A corepressor participates in LexA-independent regulation of error-prone polymerases in Acinetobacter

The DNA damage response of the multidrug-resistant pathogen Acinetobacter baumannii, which induces mutagenic UmuD′2C error-prone polymerases, differs from that of many bacteria. Acinetobacter species lack a LexA repressor, but induce gene transcription after DNA damage. One regulator, UmuDAb, binds to and represses the promoters of the multiple A. baumannii ATCC 17978 umuDC alleles and the divergently transcribed umuDAb and ddrR genes. ddrR is unique to the genus Acinetobacter and of unknown function. 5\u27 RACE (rapid amplification of cDNA ends) PCR mapping of the umuDAb and ddrR transcriptional start sites revealed that their −35 promoter elements overlapped the UmuDAb binding site, suggesting that UmuDAb simultaneously repressed expression of both genes by blocking polymerase access. This coordinated control of ddrR and umuDAb suggested that ddrR might also regulate DNA damage-inducible gene transcription. RNA-sequencing experiments in 17 978 ddrR− cells showed that ddrR regulated approximately 25 % (n=39) of the mitomycin C-induced regulon, with umuDAb coregulating 17 of these ddrR-regulated genes. Eight genes (the umuDC polymerases, umuDAb and ddrR) were de-repressed in the absence of DNA damage, and nine genes were uninduced in the presence of DNA damage, in both ddrR and umuDAb mutant strains. These data suggest ddrR has multiple roles, both as a co-repressor and as a positive regulator of DNA damage-inducible gene transcription. Additionally, 57 genes were induced by mitomycin C in the ddrR mutant but not in wild-type cells. This regulon contained multiple genes for DNA replication, recombination and repair, transcriptional regulators, RND efflux, and transport. This study uncovered another regulator of the atypical DNA damage response of this genus, to help describe how this pathogen acquires drug resistance through its expression of the error-prone polymerases under DdrR and UmuDAb control

Comparative Performance of Three Length-Based Mortality Estimators

Length‐based methods provide alternatives for estimating the instantaneous total mortality rate (Z) in exploited marine populations when data are not available for age‐based methods. We compared the performance of three equilibrium length‐based methods: the length‐converted catch curve (LCCC), the Beverton–Holt equation (BHE), and the length‐based spawning potential ratio (LB‐SPR) method. The LCCC and BHE are two historically common procedures that use length as a proxy for age. From a truncated length‐frequency distribution of fully selected animals, the LCCC estimates Z with a regression of the logarithm of catch at length by the midpoint of the length‐bins, while the BHE estimates Z as a function of the mean length. The LB‐SPR method is a likelihood‐based population dynamics model, which—unlike the LCCC and BHE—does not require data truncation. Using Monte Carlo simulations across a range of scenarios with varying mortality and life history characteristics, our study showed that neither the LCCC nor the BHE was uniformly superior in terms of bias or root mean square error across simulations, but these estimators performed better than LB‐SPR, which had the largest bias in most cases. Generally, if the ratio of natural mortality (M) to the von Bertalanffy growth rate parameter (K) is low, then the BHE is most preferred, although there is likely to be high bias and low precision. If M/K is high, then the LCCC and BHE performed better and similarly to each other. Differences in performance among commonly used truncation methods for the LCCC and BHE were small. The LB‐SPR method did not perform as well as the classical methods but may still be of interest because it provides estimates of a logistic selectivity curve. The M/K ratio provided the most contrast in the performance of the three methods, suggesting that it should be considered for predicting the likely performance of length‐based mortality estimators

Transferrable protection by gut microbes against STING-associated lung disease

STING modulates immunity by responding to bacterial and endogenous cyclic dinucleotides (CDNs). Humans and mice with STING gain-of-function mutations develop a syndrome known as STING-associated vasculopathy with onset in infancy (SAVI), which is characterized by inflammatory or fibrosing lung disease. We hypothesized that hyperresponsiveness of gain-of-function STING to bacterial CDNs might explain autoinflammatory lung disease in SAVI mice. We report that depletion of gut microbes with oral antibiotics (vancomycin, neomycin, and ampicillin [VNA]) nearly eliminates lung disease in SAVI mice, implying that gut microbes might promote STING-associated autoinflammation. However, we show that germ-free SAVI mice still develop severe autoinflammatory disease and that transferring gut microbiota from antibiotics-treated mice to germ-free animals eliminates lung inflammation. Depletion of anaerobes with metronidazole abolishes the protective effect of the VNA antibiotics cocktail, and recolonization with the metronidazole-sensitive anaerobe Bacteroides thetaiotaomicron prevents disease, confirming a protective role of a metronidazole-sensitive microbe in a model of SAVI

Homeostatic interferon-lambda response to bacterial microbiota stimulates preemptive antiviral defense within discrete pockets of intestinal epithelium

Interferon-lambda (IFN-λ) protects intestinal epithelial cells (IECs) from enteric viruses by inducing expression of antiviral IFN-stimulated genes (ISGs). Here, we find that bacterial microbiota stimulate a homeostatic ISG signature in the intestine of specific pathogen-free mice. This homeostatic ISG expression is restricted to IECs, depends on IEC-intrinsic expression of IFN-λ receptor

Human-Automation Teaming in Track Inspection

This report provides a foundational overview of how the rail industry can approach the design of human-automation teams (HATs), with the goal of improving safety and efficiency in the track inspection process. The authors present a general process for designing HATs, then explore how this design process can be applied to track inspection. The report addresses four track inspection tasks (data collection, data analysis, decision making, and action) and presents broadly applicable considerations for HATs for each task. Railroads and manufacturers may use the design process and general considerations in this report to develop requirements specific to a given inspection technology

Synthesis and reductive chemistry of bimetallic and trimetallic rare-earth metallocene hydrides with (C5H4SiMe3)1− ligands

The reductive chemistry of [Cp\u272Ln(μ–H)(THF)x]y [Ln = Y, Dy, Tb; Cp\u27 = (C5H4SiMe3)1−; x = 2, 0 and y = 2, 3] was examined to determine if these hydrides would be viable precursors for 4fn5d1 Ln2+ ions that could form 5d1-5d1 metal–metal bonded complexes. The hydrides were prepared by reaction of the chlorides, [Cp\u272Ln(μ–Cl)]2, 1-Ln, with allylmagnesium chloride to form the allyl complexes, [Cp\u272Y(η3–C3H5)(THF)], 2-Ln, which were hydrogenolyzed. The solvent-free reaction of solid 2-Ln with 60 psi of H2 gas in a Fischer-Porter apparatus produced, in the Y case, the trimetallic species, [Cp\u272Y(μ–H)]3, 3-Y, and in the Dy and Tb cases, the bimetallic complexes [Cp\u272Ln(μ–H)(THF)]2, 4-Ln (Ln = Dy, Tb). The latter complexes could be converted to 3-Dy and 3-Tb by heating under vacuum. Isopiestic data indicate that 3-Y solvates to 4-Y in THF. Reductions of 4-Y, 4-Dy, and 4-Tb with KC8 in the presence of a chelate such as 2.2.2-cryptand or 18-crown-6 all gave reaction products with intense dark colors characteristic of Ln2+ ions. In the yttrium case, with either chelating agent, the dark green product gives a rhombic EPR spectrum (g1 = 2.01, g2 = 1.99, g3 = 1.98, A = 24.1 G) at 77 K. However, the only crystallographically-characterizable products obtainable from these solutions were Ln3+polyhydride anion complexes of composition, [K(chelate)]{[Cp\u272Ln(μ–H)]3(μ–H)}

Optimism/pessimism and health-related quality of life during pregnancy across three continents: a matched cohort study in China, Ghana, and the United States

<p>Abstract</p> <p>Background</p> <p>Little is known about how optimism/pessimism and health-related quality of life compare across cultures.</p> <p>Methods</p> <p>Three samples of pregnant women in their final trimester were recruited from China, Ghana, and the United States (U.S.). Participants completed a survey that included the Life Orientation Test - Revised (LOT-R, an optimism/pessimism measure), the Short Form 12 (SF-12, a quality of life measure), and questions addressing health and demographic factors. A three-country set was created for analysis by matching women on age, gestational age at enrollment, and number of previous pregnancies. Anovas with post-hoc pairwise comparisons were used to compare results across the cohorts. Multivariate regression analysis was used to create a model to identify those variables most strongly associated with optimism/pessimism.</p> <p>Results</p> <p>LOT-R scores varied significantly across cultures in these samples, with Ghanaian pregnant women being the most optimistic and least pessimistic and Chinese pregnant women being the least optimistic overall and the least pessimistic in subscale analysis. Four key variables predicted approximately 20% of the variance in overall optimism scores: country of origin (p = .006), working for money (p = .05); level of education (p = .002), and ever being treated for emotional issues with medication (p < .001). Quality of life scores also varied by country in these samples, with the most pronounced difference occurring in the vitality measure. U.S. pregnant women reported far lower vitality scores than both Chinese and Ghanaian pregnant women in our sample.</p> <p>Conclusion</p> <p>This research raises important questions regarding what it is about country of origin that so strongly influences optimism/pessimism among pregnant women. Further research is warranted exploring underlying conceptualization of optimism/pessimism and health related quality of life across countries.</p

The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies

Reproducibility is a fundamental requirement in scientific experiments and clinical contexts. Recent publications raise concerns about the reliability of microarray technology because of the apparent lack of agreement between lists of differentially expressed genes (DEGs). In this study we demonstrate that (1) such discordance may stem from ranking and selecting DEGs solely by statistical significance (P) derived from widely used simple t-tests; (2) when fold change (FC) is used as the ranking criterion, the lists become much more reproducible, especially when fewer genes are selected; and (3) the instability of short DEG lists based on P cutoffs is an expected mathematical consequence of the high variability of the t-values. We recommend the use of FC ranking plus a non-stringent P cutoff as a baseline practice in order to generate more reproducible DEG lists. The FC criterion enhances reproducibility while the P criterion balances sensitivity and specificity

Single-cell Analysis of the Neonatal Immune System Across the Gestational Age Continuum

Although most causes of death and morbidity in premature infants are related to immune maladaptation, the premature immune system remains poorly understood. We provide a comprehensive single-cell depiction of the neonatal immune system at birth across the spectrum of viable gestational age (GA), ranging from 25 weeks to term. A mass cytometry immunoassay interrogated all major immune cell subsets, including signaling activity and responsiveness to stimulation. An elastic net model described the relationship between GA and immunome (R=0.85, p=8.75e-14), and unsupervised clustering highlighted previously unrecognized GA-dependent immune dynamics, including decreasing basal MAP-kinase/NFkB signaling in antigen presenting cells; increasing responsiveness of cytotoxic lymphocytes to interferon-a; and decreasing frequency of regulatory and invariant T cells, including NKT cells and MAIT cells. Knowledge gained from the analysis of the neonatal immune landscape across GA provides a mechanistic framework to understand the unique susceptibility of preterm infants to both hyper-inflammatory diseases and infections

(p)ppGpp and c-di-AMP Homeostasis Is Controlled by CbpB in Listeria monocytogenes

The facultative intracellular pathogen Listeria monocytogenes, like many related Firmicutes, uses the nucleotide second messenger cyclic di-AMP (c-di-AMP) to adapt to changes in nutrient availability, osmotic stress, and the presence of cell wall-acting antibiotics. In rich medium, c-di-AMP is essential; however, mutations in cbpB, the gene encoding c-di-AMP binding protein B, suppress essentiality. In this study, we identified that the reason for cbpB-dependent essentiality is through induction of the stringent response by RelA. RelA is a bifunctional RelA/SpoT homolog (RSH) that modulates levels of (p)ppGpp, a secondary messenger that orchestrates the stringent response through multiple allosteric interactions. We performed a forward genetic suppressor screen on bacteria lacking c-di-AMP to identify genomic mutations that rescued growth while cbpB was constitutively expressed and identified mutations in the synthetase domain of RelA. The synthetase domain of RelA was also identified as an interacting partner of CbpB in a yeast-2-hybrid screen. Biochemical analyses confirmed that free CbpB activates RelA while c-di-AMP inhibits its activation. We solved the crystal structure of CbpB bound and unbound to c-di-AMP and provide insight into the region important for c-di-AMP binding and RelA activation. The results of this study show that CbpB completes a homeostatic regulatory circuit between c-di-AMP and (p)ppGpp in Listeria monocytogenes.</div