Broad-Scale Redistribution of mRNA Abundance and Transcriptional Machinery in Response to Growth Rate in Salmonella Enterica Serovar Typhimurium

We have investigated the connection between the four-dimensional architecture of the bacterial nucleoid and the organism\u27s global gene expression programme. By localizing the transcription machinery and the transcriptional outputs across the genome of the model bacterium Salmonella enterica serovar Typhimurium at different stages of the growth cycle, a surprising disconnection between gene dosage and transcriptional output was revealed. During exponential growth, gene output occurred chiefly in the Ori (origin), Ter (terminus) and NSL (non-structured left) domains, whereas the Left macrodomain remained transcriptionally quiescent at all stages of growth. The apparently high transcriptional output in Ter was correlated with an enhanced stability of the RNA expressed there during exponential growth, suggesting that longer mRNA half-lives compensate for low gene dosage. During exponential growth, RNA polymerase (RNAP) was detected everywhere, whereas in stationary phase cells, RNAP was concentrated in the Ter macrodomain. The alternative sigma factors RpoE, RpoH and RpoN were not required to drive transcription in these growth conditions, consistent with their observed binding to regions away from RNAP and regions of active transcription. Specifically, these alternative sigma factors were found in the Ter macrodomain during exponential growth, whereas they were localized at the Ori macrodomain in stationary phase

Corrigendum: Calibrating spectrometers for measurements of the spectral irradiance caused by solar radiation (2020 Metrologia 57 065027)

We correct an error in equation (60) of the original publication

Calibrating spectrometers for measurements of the spectral irradiance caused by solar radiation

Measuring the spectral irradiance of solar radiation is required in many fields of science and technology. In this work, we present an in-depth discussion of the measuring procedure and required corrections for such measurements. We also describe our measurement uncertainty analysis, which is based on a Monte-Carlo procedure in accordance with the Guide to the expression of uncertainty in measurement (JCGM, Paris, 2008). For this purpose, fifteen uncertainty sources are identified, analyzed and described analytically. As a specific application example, we describe the instrumentation and procedure for determining the spectral irradiance of a solar simulator at the ISO/IEC 17 025 accredited solar cell calibration laboratory ISFH CalTeC and the corresponding measurement uncertainty analysis. Moreover, we provide a Python implementation for this calculation along with the paper. We show that for state-of-the-art instrumentation, significant uncertainty contributions arise from the reference lamp (primary calibration standard), stray light and signal-to-noise ratio. If sharp spectral features are present (which is common, e.g. for Xenon lamps), spectral bandwidth and wavelength uncertainty also contribute significantly to the overall uncertainty. © 2020 BIPM & IOP Publishing Lt

Genetic Regulation of Virulence and Antibiotic Resistance in Acinetobacter baumannii

Multidrug resistant microorganisms are forecast to become the single biggest challenge to medical care in the 21st century. Over the last decades, members of the genus Acinetobacter have emerged as bacterial opportunistic pathogens, in particular as challenging nosocomial pathogens because of the rapid evolution of antimicrobial resistances. Although we lack fundamental biological insight into virulence mechanisms, an increasing number of researchers are working to identify virulence factors and to study antibiotic resistance. Here, we review current knowledge regarding the regulation of virulence genes and antibiotic resistance in Acinetobacter baumannii. A survey of the two-component systems AdeRS, BaeSR, GacSA and PmrAB explains how each contributes to antibiotic resistance and virulence gene expression, while BfmRS regulates cell envelope structures important for pathogen persistence. A. baumannii uses the transcription factors Fur and Zur to sense iron or zinc depletion and upregulate genes for metal scavenging as a critical survival tool in an animal host. Quorum sensing, nucleoid-associated proteins, and non-classical transcription factors such as AtfA and small regulatory RNAs are discussed in the context of virulence and antibiotic resistance

Experimental Determination of the Uncertainty of the Absorption Coefficient of Crystalline Silicon

Based on a combined analysis of spectroscopic ellipsometry, reflectance and transmittance measurements as well as spectrally resolved luminescence measurements and spectral responsivity measurements, we present data of the coefficient of band-to-band absorption of crystalline silicon at 295 K in the wavelength range 250 - 1450 nm. A systematic measurement uncertainty analysis according to the "Guide to the Expression of Uncertainty in Measurements" (GUM) is carried out for each method, showing that the relative uncertainty of the absorption coefficient data so determined is of the order of 0.3% at 300 nm, 1% at 900 nm, 10% at 1200 nm and 180% at 1450 nm. The data are consolidated by comparison of measurements carried out independently at different institutions. The uncertainty of solar cell energy conversion predictions by means of simulations due to the uncertainty of the absorption coefficient data is shown to be of the order of 0.1% relative.Deutsche Bundesstiftung UmweltState of Lower Saxon

The small RNA RssR regulates myo-inositol degradation by Salmonella enterica

Small noncoding RNAs (sRNAs) with putative regulatory functions in gene expression have been identified in the enteropathogen Salmonella enterica serovar Typhimurium (S. Typhimurium). Two sRNAs are encoded by the genomic island GEI4417/4436 responsible for myo-inositol (MI) degradation, suggesting a role in the regulation of this metabolic pathway. We show that a lack of the sRNA STnc2160, termed RssR, results in a severe growth defect in minimal medium (MM) with MI. In contrast, the second sRNA STnc1740 was induced in the presence of glucose, and its overexpression slightly attenuated growth in the presence of MI. Constitutive expression of RssR led to an increased stability of the reiD mRNA, which encodes an activator of iol genes involved in MI utilization, via interaction with its 5'-UTR. SsrB, a response regulator contributing to the virulence properties of salmonellae, activated rssR transcription by binding the sRNA promoter. In addition, the absence of the RNA chaperone Hfq resulted in strongly decreased levels of RssR, attenuated S. Typhimurium growth with MI, and reduced expression of several iol genes required for MI degradation. Considered together, the extrinsic RssR allows fine regulation of cellular ReiD levels and thus of MI degradation by acting on the reiD mRNA stability

Applied system analysis and technology of designing the software

An analogy is made between the stages of applied system analysis and the stages of software Engineerin

The diversity, evolution and ecology of Salmonella in venomous snakes

BACKGROUND: Reptile-associated Salmonella bacteria are a major, but often neglected cause of both gastrointestinal and bloodstream infection in humans globally. The diversity of Salmonella enterica has not yet been determined in venomous snakes, however other ectothermic animals have been reported to carry a broad range of Salmonella bacteria. We investigated the prevalence and diversity of Salmonella in a collection of venomous snakes and non-venomous reptiles. METHODOLOGY/PRINCIPLE FINDINGS: We used a combination of selective enrichment techniques to establish a unique dataset of reptilian isolates to study Salmonella enterica species-level evolution and ecology and used whole-genome sequencing to investigate the relatedness of phylogenetic groups. We observed that 91% of venomous snakes carried Salmonella, and found that a diverse range of serovars (n = 58) were carried by reptiles. The Salmonella serovars belonged to four of the six Salmonella enterica subspecies: diarizonae, enterica, houtanae and salamae. Subspecies enterica isolates were distributed among two distinct phylogenetic clusters, previously described as clade A (52%) and clade B (48%). We identified metabolic differences between S. diarizonae, S. enterica clade A and clade B involving growth on lactose, tartaric acid, dulcitol, myo-inositol and allantoin. SIGNIFICANCE: We present the first whole genome-based comparative study of the Salmonella bacteria that colonise venomous and non-venomous reptiles and shed new light on Salmonella evolution. Venomous snakes examined in this study carried a broad range of Salmonella, including serovars which have been associated with disease in humans such as S. Enteritidis. The findings raise the possibility that venomous snakes could be a reservoir for Salmonella serovars associated with human salmonellosis

Role of a single noncoding nucleotide in the evolution of an epidemic African clade of Salmonella

Salmonella enterica serovar Typhimurium ST313 is a relatively newly emerged sequence type that is causing a devastating epidemic of bloodstream infections across sub-Saharan Africa. Analysis of hundreds ofSalmonellagenomes has revealed that ST313 is closely related to the ST19 group ofSTyphimurium that cause gastroenteritis across the world. The core genomes of ST313 and ST19 vary by only ∼1,000 SNPs. We hypothesized that the phenotypic differences that distinguish AfricanSalmonellafrom ST19 are caused by certain SNPs that directly modulate the transcription of virulence genes. Here we identified 3,597 transcriptional start sites of the ST313 strain D23580, and searched for a gene-expression signature linked to pathogenesis ofSalmonellaWe identified a SNP in the promoter of thepgtEgene that caused high expression of the PgtE virulence factor in AfricanS.Typhimurium, increased the degradation of the factor B component of human complement, contributed to serum resistance, and modulated virulence in the chicken infection model. We propose that high levels of PgtE expression by AfricanSTyphimurium ST313 promote bacterial survival and dissemination during human infection. Our finding of a functional role for an extragenic SNP shows that approaches used to deduce the evolution of virulence in bacterial pathogens should include a focus on noncoding regions of the genome

Mid-depth equatorial tracer tongues in a model of the Atlantic Ocean

Observational estimates of middepth tracer tongues in the equatorial Atlantic are reviewed and are compared with results from several eddy-resolving model simulations. Local maxima of chlorofluorocarbon (CFC) concentrations along the equator at around 1500 m depth are related to mean eastward jet structures in the models at similar depth ranges and can also be identified in several simulated tracer distributions. Similar to the observations, strong eastward jets are located in the simulations 1°–2° north and south of the equator. The model simulations show, in addition, consistent with the CFC observations, weaker jets at around 4°–6°N/S and 8°–10°N/S, suggestive of a large-scale alternating eastward/westward current system in the western tropical Atlantic in this depth range. Lagrangian transport estimates in the model using float diagnostics show a transport of 1–3 Sv in each of the eastward jets 1°–2°N/S off the equator compared to 3–12 Sv throughflow into the South Atlantic, with no seasonal cycle apparent in the transport fractioning. Comparing different model solutions reveals the choice of the subgrid-scale mixing parameterization as important for the amplitudes of the jets. Enhanced (reduced) diapycnal mixing is related to stronger (weaker) jets