Expansion and re-classification of the extracytoplasmic function (ECF) σ factor family.

Extracytoplasmic function σ factors (ECFs) represent one of the major bacterial signal transduction mechanisms in terms of abundance, diversity and importance, particularly in mediating stress responses. Here, we performed a comprehensive phylogenetic analysis of this protein family by scrutinizing all proteins in the NCBI database. As a result, we identified an average of ∼10 ECFs per bacterial genome and 157 phylogenetic ECF groups that feature a conserved genetic neighborhood and a similar regulation mechanism. Our analysis expands previous classification efforts ∼50-fold, enriches many original ECF groups with previously unclassified proteins and identifies 22 entirely new ECF groups. The ECF groups are hierarchically related to each other and are further composed of subgroups with closely related sequences. This two-tiered classification allows for the accurate prediction of common promoter motifs and the inference of putative regulatory mechanisms across subgroups composing an ECF group. This comprehensive, high-resolution description of the phylogenetic distribution of the ECF family, together with the massive expansion of classified ECF sequences and an openly accessible data repository called 'ECF Hub' (https://www.computational.bio.uni-giessen.de/ecfhub), will serve as a powerful hypothesis-generator to guide future research in the field.

H2S sensing for breath analysis with Au functionalized ZnO nanowires.

This work presents a H2S selective resistive gas sensor design based on a chemical field effect transistor (ChemFET) with open gate formed by hundreds of high temperature chemical vapour deposition (CVD) grown zinc oxide nanowires (ZnO NW). The sensing ability of pristine ZnO NWs and surface functionalized ZnO NWs for H2S is analysed systematically. ZnO NWs are functionalized by deposition of discontinuous gold (Au) nanoparticle films of different thicknesses of catalyst layer ranging from 1 to 10 nm and are compared in their gas sensing properties. All experiments were performed in a temperature stabilized small volume compartment with adjustable gas mixture at room temperature. The results allow for a well-founded understanding of signal-to-noise ratio, enhanced response, and improved limit of detection due to the Au functionalisation. Comprehension and controlled application of the beneficial effects of Au catalyst on ZnO NWs allow for the detection of very low H2S concentrations down to 10 ppb, and a theoretically estimated 500 ppt in synthetic air at room temperature.

The identification and characterization of novel transcripts from RNA-seq data.

Owing greatly to the advancement of next-generation sequencing (NGS), the amount of NGS data is increasing rapidly. Although there are many NGS applications, one of the most commonly used techniques 'RNA sequencing (RNA-seq)' is rapidly replacing microarray-based techniques in laboratories around the world. As more and more of such techniques are standardized, allowing technicians to perform these experiments with minimal hands-on time and reduced experimental/operator-dependent biases, the bottleneck of such techniques is clearly visible; that is, data analysis. Further complicating the matter, increasing evidence suggests most of the genome is transcribed into RNA; however, the majority of these RNAs are not translated into proteins. These RNAs that do not become proteins are called 'noncoding RNAs (ncRNAs)'. Although some time has passed since the discovery of ncRNAs, their annotations remain poor, making analysis of RNA-seq data challenging. Here, we examine the current limitations of RNA-seq analysis using case studies focused on the detection of novel transcripts and examination of their characteristics. Finally, we validate the presence of novel transcripts using biological experiments, showing novel transcripts can be accurately identified when a series of filters is applied. In conclusion, novel transcripts that are identified from RNA-seq must be examined carefully before proceeding to biological experiments.

Lipocalin-2 ensures host defense against Salmonella Typhimurium by controlling macrophage iron homeostasis and immune response.

Lipocalin-2 (Lcn2) is an innate immune peptide with pleiotropic effects. Lcn2 binds iron-laden bacterial siderophores, chemo-attracts neutrophils and has immunomodulatory and apoptosis-regulating effects. In this study, we show that upon infection with Salmonella enterica serovar Typhimurium, Lcn2 promotes iron export from Salmonella-infected macrophages, which reduces cellular iron content and enhances the generation of pro-inflammatory cytokines. Lcn2 represses IL-10 production while augmenting Nos2, TNF-α, and IL-6 expression. Lcn2(-/-) macrophages have elevated IL-10 levels as a consequence of increased iron content. The crucial role of Lcn-2/IL-10 interactions was further demonstrated by the greater ability of Lcn2(-/-) IL-10(-/-) macrophages and mice to control intracellular Salmonella proliferation in comparison to Lcn2(-/-) counterparts. Overexpression of the iron exporter ferroportin-1 in Lcn2(-/-) macrophages represses IL-10 and restores TNF-α and IL-6 production to the levels found in wild-type macrophages, so that killing and clearance of intracellular Salmonella is promoted. Our observations suggest that Lcn2 promotes host resistance to Salmonella Typhimurium infection by binding bacterial siderophores and suppressing IL-10 production, and that both functions are linked to its ability to shuttle iron from macrophages.

A MoClo-Compatible Toolbox of ECF Sigma Factor-Based Regulatory Switches for Proteobacterial Chassis.

The construction of complex synthetic gene circuits with predetermined and reliable output depends on orthogonal regulatory parts that do not inadvertently interfere with the host machinery or with other circuit components. Previously, extracytoplasmic function sigma factors (ECFs), a diverse group of alternative sigma factors with distinct promoter specificities, were shown to have great potential as context-independent regulators, but so far, they have only been used in a few model species. Here, we show that the alphaproteobacterium Sinorhizobium meliloti, which has been proposed as a plant-associated bacterial chassis for synthetic biology, has a similar phylogenetic ECF acceptance range as the gammaproteobacterium Escherichia coli. A common set of orthogonal ECF-based regulators that can be used in both bacterial hosts was identified and used to create 2-step delay circuits. The genetic circuits were implemented in single copy in E. coli by chromosomal integration using an established method that utilizes bacteriophage integrases. In S. meliloti, we demonstrated the usability of single-copy pABC plasmids as equivalent carriers of the synthetic circuits. The circuits were either implemented on a single pABC or modularly distributed on 3 such plasmids. In addition, we provide a toolbox containing pABC plasmids compatible with the Golden Gate (MoClo) cloning standard and a library of basic parts that enable the construction of ECF-based circuits in S. meliloti and in E. coli. This work contributes to building a context-independent and species-overarching ECF-based toolbox for synthetic biology applications.

Commissioning of the novel Continuous Angle Multi-energy Analysis spectrometer at the Paul Scherrer Institut.

We report on the commissioning results of the cold neutron multiplexing secondary spectrometer CAMEA (Continuous Angle Multi-Energy Analysis) at the Swiss Spallation Neutron Source at the Paul Scherrer Institut, Switzerland. CAMEA is optimized for efficient data acquisition of scattered neutrons in the horizontal scattering plane, allowing for detailed and rapid mapping of low-energy excitations under extreme sample environment conditions.

Multiparametric ultrasound in torsion of the testicular appendages: a reliable diagnostic tool?

AIM: Torsion of the testicular appendages represents the most common cause of an acute scrotum in prepubertal boys. Its sonographic appearances on gray-scale US and color Doppler US have already been presented in several studies. The aim of this analysis was to expand those already established techniques with strain elastography and thus present typical features of this entity on multiparametric US. MATERIAL AND METHODS: Retrospective analysis of all patients presented to the urological department with an acute scrotum between January 2018 and July 2020 identified eleven patients 6-17 years old (mean, 11.1 years), discharged with the diagnosis torsion of the testicular appendages that were examined with a high-end ultrasound device. Results: On gray-scale US all patients showed a round lesion with heterogenous echotexture adjacent to the upper pole of the testis/epididymis with a diameter of 4 to 11.1 mm (mean, 7.7 mm). Scrotal skin thickening and a concomitant hydrocele were found in 9 (81.8%) and 7 (63.6%) cases, respectively. On color Doppler images, all torsed appendages were avascular and in 9 (81.8%) patients we observed hyperemia of the adjacent epididymis. Strain elastography showed increased tissue stiffness in all documented images. CONCLUSION: Torsion of the testicular appendages has a set of features on multiparametric US. Awareness of this features can facilitate diagnosis of torsion of the testicular appendages and reduce unnecessary surgicalscrotal exploration or unwarranted antibiotic treatment.

Multiplex bacterial PCR in the bronchoalveolar lavage fluid of non-intubated patients with suspected pulmonary infection: a quasi-experimental study.

Background: Early pathogen identification in pulmonary infection is crucial to guide antibacterial therapy and decrease length of hospital stay. We hypothesise that compared to conventional diagnostic methods, a multiplex bacterial polymerase chain reaction assay has a higher diagnostic yield in bronchoalveolar lavage (BAL) fluid and improved clinical outcomes in patients with suspicion of pulmonary infection. Methods: A prospective, monocentric, quasi-experimental, observational study was carried out. Unselected patients with suspected pulmonary infection who underwent bronchoscopy with BAL were included in the study over a period of 1 year. In addition to conventional diagnostic methods, a multiplex PCR bacterial assay was performed in BAL on a 2 week on: 1 week off pre-determined schedule. No therapeutic recommendations were provided to the treating physician. Results: 605 cases were included, 54% of whom were immunosuppressed. Conventional diagnostic methods detected 56% of the bacteria evidenced by PCR. PCR failed to detect bacteria in 4% of the cases with a positive conventional diagnostic result. After bronchoscopy, 42% of the patients received antibacterial therapy for pulmonary infection for a median of 12 antibiotic days. There was no statistically significant difference in length of hospital stay (median 8 versus 8; p=0.839), antibiotic exposure (median 11 versus 14; p=0.362) or number of antibiotics prescribed (median 2 versus 2; p=0.595) between the two groups. Conclusions: A multiplex bacterial PCR detected more bacteria in BAL fluid than conventional diagnostic methods. However, without a specific antibiotic stewardship approach and a clear understanding of the clinical implications of a positive or negative PCR result, the PCR results did not influence clinical outcomes.

Thermoelectrically-Cooled InAs/GaSb Type-II Superlattice Detectors as an Alternative to HgCdTe in a Real-Time Mid-Infrared Backscattering Spectroscopy System.

We report on the development of thermoelectrically cooled (TE-cooled) InAs/GaSb type-II superlattice (T2SL) single element infrared (IR) photodetectors and exemplify their applicability for real-time IR spectroscopy in the mid-infrared in a possible application. As the European Union's Restriction of Hazardous Substances (RoHS) threatens the usage of the state-of-the-art detector material mercury cadmium telluride (MCT), RoHS-compatible alternatives to MCT have to be established for IR detection. We use bandgap engineered InAs/GaSb T2SLs to tailor the temperature-dependent bandgap energy for detection throughout the required spectral range. Molecular beam epitaxy of superlattice samples is performed on GaAs substrates with a metamorphic GaAsSb buffer layer. Photolithographic processing yields laterally-operated T2SL photodetectors. Integrated in a TE-cooled IR detector module, such T2SL photodetectors can be an alternative to MCT photodetectors for spectroscopy applications. Here, we exemplify this by exchanging a commercially available MCT-based IR detector module with our T2SL-based IR detector module in a real-time mid-infrared backscattering spectroscopy system for substance identification. The key detector requirements imposed by the spectroscopy system are a MHz-bandwidth, a broad spectral response, and a high signal-to-noise ratio, all of which are covered by the reported T2SL-based IR detector module. Hence, in this paper, we demonstrate the versatility of TE-cooled InAs/GaSb T2SL photodetectors and their applicability in an IR spectroscopy system.

Increasing workflow development speed and reproducibility with Vectools.

Despite advances in bioinformatics, custom scripts remain a source of difficulty, slowing workflow development and hampering reproducibility. Here, we introduce Vectools, a command-line tool-suite to reduce reliance on custom scripts and improve reproducibility by offering a wide range of common easy-to-use functions for table and vector manipulation. Vectools also offers a number of vector related functions to speed up workflow development, such as simple machine learning and common statistics functions.

ANGIOGENES: knowledge database for protein-coding and noncoding RNA genes in endothelial cells.

Increasing evidence indicates the presence of long noncoding RNAs (lncRNAs) is specific to various cell types. Although lncRNAs are speculated to be more numerous than protein-coding genes, the annotations of lncRNAs remain primitive due to the lack of well-structured schemes for their identification and description. Here, we introduce a new knowledge database "ANGIOGENES" (http://angiogenes.uni-frankfurt.de) to allow for in silico screening of protein-coding genes and lncRNAs expressed in various types of endothelial cells, which are present in all tissues. Using the latest annotations of protein-coding genes and lncRNAs, publicly-available RNA-seq data was analyzed to identify transcripts that are expressed in endothelial cells of human, mouse and zebrafish. The analyzed data were incorporated into ANGIOGENES to provide a one-stop-shop for transcriptomics data to facilitate further biological validation. ANGIOGENES is an intuitive and easy-to-use database to allow in silico screening of expressed, enriched and/or specific endothelial transcripts under various conditions. We anticipate that ANGIOGENES serves as a starting point for functional studies to elucidate the roles of protein-coding genes and lncRNAs in angiogenesis.