Expanding the Boolean logic of the prokaryotic transcription factor XylR by functionalization of permissive sites with a protease-target sequence

The σ54-dependent prokaryotic regulator XylR implements a one-input/one-output actuator that transduces the presence of the aromatic effector m-xylene into transcriptional activation of the cognate promoter Pu. Such a signal conversion involves the effector-mediated release of the intramolecular repression of the N-terminal A domain on the central C module of XylR. On this background, we set out to endow this regulator with additional signal-sensing capabilities by inserting a target site of the viral protease NIa in permissive protein locations that once cleaved in vivo could either terminate XylR activity or generate an effector-independent, constitutive transcription factor. To find optimal protein positions to this end, we saturated the xylR gene DNA with a synthetic transposable element designed for randomly delivering in-frame polypeptides throughout the sequence of any given protein. This Tn5-based system supplies the target gene with insertions of a selectable marker that can later be excised, leaving behind the desired (poly) peptides grafted into the protein structure. Implementation of such knock-in-leave-behind (KILB) method to XylR was instrumental to produce a number of variants of this transcription factor (TF) that could compute in vivo two inputs (m-xylene and protease) into a single output following a logic that was dependent on the site of the insertion of the NIa target sequence in the TF. Such NIa-sensitive XylR specimens afforded the design of novel regulatory nodes that entered protease expression as one of the signals recognized in vivo for controlling Pu. This approach is bound to facilitate the functionalization of TFs and other proteins with new traits, especially when their forward engineering is made difficult by, for example, the absence of structural data.This study was supported by the BIO and FEDER CONSOLIDER-INGENIO Program of the Spanish Ministry of Science and Innovation, the MICROME, ST-FLOW and ARYSIS Contracts of the EU, and the PROMT Project of the CAM.Peer reviewe

pBAM1: an all-synthetic genetic tool for analysis and construction of complex bacterial phenotypes

<p>Abstract</p> <p>Background</p> <p>Since publication in 1977 of plasmid pBR322, many breakthroughs in Biology have depended on increasingly sophisticated vector platforms for analysis and engineering of given bacterial strains. Although restriction sites impose a certain format in the procedures for assembling cloned genes, every attempt thus far to standardize vector architecture and nomenclature has ended up in failure. While this state of affairs may still be tolerable for traditional one-at-a-time studies of single genes, the onset of systems and synthetic biology calls for a simplification -along with an optimization- of the currently unwieldy pool of genetic tools.</p> <p>Results</p> <p>The functional DNA sequences present in the natural bacterial transposon Tn<it>5 </it>have been methodically edited and refactored for the production of a multi-purpose genetic tool named pBAM1, which allows a range of manipulations in the genome of Gram-negative bacteria. This all-synthetic construct enhances the power of mini-transposon vectors for either de-construction or re-construction of phenotypes <it>á la carte </it>by incorporating features inspired in systems engineering: modularity, re-usability, minimization, and compatibility with other genetic tools. pBAM1 bears an streamlined, restriction site-freed and narrow-host range replication frame bearing the sequences of R6K <it>oriV</it>, <it>oriT </it>and an ampicillin resistance marker. These go along with a business module that contains a host-independent and hyperactive transposition platform for <it>in vivo </it>or <it>in vitro </it>insertion of desired DNA into the genome of the target bacterium. All functional sequences were standardized for a straightforward replacement by equivalent counterparts, if required. pBAM1 can be delivered into recipient cells by either mating or electroporation, producing transposon insertion frequencies of 1.8 × 10^-3and 1.02 × 10^-7, respectively in the soil bacterium <it>Pseudomonas putida</it>. Analyses of the resulting clones revealed a 100% of unique transposition events and virtually no-cointegration of the donor plasmid within the target genome.</p> <p>Conclusions</p> <p>This work reports the design and performance of an all-synthetic mini-transposon vector. The power of the new system for both identification of new functions or for the construction of desired phenotypes is shown in a genetic survey of hyper-expressed proteins and regulatory elements that influence the expression of the σ⁵⁴-dependent <it>Pu </it>promoter of <it>P. putida</it>.</p

Mechanism of Transcription Activation at the comG Promoter by the Competence Transcription Factor ComK of Bacillus subtilis

The development of genetic competence in Bacillus subtilis is regulated by a complex signal transduction cascade, which results in the synthesis of the competence transcription factor, encoded by comK. ComK is required for the transcription of the late competence genes that encode the DNA binding and uptake machinery and of genes required for homologous recombination. In vivo and in vitro experiments have shown that ComK is responsible for transcription activation at the comG promoter. In this study, we investigated the mechanism of this transcription activation. The intrinsic binding characteristics of RNA polymerase with and without ComK at the comG promoter were determined, demonstrating that ComK stabilizes the binding of RNA polymerase to the comG promoter. This stabilization probably occurs through interactions with the upstream DNA, since a deletion of the upstream DNA resulted in an almost complete abolishment of stabilization of RNA polymerase binding. Furthermore, a strong requirement for the presence of an extra AT box in addition to the common ComK-binding site was shown. In vitro transcription with B. subtilis RNA polymerase reconstituted with wild-type -subunits and with C-terminal deletion mutants of the -subunits was performed, demonstrating that these deletions do not abolish transcription activation by ComK. This indicates that ComK is not a type I activator. We also show that ComK is not required for open complex formation. A possible mechanism for transcription activation is proposed, implying that the major stimulatory effect of ComK is on binding of RNA polymerase.Peer reviewe

Managing Vulvodynia with Central Sensitization: Challenges and Strategies

Background: Vulvodynia is defined as a chronic idiopathic vulvar pain condition. This study aimed to investigate the effect of central sensitization on the prognosis of neuromodulator treatment for vulvodynia. Method: A total of 105 patients with vulvodynia who underwent pelvic mapping pain exploration were included and scored according to the Convergence PP Criteria for pelvic pain and central sensitization. The patients were treated according to chronic pelvic pain guidelines, and their response to treatment was evaluated. Results: A total of 35 out 105 patients (33%) with vulvodynia had central sensitization, which was associated with comorbidities, dyspareunia, pain with micturition, and pain with defecation. Dyspareunia and pain with defecation were independent prognostic factors for central sensitization. Patients with central sensitization experienced more pain during intercourse, urination, or defecation, had more comorbidities, and responded worse to treatment. They required more treatment, with a longer response time (over 2 months). Patients with localized vulvodynia were treated with physiotherapy and lidocaine, while patients with generalized vulvodynia were treated with neuromodulators. Amitriptyline was effective in treating patients with generalized spontaneous vulvodynia and dyspareunia. Conclusions: Overall, this study highlights the importance of considering central sensitization in the diagnosis and treatment of vulvodynia and the need for individualized treatment based on the patient’s symptoms and underlying mechanisms. Vulvodynia patients with central sensitization had more pain during intercourse, urination, or defecation, and responded worse to treatment, requiring more time and medicatio

The Metabolic Redox Regime of <i>Pseudomonas putida</i> Tunes Its Evolvability toward Novel Xenobiotic Substrates

Some environmental bacteria evolve with new capacities for the aerobic biodegradation of chemical pollutants by adapting preexisting redox reactions to novel compounds. The process typically starts by cooption of enzymes from an available route to act on the chemical structure of the substrate-to-be. The critical bottleneck is generally the first biochemical step, and most of the selective pressure operates on reshaping the initial reaction. The interim uncoupling of the novel substrate to preexisting Rieske nonheme iron oxygenases usually results in formation of highly mutagenic ROS. In this work, we demonstrate that the background metabolic regime of the bacterium that hosts an evolving catabolic pathway (e.g., biodegradation of the xenobiotic 2,4-DNT) determines whether the cells either adopt a genetic diversification regime or a robust ROS-tolerant status. Furthermore, our results offer new perspectives to the rational design of efficient whole-cell biocatalysts, which are pursued in contemporary metabolic engineering.During evolution of biodegradation pathways for xenobiotic compounds involving Rieske nonheme iron oxygenases, the transition toward novel substrates is frequently associated with faulty reactions. Such events release reactive oxygen species (ROS), which are endowed with high mutagenic potential. In this study, we evaluated how the operation of the background metabolic network by an environmental bacterium may either foster or curtail the still-evolving pathway for 2,4-dinitrotoluene (2,4-DNT) catabolism. To this end, the genetically tractable strain Pseudomonas putida EM173 was implanted with the whole genetic complement necessary for the complete biodegradation of 2,4-DNT (recruited from the environmental isolate Burkholderia sp. R34). By using reporter technology and direct measurements of ROS formation, we observed that the engineered P. putida strain experienced oxidative stress when catabolizing the nitroaromatic substrate. However, the formation of ROS was neither translated into significant activation of the SOS response to DNA damage nor did it result in a mutagenic regime (unlike what has been observed in Burkholderia sp. R34, the original host of the pathway). To inspect whether the tolerance of P. putida to oxidative challenges could be traced to its characteristic reductive redox regime, we artificially altered the NAD(P)H pool by means of a water-forming, NADH-specific oxidase. Under the resulting low-NAD(P)H status, catabolism of 2,4-DNT triggered a conspicuous mutagenic and genomic diversification scenario. These results indicate that the background biochemical network of environmental bacteria ultimately determines the evolvability of metabolic pathways. Moreover, the data explain the efficacy of some bacteria (e.g., pseudomonads) to host and evolve with new catabolic routes

Hysteroscopic versus histopathological agreement in the diagnosis of chronic endometritis: results from a retrospective observational study

Purpose: To evaluate the agreement rate between hysteroscopy and pathological examination in case of chronic endometritis. Methods: A retrospective observational study carried out at Gynecology and Obstetrics Department, Puerta de Hierro Hospital, Autónoma University of Madrid, Spain, from January 2021 to June 2022 was performed by obtaining data from 115 medical records of women who underwent office hysteroscopies that was compared with the findings of final histological examination of endometrial biopsy. Cohen's kappa index was used to evaluate this agreement rate. In addition, sensitivity, specificity, positive and negative predictive value and diagnostic accuracy were obtained. Results: The agreement between hysteroscopic findings and histological examination showed a modest result with a Cohen's kappa index of 34%. In addition, we obtained a specificity of 70% and a sensitivity of 64%. The positive and negative predictive value were 60.8% and 73.4%, respectively. An excellent agreement rate (100%) between histological and hysteroscopic results was observed in presence of hyperemia and micropolyps. Conclusion: Although the sample size is not as large as that of other studies published so far, the first glance of our experience is that hysteroscopic signs are not yet sufficient to make an accurate diagnosis of chronic endometritis, thus requiring a histopathological confirmation to make it

Complications of Pessaries Amenable to Surgical Correction: Two Case Reports and a Systematic Review of the Literature

Forty percent of women will experience prolapse in their lifetime. Vaginal pessaries are considered the first line of treatment in selected patients. Major complications of vaginal pessaries rarely occur. Methods: PubMed and Embase were searched from 1961 to 2022 for major complications of vaginal pessaries using Medical Subject Headings (MeSH) and free-text terms. The keywords were pessary or pessaries and: vaginal discharge, incontinence, entrapment, urinary infections, fistula, complications, and vaginal infection. The exclusion criteria were other languages than English, pregnancy, complications without a prior history of pessary placement, pessaries unregistered for clinical practice (herbal pessaries), or male patients. The extracted data included symptoms, findings upon examination, infection, type of complication, extragenital symptoms, and treatment. Results: We identified 1874 abstracts and full text articles; 54 were assessed for eligibility and 49 met the inclusion criteria. These 49 studies included data from 66 patients with pessary complications amenable to surgical correction. Clavien–Dindo classification was used to grade the complications. Most patients presented with vaginal symptoms such as bleeding, discharge, or ulceration. The most frequent complications were pessary incarceration and fistulas. Surgical treatment included removal of the pessary under local or general anesthesia, fistula repair, hysterectomy and vaginal repair, and the management of bleeding. Conclusions: Pessaries are a reasonable and durable treatment for pelvic organ prolapse. Complications are rare. Routine follow-ups are necessary. The ideal patient candidate must be able to remove and reintroduce their pessary on a regular basis; if not, this must be performed by a healthcare worker at regular interval

Evaluation of the In Vitro Antimicrobial Efficacy against Staphylococcus aureus and epidermidis of a Novel 3D-Printed Degradable Drug Delivery System Based on Polycaprolactone/Chitosan/Vancomycin—Preclinical Study

Acute and chronic bone infections, especially those caused by methicillin-resistant Staphylococcus aureus (MRSA), remains a major complication and therapeutic challenge. It is documented that local administration of vancomycin offers better results than the usual routes of administration (e.g., intravenous) when ischemic areas are present. In this work, we evaluate the antimicrobial efficacy against S. aureus and S. epidermidis of a novel hybrid 3D-printed scaffold based on polycaprolactone (PCL) and a chitosan (CS) hydrogel loaded with different vancomycin (Van) concentrations (1, 5, 10, 20%). Two cold plasma treatments were used to improve the adhesion of CS hydrogels to the PCL scaffolds by decreasing PCL hydrophobicity. Vancomycin release was measured by means of HPLC, and the biological response of ah-BM-MSCs growing in the presence of the scaffolds was evaluated in terms of cytotoxicity, proliferation, and osteogenic differentiation. The PCL/CS/Van scaffolds tested were found to be biocompatible, bioactive, and bactericide, as demonstrated by no cytotoxicity (LDH activity) or functional alteration (ALP activity, alizarin red staining) of the cultured cells and by bacterial inhibition. Our results suggest that the scaffolds developed would be excellent candidates for use in a wide range of biomedical fields such as drug delivery systems or tissue engineering applications.FarmaciaMedicin

SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes

10 Pág.The SEVA platform (https://seva-plasmids.com) was launched one decade ago, both as a database (DB) and as a physical repository of plasmid vectors for genetic analysis and engineering of Gram-negative bacteria with a structure and nomenclature that follows a strict, fixed architecture of functional DNA segments. While the current update keeps the basic features of earlier versions, the platform has been upgraded not only with many more ready-to-use plasmids but also with features that expand the range of target species, harmonize DNA assembly methods and enable new applications. In particular, SEVA 4.0 includes (i) a sub-collection of plasmids for easing the composition of multiple DNA segments with MoClo/Golden Gate technology, (ii) vectors for Gram-positive bacteria and yeast and [iii] off-the-shelf constructs with built-in functionalities. A growing collection of plasmids that capture part of the standard-but not its entirety-has been compiled also into the DB and repository as a separate corpus (SEVAsib) because of its value as a resource for constructing and deploying phenotypes of interest. Maintenance and curation of the DB were accompanied by dedicated diffusion and communication channels that make the SEVA platform a popular resource for genetic analyses, genome editing and bioengineering of a large number of microorganisms.The SEVA repository has been developed and maintained with funds of the SYCOLIM [ERA-COBIOTECH 2018-PCI2019-111859-2] Project of the Spanish Ministry of Science and Innovation, SYNBIO4FLAV [H2020-NMBP-TR-IND/H2020-NMBP-BIO-2018-814650]; MIX-UP [MIX-UP H2020-BIO-CN-2019-870294] Contracts of the European Union; BIOSINT-CM [Y2020/TCS-6555] Project of the Comunidad de Madrid-European Structural and Investment Funds (FSE, FECER); P.I.N. acknowledges financial support by the Novo Nordisk Foundation [NNF20CC0035580, TARGET (NNF21OC0067996]; European Union's Horizon 2020 Research and Innovation Programme [814418 (SinFonia)]; M.H.H.N. acknowledges funding by the Novo Nordisk Foundation [NNF20CC0035580]; P.D. was funded by Czech Science Foundation Project 22-12505S; A.G.M. was supported by the Grants BioSinT-CM [Y2020/TCS-6555]; CONTEXT (Atracción de Talento Program) [2019-T1/BIO-14053] Projects of the Comunidad de Madrid, MULTI-SYSBIO [PID2020-117205GA-I00]; Severo Ochoa Program for Centres of Excellence in R&D [CEX2020-000999-S] funded by MCIN/AEI/10.13039/501100011033 and the ECCO (ERC-2021-COG-101044360) Contract of the EU. Funding for open access charge: European Commission Grant SYNBIO4FLAV [H2020-NMBP-TR-IND/H2020-NMBP-BIO-2018-814650].With funding from the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2020‐000999‐S) .Peer reviewe

The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes

The 'Standard European Vector Architecture' database (SEVA-DB, http://seva.cnb.csic.es) was conceived as a user-friendly, web-based resource and a material clone repository to assist in the choice of optimal plasmid vectors for de-constructing and re-constructing complex prokaryotic phenotypes. The SEVA-DB adopts simple design concepts that facilitate the swapping of functional modules and the extension of genome engineering options to microorganisms beyond typical laboratory strains. Under the SEVA standard, every DNA portion of the plasmid vectors is minimized, edited for flaws in their sequence and/or functionality, and endowed with physical connectivity through three inter-segment insulators that are flanked by fixed, rare restriction sites. Such a scaffold enables the exchangeability of multiple origins of replication and diverse antibiotic selection markers to shape a frame for their further combination with a large variety of cargo modules that can be used for varied end-applications. The core collection of constructs that are available at the SEVA-DB has been produced as a starting point for the further expansion of the formatted vector platform. We argue that adoption of the SEVA format can become a shortcut to fill the phenomenal gap between the existing power of DNA synthesis and the actual engineering of predictable and efficacious bacteria