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Papers by Laura Jenniches

Proceedings of the National Academy of Sciences of the United States of America, Jun 15, 2021

RNA decay is a crucial mechanism for regulating gene expression in response to environmental stre... more RNA decay is a crucial mechanism for regulating gene expression in response to environmental stresses. In bacteria, RNA-binding proteins (RBPs) are known to be involved in post- transcriptional regulation, but their global impact on RNA half-lives has not been extensively studied. To shed light on the role of the major RBPs ProQ and CspC/E in maintaining RNA stability, we performed RNA sequencing ofSalmonella entericaover a time course following treatment with the transcription initiation inhibitor rifampicin (RIF-seq) in the presence and absence of these RBPs. We develop a hierarchical Bayesian model that corrects for confounding factors in rifampicin RNA stability assays and enables us to identify differentially decaying transcripts transcriptome-wide. Our analysis revealed that the median RNA half-life inSalmonellain early stationary phase is less than 1 minute, a third of previous estimates. We found that over half of the 500 most long-lived transcripts are bound by at least one...

To compare theoretical predictions and experimental results, we require not only a precise knowle... more To compare theoretical predictions and experimental results, we require not only a precise knowledge of the observables themselves, but also a good understanding of the uncertainty introduced by missing higher orders in perturbative QCD. In this work, we present a method which combines effective field theories and perturbative QCD to predict the effect of New Physics on measurements at the LHC and at other future colliders. We use heavy-quark, heavy-scalar and soft-collinear effective theory to calculate a three-body cascade decay at NLO QCD in the expansion-by-regions formalism. The second project focuses on theoretical uncertainties in perturbative QCD. We perform a study of theoretical uncertainties obtained using the traditional scale-variation and the Cacciari-Houdeau approach [1], which uses Bayesian statistics to estimate missing-higher-order uncertainties. In addition, we discuss an extension of the Cacciari-Houdeau approach to observables with hadrons in the initial state.

Nature Communications, 2020

Bacteria of the genus Bacteroides are common members of the human intestinal microbiota and impor... more Bacteria of the genus Bacteroides are common members of the human intestinal microbiota and important degraders of polysaccharides in the gut. Among them, the species Bacteroides thetaiotaomicron has emerged as the model organism for functional microbiota research. Here, we use differential RNA sequencing (dRNA-seq) to generate a single-nucleotide resolution transcriptome map of B. thetaiotaomicron grown under defined laboratory conditions. An online browser, called ‘Theta-Base’ (www.helmholtz-hiri.de/en/datasets/bacteroides), is launched to interrogate the obtained gene expression data and annotations of ~4500 transcription start sites, untranslated regions, operon structures, and 269 noncoding RNA elements. Among the latter is GibS, a conserved, 145 nt-long small RNA that is highly expressed in the presence of N-acetyl-D-glucosamine as sole carbon source. We use computational predictions and experimental data to determine the secondary structure of GibS and identify its target gen...

Frontiers in Cellular and Infection Microbiology, 2020

Enterococcus faecalisandfaeciumare two major representative clinical strains of the Enterococcus ... more Enterococcus faecalisandfaeciumare two major representative clinical strains of the Enterococcus genus and are sadly notorious to be part of the top agents responsible for nosocomial infections. Despite their critical implication in worldwide public healthcare, essential and available resources such as deep transcriptome annotations remain poor, which also limits our understanding of post-transcriptional control small regulatory RNA (sRNA) functions in these bacteria. Here, using the dRNA-seq technique in combination with ANNOgesic analysis, we successfully mapped and annotated transcription start sites (TSS) of bothE. faecalis V583andE. faecium AUS0004at single nucleotide resolution. Analyzing bacteria in late exponential phase, we capture ~40% (E. faecalis) and 43% (E. faecium) of the annotated protein-coding genes, determine 5′ and 3′ UTR (untranslated region) length, and detect instances of leaderless mRNAs. The transcriptome maps revealed sRNA candidates in both bacteria, some ...

ABSTRACTThe Gram-positive human pathogen Clostridioides difficile has emerged as the leading caus... more ABSTRACTThe Gram-positive human pathogen Clostridioides difficile has emerged as the leading cause of antibiotic-associated diarrhea. Despite growing evidence for a role of Hfq in RNA-based gene regulation in C. difficile, little is known about the bacterium’s transcriptome architecture and mechanisms of post-transcriptional control. Here, we have applied a suite of RNA-centric techniques, including transcription start site mapping, transcription termination mapping and Hfq RIP-seq, to generate a single-nucleotide resolution RNA map of C. difficile 630. Our transcriptome annotation provides information about 5’ and 3’ untranslated regions, operon structures and non-coding regulators, including 42 sRNAs. These transcriptome data are accessible via an open-access browser called ‘Clost-Base’. Our results indicate functionality of many conserved riboswitches and predict novel cis-regulatory elements upstream of MDR-type ABC transporters and transcriptional regulators. Recent studies hav...

Proceedings of 13th International Symposium on Radiative Corrections (Applications of Quantum Field Theory to Phenomenology) — PoS(RADCOR2017), 2018

We discuss the computation of the next-to-leading order electroweak corrections to Higgs-boson pr... more We discuss the computation of the next-to-leading order electroweak corrections to Higgs-boson production through gluon fusion in the Two-Higgs-Doublet Model. In particular, we focus on the production of a neutral, scalar Higgs boson. We provide results in different renormalization schemes. Our results can also be used in order to describe the corresponding electroweak corrections of the Higgs-boson decay into two gluons at next-to-leading order.

Journal of High Energy Physics, 2018

We have computed the two-loop, electroweak corrections to the production of a light and a heavy n... more We have computed the two-loop, electroweak corrections to the production of a light and a heavy neutral, scalar Higgs-boson through the important gluon fusion process in the Two-Higgs-Doublet Model. We provide our results in various renormalization schemes for different scenarios and benchmark points, which will be valuable for experimental studies at the LHC. We describe the technicalities of our two-loop calculation and augment it by a phenomenological discussion. Our results are also applicable to the gluonic neutral, scalar Higgs-boson decays.

Physics Letters B, 2017

Kinematic edges of cascade decays of new particles produced in high-energy collisions may provide... more Kinematic edges of cascade decays of new particles produced in high-energy collisions may provide important constraints on the involved particles' masses. For the exemplary case of gluino decayg → qqχ into a pair of quarks and a neutralino through a squark resonance, we study the hadronic invariant mass distribution in the vicinity of the kinematic edge. We perform a next-to-leading order calculation in the strong coupling α s and the ratio of squark width and squark mass Γq/mq, based on a systematic expansion in Γq/mq. The separation into hard, collinear and soft contributions elucidates the process-dependent and universal features of distributions in the edge region, represented by on-shell decay matrix elements, universal jet functions and a soft function that depends on the resonance propagator and soft Wilson lines.

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Journal of High Energy Physics, 2016

We present a consistent renormalization scheme for the CP-conserving Two-Higgs-Doublet Model base... more We present a consistent renormalization scheme for the CP-conserving Two-Higgs-Doublet Model based on MS renormalization of the mixing angles and the soft-Z 2symmetry-breaking scale M sb in the Higgs sector. This scheme requires to treat tadpoles fully consistently in all steps of the calculation in order to provide gauge-independent Smatrix elements. We show how bare physical parameters have to be defined and verify the gauge independence of physical quantities by explicit calculations in a general R ξ-gauge. The procedure is straightforward and applicable to other models with extended Higgs sectors. In contrast to the proposed scheme, the MS renormalization of the mixing angles combined with popular on-shell renormalization schemes gives rise to gauge-dependent results already at the one-loop level. We present explicit results for electroweak NLO corrections to selected processes in the appropriately renormalized Two-Higgs-Doublet Model and in particular discuss their scale dependence.

Journal of High Energy Physics, 2015

We consider two approaches to estimate and characterise the theoretical uncertainties stemming fr... more We consider two approaches to estimate and characterise the theoretical uncertainties stemming from the missing higher orders in perturbative calculations in Quantum Chromodynamics: the traditional one based on renormalisation and factorisation scale variation, and the Bayesian framework proposed by Cacciari and Houdeau. We estimate uncertainties with these two methods for a comprehensive set of more than thirty different observables computed in perturbative Quantum Chromodynamics, and we discuss their performance in properly estimating the size of the higher order terms that are known. We find that scale variation with the conventional choice of varying scales within a factor of two of a central scale gives uncertainty intervals that tend to be somewhat too small to be interpretable as 68% confidence-level-heuristic ones. We propose a modified version of the Bayesian approach of Cacciari and Houdeau which performs well for non-hadronic observables and, after an appropriate choice of the relevant expansion parameter for the perturbative series, for hadronic ones too.

For the purpose of understanding recent cosmic ray measurements in the energy region below 10 GeV... more For the purpose of understanding recent cosmic ray measurements in the energy region below 10 GeV it is important to obtain good knowledge of the charge-sign dependent modulation caused by interplanetary magnetic fields. Existing three-dimensional time-dependent models of the heliosphere can be constrained further using series of measurements of the low-energy cosmic ray fluxes over the course of a solar