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Ralstonia solanacearum species complex (RSSC) strains are bacteria that colonize plant xylem tissue and cause vascular wilt diseases. However, individual strains vary in host range, optimal disease temperatures and physiological traits. To increase our understanding of the evolution, diversity and biology of the RSSC, we performed a meta-analysis of 100 representative RSSC genomes. These 100 RSSC genomes contain 4940 genes on average, and a pangenome analysis found that there are 3262 genes in the core genome (~60 % of the mean RSSC genome) with 13 128 genes in the extensive flexible genome. A core genome phylogenetic tree and a whole-genome similarity matrix aligned with the previously named species ( R. solanacearum , R. pseudosolanacearum , R. syzygii ) and phylotypes (I–IV). These analyses also highlighted a third unrecognized sub-clade of phylotype II. Additionally, we identified differences between phylotypes with respect to gene content and recombination rate, and we delineated population clusters based on the extent of horizontal gene transfer. Multiple analyses indicate that phylotype II is the most diverse phylotype, and it may thus represent the ancestral group of the RSSC. We also used our genome-based framework to test whether the RSSC sequence variant (sequevar) taxonomy is a robust method to define within-species relationships of strains. The sequevar taxonomy is based on alignments of a single conserved gene (egl). Although sequevars in phylotype II describe monophyletic groups, the sequevar system breaks down in the highly recombinogenic phylotype I, which highlights the need for an improved, cost-effective method for genotyping strains in phylotype I. Finally, we enabled quick and precise genome-based identification of newly sequenced RSSC strains by assigning Life Identification Numbers (LINs) to the 100 strains and by circumscribing the RSSC and its sub-groups in the LINbase Web service.

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 di [ABSTRACT FROM AUTHOR]

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 β-Galactosidase and porcine reproductive respiratory virus infection. Data support the preclinical development of PMCs for imaging and delivery targeting cancer and infectious disease. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 (C max ) 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Background: Health costs have risen everywhere, worldwide, and nurses play a pivotal role in cost savings and in contributing to the fi nancial 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 fi elds of nursing, through the use of continuing education courses and workshops. [ABSTRACT FROM AUTHOR]

Background: A common, early postpartum concern of the breastfeeding mother is nipple pain. Because of a lack of effective treatment and opposing results about lanolin, we decided to compare the effect of lanolin ointment and aloe Vera gel on nipple soreness treatment. Methods: This clinical blind trial was performed in Mashhad, Iran, from February 2008 to May 2009. Sampling was nonrandom and purposive, and then samples were divided randomly into two groups. After first applying the preparation on their arms to check for allergy symptoms, mothers were instructed to then rub the preparation on their nipples three times a day for seven consecutive days, each application performed after feeding the baby. Mothers were to let the preparation dry and not to wash it before the next feeding. Researcher pretreatment at the third and seventh day filled out the Storr scale with interviews and examinations. There were no complications in mothers and infants because of the drug's usage The data was then analyzed with Spss 11.5 and Mann-Whitney, Student's t-test, and t-paired tests. Results: A total of 100 samples enrolled with 50 samples in the lanolin group and 50 samples in the aloe vera group. In aloe Vera group Nipple soreness scoring decreased significantly at the third day versus pretreatment (p=0.00) and also at the seventh day versus pretreatment and the third day (p=0.000). Nipple soreness scoring decreased significantly at the third day versus pretreatment (p=0.00) and also at the seventh day versus pretreatment and the third day (p=0.000, p=0.001). The two groups were homogenous at the pretreatment day (p=0.711), but there was a significant difference between the two groups at the third and seventh day (p=0.048, p=0.003). Conclusion: Aloe Vera is more effective than lanolin on nipple soreness healing. [ABSTRACT FROM AUTHOR]

Most Ralstonia solanacearum species complex strains cause bacterial wilts in tropical or subtropical zones, but the group known as race 3 biovar 2 (R3bv2) is cool virulent and causes potato brown rot at lower temperatures. R3bv2 has invaded potato-growing regions around the world but is not established in the United States. Phylogenetically, R3bv2 corresponds to a subset of the R. solanacearum phylotype IIB clade, but little is known about the distribution of the cool virulence phenotype within phylotype IIB. Therefore, genomes of 76 potentially cool virulent phylotype IIB strains and 30 public genomes were phylogenetically analyzed. A single clonal lineage within the sequevar 1 subclade of phylotype IIB that originated in South America has caused nearly all brown rot outbreaks worldwide. To correlate genotypes with relevant phenotypes, we quantified virulence of 10 Ralstonia strains on tomato and potato at both 22 and 28°C. Cool virulence on tomato did not predict cool virulence on potato. We found that cool virulence is a quantitative trait. Strains in the sequevar 1 pandemic clonal lineage caused the most disease, whereas other R3bv2 strains were only moderately cool virulent. However, some non-R3bv2 strains were highly cool virulent and aggressively colonized potato tubers. Thus, cool virulence is not consistently correlated with strains historically classified as the R3bv2 group. To aid in the detection of sequevar 1 strains, this group was genomically delimited in the LINbase web server, and a sequevar 1 diagnostic primer pair was developed and validated. We discuss implications of these results for the R3bv2 definition., Competing Interests: The author(s) declare no conflict of interest.

As a central organizing principle of biology, bacteria and archaea are classified into a hierarchical structure across taxonomic ranks from kingdom to subspecies. Traditionally, this organization was based on observable characteristics of form and chemistry but recently, bacterial taxonomy has been robustly quantified using comparisons of sequenced genomes, as exemplified in the Genome Taxonomy Database (GTDB). Such genome-based taxonomies resolve genomes down to genera and species and are useful in many contexts yet lack the flexibility and resolution of a fine-grained approach. The Life Identification Number (LIN) approach is a common, quantitative framework to tie existing (and future) bacterial taxonomies together, increase the resolution of genome-based discrimination of taxa, and extend taxonomic identification below the species level in a principled way. Utilizing LINgroup as an organizational concept helps resolve some of the confusion and unforeseen negative effects resulting from nomenclature changes of microorganisms that are closely related by overall genomic similarity (often due to genome-based reclassification). Our experimental results demonstrate the value of LINs and LINgroups in mapping between taxonomies, translating between different nomenclatures, and integrating them into a single taxonomic framework. They also reveal the robustness of LIN assignment to hyper-parameter changes when considering within-species taxonomic groups.

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.

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., Competing Interests: Life Identification Number and LIN are registered trademarks of This Genomic Life Inc. Lenwood S Heath and Boris A Vinatzer report in accordance with Virginia Tech policies and procedures and their ethical obligation as researchers, that they have a financial interest in This Genomic Life Inc that may be affected by the research reported in this manuscript. They have disclosed those interests fully to Virginia Tech, and they have in place an approved plan for managing any potential conflicts arising from this relationship., (© 2021 Tian et al.)

Ralstonia solanacearum phylotype II sequevar 1 ( Rs II-1, formerly race 3 biovar 2) causes tomato bacterial wilt, potato brown rot, and Southern wilt of geranium. Strains in Rs II-1 cause wilting in potato and tomato at cooler temperatures than tropical lowland R. solanacearum strains. Although periodically introduced, Rs II-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 Rs II-1 isolate introduced to the United States in geranium cuttings in spring 2020. UW848 belongs to the near-clonal cluster of Rs II-1 global pandemic strains.