Sequencing and characterization of Helcococcus ovis: a comprehensive comparative genomic analysis of virulence.

BACKGROUND: Helcococcus ovis (H. ovis) is an emerging bacterial pathogen that commonly causes opportunistic respiratory, mammary, and uterine infections across mammalian hosts. This study applied long- and short-read whole genome sequencing technologies to identify virulence factors in five H. ovis isolates with low, medium, and high virulence phenotypes. RESULTS: The resulting assemblies contained one circular chromosome ranging from 1,744,566 to 1,850,083 bp in length and had a mean GC content of 27.6%. Phylogenetic and nucleotide identity analyses found low virulence strain KG38 to be part of a clade that forms an outgroup apart from the rest of the H. ovis taxon. Assembling the first complete genomes of the species revealed major genomic rearrangements in KG38. One to six prophage regions were identified in each genome. A novel pathogenicity island was found exclusively in the two high virulence strains (KG37 and KG104), along with two hypothetical transmembrane proteins designated as putative VFs. Finally, three zinc ABC transporters and three Type-II/IV secretion systems were identified as possible virulence determinants in this species. The low virulence strain KG38 has fewer intact paralogs of these operons in its genome compared to the higher virulence isolates, which strongly suggests a role in virulence. This strain is also missing four putative virulence factors (VFs) found in other isolates associated with adherence (collagen adhesin precursor), immune evasion (choline-binding protein A and a PspA-like hypothetical protein) and cell wall synthesis (glycerol-3-phosphate cytidylyltransferase). CONCLUSIONS: In this study, we assembled reference-quality complete genomes for five H. ovis strains to identify putative virulence factors. Phylogenetic analyses of H. ovis isolates revealed the presence of a clade representing a potentially novel species within the genus Helcococcus. A novel pathogenicity island and two hypothetical transmembrane proteins were found exclusively in high-virulence strains. The identification of Zinc ABC transporters and Type-II/IV secretion systems as possible virulence determinants, along with the differences in operon content between the low and high virulence isolates, strongly suggests they also play a role in the bacterium's pathogenicity. Taken together, these findings are a valuable first step toward deciphering the pathogenesis of H. ovis infections.

Heat abatement during the pre-weaning period: effects on growth, feed efficiency, metabolites, and insulin of male Holstein calves.

Heat stress abatement strategies for pre-weaned dairy calves are seldom evaluated. An experiment was conducted to evaluate the effects of housing calves under a barn and provision of fans to calves housed under a barn on calfhood performance. The experiment was conducted in a dairy in southern Georgia, USA. Male Holstein calves (n = 60; 0 to 68 day of age) were assigned randomly at birth (day 0) to 1 of 3 treatments: hutch outdoors with 50% of its area covered with plywood (control = 20), hutch in a barn with no cooling (SH = 21), and hutch in a barn with ceiling fans (SHF = 19). Body weight (BW) was measured at birth, and total serum protein and wither-height were measured 24 to 48 h after birth. A sub-set of hutches was evaluated for air speed and temperature, and rectal temperature (RT) and respiratory frequency (RF) of calves housed in these hutches were measured at 0900 and 1500 h. Intakes of liquid feed (days 14 to 63) and starter (days 14 to 68) were recorded daily, BW and wither-height were measured weekly, and feed efficiency was calculated weekly. Blood was sampled on days 1, 14, 28, 42, 49, 52, 56, 58, 63, and 65 for the measurement of fatty acids, ß-hydroxybutyrate, glucose, and insulin. The SHF treatment resulted in air velocity 0.56 to 0.83 m/s greater (P < 0.01) than the control and SH treatments, respectively, whereas the control treatment resulted in air temperature 1.2 to 3.2 °C greater (P < 0.01) than the SH and SHF treatments, respectively. The RT of calves in the control treatment was 0.1 to 1.1 °C greater (P ≤ 0.03) than the SH and SHF treatments, respectively, and the control treatment resulted in RF 39.4 to 60.2 mov/min greater (P < 0.01) than the SH and SHF treatments, respectively. Treatment did not (P ≥ 0.27) affect feed efficiency and concentrations of metabolites and insulin, but calves in the control treatment were 2.6 cm shorter (P = 0.03) than calves in the SHF treatments at weaning. Provision of fans to calves housed under a barn reduced RT, RF, but only had a minute impact on wither-height.

Optimization and Testing of a Commercial Viability PCR Protocol to Detect Escherichia coli in Whole Blood.

Bacteremia, specifically if progressed to sepsis, poses a time-sensitive threat to human and animal health. Escherichia coli is a main causative agent of sepsis in humans. The objective was to evaluate a propidium monoazide (PMA)-based viability PCR (vPCR) protocol to detect and quantify live E. coli from whole blood. We optimized the protocol by adding a eukaryotic-specific lysis step prior to PMA exposure, then used spiking experiments to determine the lower limit of detection (LOD) and linear range of quantification. We also compared the vPCR quantification method to standard colony count of spiked inoculum. Lastly, we calculated percent viability in spiked samples containing 50% live cells or 0% live cells. The LOD was 102 CFU/mL for samples containing live cells only and samples with mixed live and heat-killed cells. The linear range of quantification was 102 CFU/mL to 108 CFU/mL (R2 of 0.997) in samples containing only live cells and 103 CFU/mL to 108 CFU/mL (R2 of 0.998) in samples containing live plus heat-killed cells. A Bland-Altman analysis showed that vPCR quantification overestimates compared to standard plate count of the spiked inoculum, with an average bias of 1.85 Log10 CFU/mL across the linear range when only live cells were present in the sample and 1.98 Log10 CFU/mL when live plus heat-killed cells were present. Lastly, percent viability calculations showed an average 89.5% viable cells for samples containing 50% live cells and an average 19.3% for samples containing 0% live cells. In summary, this optimized protocol can detect and quantify viable E. coli in blood in the presence of heat-killed cells. Additionally, the data presented here provide the groundwork for further development of vPCR to detect and quantify live bacteria in blood in clinical settings.

Validation of a fully automated chemiluminescent immunoassay for cattle serum and plasma progesterone measurement.

Introduction: Monitoring circulating progesterone concentration ([P4]) is an important component of basic and applied reproduction research and clinical settings. IMMULITE® 2000 XPi (Siemens Healthineers, Cary, NC) is a newly upgraded fully automated immunoassay system marketed for human use to measure concentrations of different measurands including P4. Objectives: Our objective was therefore to characterize the analytical performance of the IMMULITE® 2000 XPi P4 immunoassay (IPI) across the reportable range in serum and plasma of cattle. Methods: The IPI validation protocols included characterization of the method linearity, within-run, and between-run precision through calculation of the coefficient of variation (CV). The method accuracy was assessed through the calculation of the spiking-recovery (SR) bias across the reportable range (0.2-40.0 ng/mL). Passing-Bablok regression and Bland-Altman plots were used to determine the interlaboratory bias for two laboratories. Three types of observed total error (TEo) were calculated based on the considered type of bias, TEoSR (spiking-recovery), TEoRB (range-based bias), and TEoAB (average-based bias). Results: The IPI was linearly related to the true value (R 2 = 0.997) across the reportable range. The within-run and between-run precision (CV%) of the IPI for both serum and plasma [P4] of clinical relevance (1, 2, 5, and 10 ng/mL) were <5 and <10%, respectively. The TEo reported here for serum and plasma at [P4] of 1 and 5 ng/mL was ~20 and 25%, respectively. Of interest, the three types of TEo were relatively similar regardless of the considered bias. Conclusions: We concluded that the automated IPI provides a precise, accurate, reliable, and safe method for measuring [P4] in both serum and plasma of cattle. Consistent with the manufacturer's recommendations, the serum matrix is more accurate than plasma.

Analytical Validation of the IMMULITE® 2000 XPi Progesterone Assay for Quantitative Analysis in Ovine Serum.

Monitoring circulating progesterone (P4) concentration is an important component of basic and applied reproduction research and clinical settings. IMMULITE® 2000 XPi (Siemens) is a newly upgraded fully automated immunoassay system marketed for human use to measure concentrations of different analytes including P4. Our objective was therefore to characterize the analytical performance of the IMMULITE® 2000 XPi P4 immunoassay across the reportable range in ovine serum. This validation of analytical performance included determining (1) linearity, (2) precision through within-run, and between-run coefficient of variation (CV) calculations, (3) accuracy through bias calculations for spiking-recovery bias and interlaboratory (range and average based) bias for two laboratories across the reportable range (0.2−40 ng/mL). The average within-run and between-run precision (CV%) across the reportable range of the IMMULITE® 2000 XPi P4 immunoassay for serum P4 concentration were both <5%, ranging between 2−8%. The average Observed Total Analytic Error (TEo) reported here for serum P4 concentration across the reportable range was ~30%, ranging from 14.8−59.4%, regardless of the considered bias. Based on these data we conclude that the automated IMMULITE® 2000 XPi P4 immunoassay provides a precise, accurate, reliable, and safe method for measuring P4 concentration ovine serum.

Ovulatory response to GnRH agonist during early and late fall in mares.

This study aimed to assess the ovulatory response of deslorelin acetate during the fall and the response to PGF2α 8 d post-ovulation. One hundred estrous cycles from 22 mares kept in 40° latitude were evaluated. Mares were checked by transrectal ultrasonography until a preovulatory follicle was detected and ovulation induced with deslorelin acetate. Ovulation was confirmed by ultrasonography performed at 24, 36 h post-induction and then repeated at 2-h intervals post-induction. Serum progesterone concentrations and luteal tissue area were determined daily to assess CL function. A dose of PGF2α was administered 8 d post-ovulation and interval to the subsequent ovulation was observed; each mare completed up to five cycles. The effects of local climate on endpoints were analyzed. Cycles were grouped as early (Sept 13, 2020-Oct 31, 2020; n = 55; 22 mares) and late fall (Nov 1, 2020-Dec 31, 2020; n = 45; 20 mares) based on the date of induction. The overall number of cycles with ovulations between 24 and 48 h was 90%. The number of multiple ovulations were similar between early (n = 5) and late (n = 4) fall (P = 0.87). There were no differences in deemed spontaneous ovulations occurring before 24 h between early (n = 6) and late (n = 2) fall (P = 0.29). Two failures to respond to deslorelin by 48 h were recorded in early fall and none in the late fall. The interval from induction to ovulation was similar in early (40.6 ± 0.4 h) and late (41.2 ± 0.5 h) fall (P = 0.55). The percentage of mares ovulating between 36 and 48 h post-deslorelin did not vary between early and late fall (91 vs. 95%, P = 0.21), as did not for ovulation occurring between 38 h and 44 h (62 vs. 60%, P = 0.69). Edema scores varied with time relative to ovulation (P < 0.001) and were lower in late fall (P = 0.01). Progesterone concentrations varied with time (P < 0.001) but did not differ between early and late fall (P = 0.73) and correlated weakly with the luteal area (r = 0.13; P = 0.031). Follicles <35 mm at the PGF2α had a shorter interval to the next ovulation than follicles ≥ 35 mm (9.2 ± 0.5 d vs. 10.6 ± 1.2 d) (P = 0.03). Lower temperature was associated with a smaller follicle size at induction (P = 0.0021) and ovulation (P = 0.009) and lower relative humidity was associated with a larger follicle size at ovulation (P = 0.032). In conclusion, cycling mares displayed a highly efficacious response to deslorelin acetate and apparently normal luteal function during the fall, despite lower edema scores in late fall.

Detection of bulky DNA lesions: DDB2 at the interface of chromatin and DNA repair in eukaryotes.

Bulky DNA damage is corrected by the nucleotide excision repair (NER) pathway. Although the core biochemical mechanism of NER is understood, details including lesion recognition and repair in the context of chromatin remain to be elucidated. As more data become available, the complexity of lesion recognition in chromatin is becoming clear. This review will discuss current knowledge of DNA damage recognition in the context of chromatin, with a focus on the roles of chromatin remodeling and the specific lesion recognition protein DDB2 (DNA damage-binding protein 2) in chromatin repair. Additionally, we propose a model that ubiquitination-mediated DDB2 dissociation from chromatin, not its degradation, is important for GG-NER progression.

Repression of small toxic protein synthesis by the Sib and OhsC small RNAs.

The sequences encoding the QUAD1 RNAs were initially identified as four repeats in Escherichia coli. These repeats, herein renamed SIB, are conserved in closely related bacteria, although the number of repeats varies. All five Sib RNAs in E. coli MG1655 are expressed, and no phenotype was observed for a five-sib deletion strain. However, a phenotype reminiscent of plasmid addiction was observed for overexpression of the Sib RNAs, and further examination of the SIB repeat sequences revealed conserved open reading frames encoding highly hydrophobic 18- to 19-amino-acid proteins (Ibs) opposite each sib gene. The Ibs proteins were found to be toxic when overexpressed and this toxicity could be prevented by coexpression of the corresponding Sib RNA. Two other RNAs encoded divergently in the yfhL-acpS intergenic region were similarly found to encode a small hydrophobic protein (ShoB) and an antisense RNA regulator (OhsC). Overexpression of both IbsC and ShoB led to immediate changes in membrane potential suggesting both proteins affect the cell envelope. Whole genome expression analysis showed that overexpression of IbsC and ShoB, as well as the small hydrophobic LdrD and TisB proteins, has both overlapping and unique consequences for the cell.