomically circumscribe any group of prokaryotes with measurable DNA similarity and that uses the individual isolate as smallest unit. Since LINbase leverages the concept of Life Identification Numbers (LINs), which are codes assigned to individual genomes based on reciprocal average nucleotide identity, we refer to groups circumscribed in LINbase as LINgroups. Users can associate with each LINgroup a name, a short description, and a URL to a peer-reviewed publication. As soon as a LINgroup is circumscribed, any user can immediately identify query genomes as members and submit comments about the LINgroup. Most genomes currently in LINbase were imported from GenBank, but users can upload their own genome sequences as well. In conclusion, LINbase combines the resolution of LINs with the power of crowdsourcing in support of a highly resolved, genome phylogeny-based digital taxonomy. LINbase is available at http://www.LINbase.org.

Novel Data Sharing Agreement to Accelerate Big Data Translational Research Projects in the One Health Sphere.

When conducting translational research, the ability to share data generated by researchers and clinicians working with for-profit companies is essential, particularly in cases that involve "one health" data (i.e., data that could come from human, animal, or environmental sources). The 1DATA Project, a collaboration between Kansas State University and the University of Missouri, has examined and overcome some of the barriers to sharing this information for "big data" projects. This article discusses some of the obstacles we encountered, and the ways those obstacles can be surmounted via a novel form of Master Sharing Agreement. Developed in collaboration with industry partners, it is presented here as a template for expediting future one health work.

Making Sense of Pharmacovigilance and Drug Adverse Event Reporting: Comparative Similarity Association Analysis Using AI Machine Learning Algorithms in Dogs and Cats.

Drug-associated adverse events cause approximately 30 billion dollars a year of added health care expense, along with negative health outcomes including patient death. This constitutes a major public health concern. The US Food and Drug Administration (FDA) requires drug labeling to include potential adverse effects for each newly developed drug product. With the advancement in incidence of adverse drug events (ADEs) and potential adverse drug events, published studies have mainly concluded potential ADEs from labeling documents obtained from the FDA's preapproval clinical trials, and very few analyzed their research work based on reported ADEs after widespread use of a drug to animal subjects. The aforesaid procedure of deriving practice based on information from preapproval labeling may misrepresent or deprecate the incidence and prevalence of specific ADEs. In this study, we make the most of the recently disseminated ADE data by the FDA for animal drugs and devices used in animals to address this public and welfare concern. For this purpose, we implemented 5 different methods (Pearson distance, Spearman distance, cosine distance, Yule distance, and Euclidean distance) to determine the most efficient and robust approach to properly discover highly associated ADEs from the reported data and accurately exclude noise-induced reported events, while maintaining a high level of correlation precision. Our comparative analysis of ADEs based on an artificial intelligence (AI) approach for the 5 robust similarity methods revealed high ADE associations for 2 drugs used in dogs and cats. In addition, the described distance methods systematically analyzed and compared ADEs from the drug labeling sections with a specific emphasis on analyzing serious ADEs. Our finding showed that the cosine method significantly outperformed all the other methods by correctly detecting and validating ADEs based on the comparative similarity association analysis compared with ADEs reported by preapproval clinical trials, premarket testing, or postapproval complication experience of FDA-approved animal drugs.

Transmammary delivery of firocoxib to piglets reduces stress and improves average daily gain after castration, tail docking, and teeth clipping1.

Painful processing procedures in piglets such as tail docking, castration, and teeth clipping are an emerging animal welfare concern. We hypothesized that transmammary delivery of a nonsteroidal anti-inflammatory drug, firocoxib, would reduce pain associated with processing in piglets. This study compared the pharmacokinetics, efficacy, safety, and tissue residue concentrations of 4 doses of firocoxib (0.5, 1.0, 1.5, or 2.0 mg/kg) administered to sows and delivered to nursing piglets prior to processing. Sixteen sows, 5 ± 2 d postpartum, were randomly assigned to 1 of 4 treatment groups. On day 0, sows received a single intramuscular dose of firocoxib at 7 ± 1 h before piglet surgical castration, tail docking, and teeth clipping (males) or sham handling (females). Firocoxib and cortisol concentrations were determined from selected samples collected from sows and 3 piglets per litter (2 barrows and 1 gilt) at 0, 2, 4, 6, 8, 12, 24, 48, 72, 96, and 120 h after drug administration. On day 21, piglets were weighed and all animals were euthanized and necropsied. Tissues were collected from 3 piglets per litter for histological examination and drug residue analysis. Mean (±SEM) peak plasma firocoxib concentrations (Cmax) were 107.90 ± 15.18, 157.50 ± 24.91, 343.68 ± 78.89, and 452.83 ± 90.27 ng/mL in sows receiving 0.5, 1.0, 1.5, and 2.0 mg/kg firocoxib, respectively, and 9.53 ± 1.21, 31.04 ± 6.79, 53.30 ± 11.1, and 44.03 ± 7.47 ng/mL in their respective piglets. Mean plasma terminal half-life values ranged from 26 to 31 h in sows and 30 to 48 h in piglets. Barrows nursing sows that received 2.0 mg/kg firocoxib had a lower mean plasma cortisol concentration at 1 ± 1 h after processing compared with barrows nursing sows that received 1.0 mg/kg (P = 0.0416) and 0.5 mg/kg of firocoxib (P = 0.0397). From processing to weaning, litters of sows receiving 2.0 mg/kg firocoxib gained more weight than litters of sows that received 0.5 mg/kg (P = 0.008) or 1.0 mg/kg (P = 0.005). No signs of nonsteroidal anti-inflammatory drug toxicity were observed on examination of the kidney, liver, stomach, and small intestine, and concentrations of firocoxib and the descyclopropylmethyl metabolite were below the limit of detection (0.01 µg/g) in all tissues examined from sows and piglets. These findings indicate that maternal delivery of firocoxib to suckling piglets before tail docking and castration may safely reduce processing-induced stress and enhance production by increasing weaning weights.

The Effect of Fun Physical Activities on Sarcopenia Progression among Elderly Residents in Nursing Homes: a Randomized Controlled Trial.

Introduction: Immobilization in the elderly can reduce the size and strength of muscle mass and ultimately lead to sarcopenia, the severity and progression of which can be prevented by exercise. However, due to physical and mental conditions, the elderly may be unable to take full advantage of regular exercise. Therefore, fun exercise through motivation and effective participation of older adults is likely to have positive effects on decreasing the volume and power of muscle mass. The aim of this study was to determine the effect of fun physical activities on the progression of sarcopenia among elderly residents in nursing homes. Methods: This study was a two-group randomized controlled trial conducted in 2014. Sixty three older adults were recruited by the random sampling. The elderly in the fun physical exercise group did the exercise for 8 weeks, three times a week for 20 minutes at a time, and in the control group, the adults did the routine exercises. The Berg Balance Scale, a dynamometer, and the Six-Minute Walk Test were used to measure sarcopenia criteria (balance, muscle strength, distance traveled).The statistical analysis was done by SPSS version 13. Results: The results showed that the mean score of the sarcopenia criterion (balance, distance walked, muscles strength) was significantly increased in the fun physical exercise group than in the control group. Conclusion: The fun physical activity reduces sarcopenia progression through improving balance, increasing distances walked, and strengthening muscles.

Potential Information Loss Due to Categorization of Minimum Inhibitory Concentration Frequency Distributions.

A bacterial isolate's susceptibility to antimicrobial is expressed as the lowest drug concentration inhibiting its visible growth, termed minimum inhibitory concentration (MIC). The susceptibilities of isolates from a host population at a particular time vary, with isolates with specific MICs present at different frequencies. Currently, for either clinical or monitoring purposes, an isolate is most often categorized as Susceptible, Intermediate, or Resistant to the antimicrobial by comparing its MIC to a breakpoint value. Such data categorizations are known in statistics to cause information loss compared to analyzing the underlying frequency distributions. The U.S. National Antimicrobial Resistance Monitoring System (NARMS) includes foodborne bacteria at the food animal processing and retail product points. The breakpoints used to interpret the MIC values for foodborne bacteria are those relevant to clinical treatments by the antimicrobials in humans in whom the isolates were to cause infection. However, conceptually different objectives arise when inference is sought concerning changes in susceptibility/resistance across isolates of a bacterial species in host populations among different sampling points or times. For the NARMS 1996-2013 data for animal processing and retail, we determined the fraction of comparisons of susceptibility/resistance to 44 antimicrobial drugs of twelve classes of a bacterial species in a given animal host or product population where there was a significant change in the MIC frequency distributions between consecutive years or the two sampling points, while the categorization-based analyses concluded no change. The categorization-based analyses missed significant changes in 54% of the year-to-year comparisons and in 71% of the slaughter-to-retail within-year comparisons. Hence, analyses using the breakpoint-based categorizations of the MIC data may miss significant developments in the resistance distributions between the sampling points or times. Methods considering the MIC frequency distributions in their entirety may be superior for epidemiological analyses of resistance dynamics in populations.

Awareness and Performance of Iranian Nurses with Regard to Health Economics: A Cross-Sectional Study.

BACKGROUND: Health costs have risen everywhere, worldwide, and nurses play a pivotal role in cost savings and in contributing to the financial stability of hospitals. AIM: This study evaluated the awareness and performance of Iranian nursing staff, with regard to health economics. MATERIALS AND METHODS: A total of 175 nurses who worked in three teaching hospitals in Mashhad (Iran) were selected for this descriptive cross-sectional study, and data were gathered via a 27-item questionnaire. Statistical analysis was performed using one-way analysis of variance, multiple regression analysis, and Pearson's correlation coefficient. RESULTS: A total of 78% (n = 39) of nurses did not have a good awareness of health economics. The overall mean score for economic awareness was 5.9 ± 2.1 (possible range, 0-16), and for economic performance was 26.6 ± 4 (possible range, 0-44). There was a significant relationship between the economic awareness and performance of nurses, and nurses in higher positions had a greater awareness of health economics. CONCLUSIONS: Considering the inadequacy of the health economics awareness and performance of nurses, it is essential that efforts are made to enhance their knowledge and behavior with regard to economic issues and cost saving in all the fields of nursing, through the use of continuing education courses and workshops.

Prediction equations for pulmonary function values in healthy young Iranians aged 8-18 years.

OBJECTIVE: Pulmonary function test (PFT) variables are dependent on height, age and gender. In addition, there is evidence of PFT variation in different ethnic groups. Prediction equations for PFT from a healthy, non-smoking, urban young population in the city of Mashhad (north-east Iran) have been derived. METHODOLOGY: Prediction equations for normal pulmonary function were derived from 336 healthy, non-smoking subjects, including 187 males (height 103-188.5 cm) and 149 females (height 104-183 cm) aged 8-18 years. The subjects underwent measurement of spirometric flow and volume. The following variables were measured: FVC, FEV1, maximal mid-expiratory flow (MMEF), PEF, maximal expiratory flow at 75, 50 and 25% of the FVC (MEF75, MEF50, and MEF25, respectively), tidal volume (VT), inspiratory reserve volume (IRV), expiratory reserve volume (ERV), inspiratory capacity (IC), and vital capacity (VC). Regression analysis using height and age as independent variables was applied to provide predicted values for both genders. RESULTS: There were positive correlations for each pulmonary function variable with height and age. The largest positive correlations were found for FEV1 with height and age, in both genders. Comparison of PFT variables derived from the equations obtained in the present study showed significant differences to those calculated from several previously published equations (P < 0.001 for most variables). For example, the values of FVC and FEV1 derived from the equations obtained in the present study were 2.83 +/- 0.99 and 2.50 +/- 0.89 for males, and 2.41 +/- 0.54 and 2.19 +/- 0.53 for females, while the values derived from the equations of the European Community for Steel and Coal study were 3.12 +/- 1.06 and 2.62 +/- 0.89 for males and 2.79 +/- 0.67 and 3.35 +/- 0.57 for females, respectively. CONCLUSIONS: A set of PFT reference values and prediction equations for both genders has been derived using a relatively large, healthy, non-smoking Iranian young population, and has generated results that differ from several other prediction equations.