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The worldwide emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) since 2019 has highlighted the importance of rapid and reliable diagnostic testing to prevent and control the viral transmission. The monitoring of the viral spread can be performed using individual diagnostics in clinical samples and global detection of SARS-CoV-2 in wastewater samples. Reverse-transcription droplet digital PCR (RT-ddPCR) offers an attractive platform for absolute RNA quantification in comparison to the gold standard reverse transcription quantitative PCR (RT-qPCR) that only yields relative quantification results. To avoid inaccurate results due to false negatives caused by polymorphisms or point mutations that can possibly compromise the accuracy of the diagnostic tests, a multiplex RT-ddPCR method was developed by combining previously published SARS-CoV-2 detection RT-qPCR assays targeting well-conserved ORF1a and RdRp genes. These assays were successfully evaluated in silico for their inclusivity using GISAID sequences from the beginning of November 2020 to the end of February 2021. The sensitivity and specificity of the new RT-ddPCR method was evaluated and its applicability on both clinical and wastewater samples was illustrated. In conclusion, a reliable and sensitive multiplex one-step RT-ddPCR assay for reliable quantification of SARS-CoV-2 RNA in clinical and wastewater samples was developed and assessed, providing a key tool for the current health crisis.

The TCR delta enhancer (Edelta) and TCR alpha enhancer (Ealpha) play critical roles in the temporal and lineage-specific control of V(D)J recombination and transcription at the TCR alphadelta locus, working as a developmental switch controlling a transition from TCR delta to TCR alpha activity during thymocyte development. Previous experiments using a transgenic reporter substrate revealed that substitution of the 116-bp minimal Ealpha, denoted Talpha1-Talpha2, for the entire 1.4-kb Ealpha led to a premature activation of V(D)J recombination. This suggested that binding sites outside of Talpha1-Talpha2 are critical for the strict developmental regulation of TCR alpha rearrangement. We have further analyzed Ealpha to better understand the mechanisms responsible for appropriate developmental regulation in vivo. We found that a 275-bp Ealpha fragment, denoted Talpha1-Talpha4, contains all binding sites required for proper developmental regulation in vivo. This suggests that developmentally appropriate enhancer activation results from a functional interaction between factors bound to Talpha1-Talpha2 and Talpha3-Talpha4. In support of this, EMSAs reveal the formation of a large enhanceosome complex that reflects the cooperative assembly of proteins bound to both Talpha1-Talpha2 and Talpha3-Talpha4. Our data suggest that enhanceosome assembly is critical for developmentally appropriate activation of Ealpha in vivo, and that transcription factors, Sp1 and pCREB, may play unique roles in this process.

Streptococcus pneumoniae remains a major causative agent of serious human diseases. The worldwide increase of antibiotic resistant strains revealed the importance of horizontal gene transfer in this pathogen, a scenario that results in the modulation of the species-specific gene pool. We investigated genomic variation in 20 S. pneumoniae isolates representing major antibiotic-resistant clones and 10 different capsular serotypes. Variation was scored as decreased hybridization signals visualized on a high-density oligonucleotide array representing 1,968 genes of the type 4 reference strain KNR.7/87. Up to 10% of the genes appeared altered between individual isolates and the reference strain; variability within clones was below 2.1%. Ten gene clusters covering 160 kb account for half of the variable genes. Most of them are associated with transposases and are assumed to be part of a flexible gene pool within the bacterial population; other variable loci include mosaic genes encoding antibiotic resistance determinants and gene clusters related to bacteriocin production. Genomic comparison between S. pneumoniae and commensal Streptococcus mitis and Streptococcus oralis strains indicates distinct antigenic profiles and suggests a smooth transition between these species, supporting the validity of the microarray system as an epidemiological and diagnostic tool.

During thymocyte maturation, enhancers of genes encoding for TCRδ (Tcrd) and TCRα (Tcra), Eδ8, and Eα, work as a developmental switch controlling transition from Tcrd to Tcra activity at the Tcrad locus. Previous experiments revealed that an Eα fragment, Tα1-Tα2, which constitutes a well-characterized compact nucleoprotein structure led to premature activation of V(D)J recombination compared with that observed for the entire Eα or Tα1-Tα4. These experiments indicated that Tα3-Tα4 collaborates with factors bound to Tα1-Tα2 for the strict developmental regulation of Tcra rearrangement. The compact enhanceosome created on Tα1-Tα2 explained the molecular basis for requirement of intact Tα2 TCF/LEF and ets sites for enhancer function. We have created a mutant version of Eα, EαMC, in which Eδ myb and runx sites have been substituted for Tα2 runx and ets sites, that argues against the notion of a requirement for strict Eα enhanceosome structure for function. EαMC resulted in a very potent enhancer indicating that stereospecific interactions among proteins that form an Eα enhanceosome are rather flexible. Activation of V(D)J recombination by EαMC during thymocyte development resulted, however, to be premature and indistinguishable from that of Tα1-Tα2. These results indicate that Tα3-Tα4 itself is not sufficient to impart a developmental delay to a chimeric >early> enhancer, and indicate the need for functional collaboration between Tα2 runx/ets sites binding proteins and proteins bound to Tα3-Tα4 for proper developmental activation. The possibility of assembly of distinct sets of proteins on Eα might represent a more flexible form of information processing during thymocyte development. Copyright © 2009 by The American Association of Immunologists, Inc.

The modulation of host cell apoptosis by bacterial pathogens is of critical importance for the outcome of the infection process. The capacity of Bartonella henselae and B. quintana to cause vascular tumor formation in immunocompromised patients is linked to the inhibition of vascular endothelial cell (EC) apoptosis. Here, we show that translocation of BepA, a type IV secretion (T4S) substrate, is necessary and sufficient to inhibit EC apoptosis. Ectopic expression in ECs allowed mapping of the anti-apoptotic activity of BepA to the Bep intracellular delivery domain, which, as part of the signal for T4S, is conserved in other T4S substrates. The anti-apoptotic activity appeared to be limited to BepA orthologs of B. henselae and B. quintana and correlated with (i) protein localization to the host cell plasma membrane, (ii) elevated levels of intracellular cyclic adenosine monophosphate (cAMP), and (iii) increased expression of cAMP-responsive genes. The pharmacological elevation of cAMP levels protected ECs from apoptosis, indicating that BepA mediates anti-apoptosis by heightening cAMP levels by a plasma membrane–associated mechanism. Finally, we demonstrate that BepA mediates protection of ECs against apoptosis triggered by cytotoxic T lymphocytes, suggesting a physiological context in which the anti-apoptotic activity of BepA contributes to tumor formation in the chronically infected vascular endothelium., Synopsis The capacity of infected host cells to die by apoptosis (programmed cell death) is critical for controlling pathogen replication and survival. Bacterial pathogens have thus developed strategies to inhibit host cell apoptosis, allowing them to preserve their cellular habitat during chronic infection. For instance, the capacity of the facultative intracellular pathogen Bartonella henselae to trigger tumor formation as a consequence of chronic infection of the human vasculature is linked to the inhibition of endothelial cell apoptosis. This study describes the identification and functional characterization of the anti-apoptotic bacterial effector protein BepA of B. henselae, which is shown to be sufficient to inhibit endothelial cell apoptosis, i.e., as triggered by activated cytotoxic T lymphocytes. Upon translocation into endothelial cells via a bacterial type IV secretion system, BepA localizes to the plasma membrane, where it triggers the production of second messenger cyclic adenosine monophosphate in quantities effective for blocking apoptosis. Strikingly, the capacity of BepA to mediate membrane localization, cyclic adenosine monophosphate production, and the resulting inhibition of apoptosis is confined to a conserved domain that originally evolved in bacteria as a signal for type IV secretion. This study thus highlights the convergent evolution of an anti-apoptotic effector protein of purely bacterial origin.

The ciaR - ciaH system is one of 13 two-component signal-transducing systems of the human pathogen Streptococcus pneumoniae . Mutations in the histidine protein kinase CiaH confer increased resistance to beta-lactam antibiotics and interfere with the development of genetic competence. In order to identify the genes controlled by the cia system, the cia regulon, DNA fragments targeted by the response regulator CiaR were isolated from restricted chromosomal DNA using the solid-phase DNA binding assay and analyzed by hybridization to an oligonucleotide microarray representing the S. pneumoniae genome. A set of 18 chromosomal regions containing 26 CiaR target sites were detected and proposed to represent the minimal cia regulon. The putative CiaR target loci included genes important for the synthesis and modification of cell wall polymers, peptide pheromone and bacteriocin production, and the htrA-spo0J region. In addition, the transcription profile of cia loss-of-function mutants and those with an apparent activated cia system representing the off and on states of the regulatory system were analyzed. The transcript analysis confirmed the cia -dependent expression of seven putative target loci and revealed three additional cia -regulated loci. Five putative target regions were silent under all conditions, and for the remaining three regions, no cia -dependent expression could be detected. Furthermore, the competence regulon, including the comCDE operon required for induction of competence, was completely repressed by the cia system.