Effects of Tylosin, a Direct-Fed Microbial and Feedlot Pen Environment on Phenotypic Resistance among Enterococci Isolated from Beef Cattle Feces

In two sequential replicates (n = 90 and n = 96 feedlot finisher cattle, respectively) we measured the impact of an Enterococcus faecium-based probiotic (DFM) and an altered feedlot pen environment on antimicrobial resistance among fecal enterococci in cattle fed (or, not fed) the macrolide tylosin. Diluted fecal samples were spiral-plated on plain and antibiotic-supplemented m-Enterococcus agar. In the first replicate, tylosin significantly (p < 0.05) increased the relative quantity of erythromycin-resistant enterococci. This effect was diminished in cattle fed the DFM in conjunction with tylosin, indicating a macrolide susceptible probiotic may help mitigate resistance. A similar observed effect was not statistically significant (p > 0.05) in the second replicate. Isolates were speciated and resistance phenotypes were obtained for E. faecium and E. hirae. Susceptible strains of bacteria fed as DFM may prove useful for mitigating the selective effects of antibiotic use; however, the longer-term sustainability of such an approach remains unclear.

The role of pseudo-overdominance in maintaining inbreeding depression

Classical models ignoring linkage predict that deleterious recessive mutations purge or fix within inbred populations, yet these often retain moderate to high segregating load. True overdominance generates balancing selection that sustains inbreeding depression even in inbred populations but is rare. In contrast, arrays of mildly deleterious recessives linked in repulsion may occur commonly enough to generate pseudo-overdominance and sustain segregating load. We used simulations to explore how long pseudo-overdominant regions (POD's) persist following their creation via hybridization between populations fixed for alternative mutations at linked loci. Balancing haplotype loads, tight linkage, and moderate to strong cumulative selective effects serve to maintain POD's, suggesting that POD's may most often arise and persist in low recombination regions (e.g., inversions). Selection and drift unbalance the load, eventually eliminating POD's, but this process is very slow when pseudo-overdominance is strong. Background selection across the genome accelerates the loss of weak POD's but reinforces strong POD's in inbred populations by disfavoring homozygotes. Further modeling and studies of POD dynamics within populations could help us understand how POD's affect persistence of the load and how inbred mating systems evolve.

Extreme purifying selection against point mutations in the human genome

Genome sequencing of tens of thousands of human individuals has recently enabled the measurement of large selective effects for mutations to protein-coding genes. Here we describe a new method, called ExtRaINSIGHT, for measuring similar selective effects at individual sites in noncoding as well as in coding regions of the human genome. ExtRaINSIGHT estimates the prevalance of strong purifying selection, or "ultraselection" (λs), as the fractional depletion of rare single-nucleotide variants (minor allele frequency <0.1%) in a target set of genomic sites relative to matched sites that are putatively neutrally evolving, in a manner that controls for local variation and neighbor-dependence in mutation rate. We show using simulations that, above an appropriate threshold, λs is closely related to the average site-specific selection coefficient against heterozygous point mutations, as predicted at mutation-selection balance. Applying ExtRaINSIGHT to 71,702 whole genome sequences from gnomAD v3, we find particularly strong evidence of ultraselection in evolutionarily ancient miRNAs and neuronal protein-coding genes, as well as at splice sites. Moreover, our estimated selection coefficient against heterozygous amino-acid replacements across the genome (at 1.4%) is substantially larger than previous estimates based on smaller sample sizes. By contrast, we find weak evidence of ultraselection in other noncoding RNAs and transcription factor binding sites, and only modest evidence in ultraconserved elements and human accelerated regions. We estimate that ~0.3-0.5% of the human genome is ultraselected, with one third to one half of ultraselected sites falling in coding regions. These estimates suggest ~0.3-0.4 lethal or nearly lethal de novo mutations per potential human zygote, together with ~2 de novo mutations that are more weakly deleterious. Overall, our study sheds new light on the genome-wide distribution of fitness effects for new point mutations by combining deep new sequencing data sets and classical theory from population genetics.

Breast fibroadenomas are less frequent in women with uterine fibroids

BACKGROUND: The etiology and incidence of Fibroadenoma (FA) as the most frequent benign breast mass and uterine fibroma (UF) as the most benign gynecological disorders are unknown. OBJECTIVE: Considering the dependency of FA and UF to sex hormones, our objective was to investigate the association of these two neoplasms. METHODS: Among women attending the hospital Gynecology Clinic, those with typical uterine fibroids in their pelvic ultrasound constituted cases and those with no pathology the controls. All participants underwent breast ultrasound for FA. Criteria for diagnosis of FA were a typical image for lumps <2 cm in women aged <40 and <1 cm in ages ≥ 40, and a histologic diagnosis for all other participants or larger lumps. RESULTS: The mean age of cases and controls was 42.4 and 41.7 years, respectively. FA were detected in 140 (23%) of all participants; 19.7% of the cases, and 26.2% of the controls (p = 0.07). FA and UF had a borderline reverse association (OR = 0.69, 95% CI = 0.46–1.02, p = 0.07). CONCLUSION: The incidence of FA is lower in patients with UF. Further studies are needed to find the selective effects of estrogen and progesterone on hormonal receptors of these two tumors.

"Is That Your Final Decision? Multi-Stage Profiling, Selective Effects, and Article 22 of the GDPR"

•Provisions in many data protection laws require a legal basis, or at the very least safeguards, for significant, solely automated decisions; Article 22 of the GDPR is the most notable. •Little attention has been paid to Article 22 in light of decision-making processes with multiple stages, potentially both manual and automated, and which together might impact upon decision subjects in different ways. •Using stylised examples grounded in real-world systems, we raise five distinct complications relating to interpreting Article 22 in the context of such multi-stage profiling systems. •These are: the potential for selective automation on subsets of data subjects despite generally adequate human input; the ambiguity around where to locate the decision itself; whether ‘significance’ should be interpreted in terms of any potential effects or only selectively in terms of realised effects; the potential for upstream automation processes to foreclose downstream outcomes despite human input; and that a focus on the final step may distract from the status and importance of upstream processes. •We argue that the nature of these challenges will make it difficult for courts or regulators to distil a set of clear, fair and consistent interpretations for many realistic contexts.

Cytokines Stimulated by IL-33 in Human Skin Mast Cells: Involvement of NF-κB and p38 at Distinct Levels and Potent Co-Operation with FcεRI and MRGPRX2

The IL-1 family cytokine IL-33 activates and re-shapes mast cells (MCs), but whether and by what mechanisms it elicits cytokines in MCs from human skin remains poorly understood. The current study found that IL-33 activates CCL1, CCL2, IL-5, IL-8, IL-13, and TNF-α, while IL-1β, IL-6, IL-31, and VEGFA remain unaffected in cutaneous MCs, highlighting that each MC subset responds to IL-33 with a unique cytokine profile. Mechanistically, IL-33 induced the rapid (1–2 min) and durable (2 h) phosphorylation of p38, whereas the phosphorylation of JNK was weaker and more transient. Moreover, the NF-κB pathway was potently activated, as revealed by IκB degradation, increased nuclear abundance of p50/p65, and vigorous phosphorylation of p65. The activation of NF-κB occurred independently of p38 or JNK. The induced transcription of the cytokines selected for further study (CCL1, CCL2, IL-8, TNF-α) was abolished by interference with NF-κB, while p38/JNK had only some cytokine-selective effects. Surprisingly, at the level of the secreted protein products, p38 was nearly as effective as NF-κB for all entities, suggesting post-transcriptional involvement. IL-33 did not only instruct skin MCs to produce selected cytokines, but it also efficiently co-operated with the allergic and pseudo-allergic/neurogenic activation networks in the production of IL-8, TNF-α, CCL1, and CCL2. Synergism was more pronounced at the protein than at the mRNA level and appeared stronger for MRGPRX2 ligands than for FcεRI. Our results underscore the pro-inflammatory nature of an acute IL-33 stimulus and imply that especially in combination with allergens or MRGPRX2 agonists, IL-33 will efficiently amplify skin inflammation and thereby aggravate inflammatory dermatoses.