RNAIII is linked with the pentose phosphate pathway through the activation of RpiRc in Staphylococcus aureus

Staphylococcus aureus RNAIII is a dual-function regulatory RNA that controls the expression of multiple virulence genes and especially the transition from adhesion to the production of exotoxins. However, its contribution to S. aureus central metabolism remains unclear. Using MS2-affinity purification coupled with RNA sequencing, we uncovered more than 50 novel RNAIII-mRNA interactions. Among them, we demonstrate that RNAIII is a major activator of the rpiRc gene, encoding a regulator of the pentose phosphate pathway (PPP). RNAIII binds the 5' UTR of rpiRc mRNA to favor ribosome loading, leading to an increased expression of RpiRc and, subsequently, of two PPP enzymes. Finally, we show that RNAIII and RpiRc are involved in S. aureus fitness in media supplemented with various carbohydrate sources related to PPP and glycolysis. Collectively, our data depict an unprecedented phenotype associated with the RNAIII regulon, especially the direct implication of RNAIII in central metabolic activity modulation. These findings show that the contribution of RNAIII in Staphylococcus aureus adaptation goes far beyond what was initially reported.

IMPORTANCE

Staphylococcus aureus is a major human pathogen involved in acute and chronic infections. Highly recalcitrant to antibiotic treatment, persistent infections are mostly associated with the loss of RNAIII expression, a master RNA regulator responsible for the switch from colonization to infection. Here, we used the MS2 affinity purification coupled with RNA sequencing approach to identify novel mRNA targets of RNAIII and uncover novel functions. We demonstrate that RNAIII is an activator of the expression of genes involved in the pentose phosphate pathway and is implicated in the adjustment of bacterial fitness as a function of carbohydrate sources. Taken together, our results demonstrate an unprecedented role of RNAIII that goes beyond the knowledge gained so far and contributes to a better understanding of the role of RNAIII in bacterial adaptation expression and the coordination of a complex regulatory network.

The male pachynema-specific protein MAPS drives phase separation in vitro and regulates sex body formation and chromatin behaviors in vivo

Dynamic chromosome remodeling and nuclear compartmentalization take place during mammalian meiotic prophase I. We report here that the crucial roles of male pachynema-specific protein (MAPS) in pachynema progression might be mediated by its liquid-liquid phase separation in vitro and in cellulo. MAPS forms distinguishable liquid phases, and deletion or mutations of its N-terminal amino acids (aa) 2-9 disrupt its secondary structure and charge properties, impeding phase separation. Maps-/- pachytene spermatocytes exhibit defects in nucleus compartmentalization, including defects in forming sex bodies, altered nucleosome composition, and disordered chromatin accessibility. MapsΔ2-9/Δ2-9 male mice expressing MAPS protein lacking aa 2-9 phenocopy Maps-/- mice. Moreover, a frameshift mutation in C3orf62, the human counterpart of Maps, is correlated with nonobstructive azoospermia in a patient exhibiting pachynema arrest in spermatocyte development. Hence, the phase separation property of MAPS seems essential for pachynema progression in mouse and human spermatocytes.

Multiple antigen presenting system (MAPS): state of the art and potential applications

INTRODUCTION

Technological innovations have been instrumental in advancing vaccine design and protective benefit. Improvements in the safety, tolerability, and efficacy/effectiveness profiles have profoundly reduced vaccine-preventable global disease morbidity and mortality. Here we present an original vaccine platform, the Multiple Antigen Presenting System (MAPS), that relies on high-affinity interactions between a biotinylated polysaccharide (PS) and rhizavidin-fused pathogen-specific proteins. MAPS allows for flexible combinations of various PS and protein components.

AREAS COVERED

This narrative review summarizes the underlying principles of MAPS and describes its applications for vaccine design against bacterial and viral pathogens in non-clinical and clinical settings.

EXPERT OPINION

The utilization of high-affinity non-covalent biotin-rhizavidin interactions in MAPS allows for combining multiple PS and disease-specific protein antigens in a single vaccine. The modular design enables a simplified exchange of vaccine components. Published studies indicate that MAPS technology may support enhanced immunogenic breadth (covering more serotypes, inducing B- and T-cell responses) beyond that which may be elicited via PS- or protein-based conjugate vaccines. Importantly, a more detailed characterization of MAPS-based candidate vaccines is warranted, especially in clinical studies. It is anticipated that MAPS-based vaccines could be adapted and leveraged across numerous diseases of global public health importance.

Exploring continuity of care for women with prenatal diagnosis of congenital anomaly: A mixed method study

AIMS

To map the pathway and service provision for pregnant women whose newborns require admission into the surgical neonatal intensive care unit at or soon after birth, and to examine the nature of continuity of care (COC) provided and the facilitators and barriers to woman- and family-centred care from the perspective of women/parents and health professionals.

BACKGROUND

Limited research exists on current service and care pathways for families whose babies are diagnosed with congenital abnormality requiring surgery.

DESIGN

A mixed method sequential design adhering to EQUATOR guidelines for Good Reporting of a Mixed Methods Study.

METHODS

Data collection methods included: (1) a workshop with health professionals (n = 15), (2) retrospective maternal record review (n = 20), prospective maternal record review (17), (3) interviews with pregnant women given a prenatal diagnosis of congenital anomaly (n = 17) and (4) interviews with key health professionals (n = 7).

RESULTS/FINDINGS

Participants perceived care delivered by state-based services as problematic prior to admission into the high-risk midwifery COC model. Once admitted to the high-risk maternity team women described care 'like a breath of fresh air' with a 'contrast in support', where they felt supported in their decisions.

CONCLUSION

This study highlights provision of COC, in particular relational continuity between health providers and women as essential to achieve optimal outcomes.

RELEVANCE TO CLINICAL PRACTICE

Provision of individualised COC offers an opportunity for perinatal services to reduce the negative consequences of pregnancy-related stress associated with diagnosis of foetal anomaly.

PATIENT OR PUBLIC CONTRIBUTION

No patient or public was involved in the design, analysis, preparation or writing of this review.

Predicting Environmental and Ecological Drivers of Human Population Structure

Landscape, climate, and culture can all structure human populations, but few existing methods are designed to simultaneously disentangle among a large number of variables in explaining genetic patterns. We developed a machine learning method for identifying the variables which best explain migration rates, as measured by the coalescent-based program MAPS that uses shared identical by descent tracts to infer spatial migration across a region of interest. We applied our method to 30 human populations in eastern Africa with high-density single nucleotide polymorphism array data. The remarkable diversity of ethnicities, languages, and environments in this region offers a unique opportunity to explore the variables that shape migration and genetic structure. We explored more than 20 spatial variables relating to landscape, climate, and presence of tsetse flies. The full model explained ∼40% of the variance in migration rate over the past 56 generations. Precipitation, minimum temperature of the coldest month, and elevation were the variables with the highest impact. Among the three groups of tsetse flies, the most impactful was fusca which transmits livestock trypanosomiasis. We also tested for adaptation to high elevation among Ethiopian populations. We did not identify well-known genes related to high elevation, but we did find signatures of positive selection related to metabolism and disease. We conclude that the environment has influenced the migration and adaptation of human populations in eastern Africa; the remaining variance in structure is likely due in part to cultural or other factors not captured in our model.

DECAL: A Reconfigurable Monolithic Active Pixel Sensor for Tracking and Calorimetry in a 180 nm Image Sensor Process

In this paper, we describe DECAL, a prototype Monolithic Active Pixel Sensor (MAPS) device designed to demonstrate the feasibility of both digital calorimetry and reconfigurability in ASICs for particle physics. The goal of this architecture is to help reduce the development and manufacturing costs of detectors for future colliders by developing a chip that can operate both as a digital silicon calorimeter and a tracking chip. The prototype sensor consists of a matrix of 64 × 64 55 μm pixels, and provides a readout at 40 MHz of the number of particles which have struck the matrix in the preceding 25 ns. It can be configured to report this as a total sum across the sensor (equivalent to the pad of an analogue calorimeter) or the sum per column (equivalent to a traditional strip detector). The design and operation of the sensor are described, and the results of chip characterisation are reported and compared to simulations.

The male germline-specific protein MAPS is indispensable for pachynema progression and fertility

Meiosis is a specialized cell division that creates haploid germ cells from diploid progenitors. Through differential RNA expression analyses, we previously identified a number of mouse genes that were dramatically elevated in spermatocytes, relative to their very low expression in spermatogonia and somatic organs. Here, we investigated in detail 1700102P08Rik, one of these genes, and independently conclude that it encodes a male germline-specific protein, in agreement with a recent report. We demonstrated that it is essential for pachynema progression in spermatocytes and named it male pachynema-specific (MAPS) protein. Mice lacking Maps (Maps ^-/- ) suffered from pachytene arrest and spermatocyte death, leading to male infertility, whereas female fertility was not affected. Interestingly, pubertal Maps ^-/- spermatocytes were arrested at early pachytene stage, accompanied by defects in DNA double-strand break (DSB) repair, crossover formation, and XY body formation. In contrast, adult Maps ^-/- spermatocytes only exhibited partially defective crossover but nonetheless were delayed or failed in progression from early to mid- and late pachytene stage, resulting in cell death. Furthermore, we report a significant transcriptional dysregulation in autosomes and XY chromosomes in both pubertal and adult Maps ^-/- pachytene spermatocytes, including failed meiotic sex chromosome inactivation (MSCI). Further experiments revealed that MAPS overexpression in vitro dramatically decreased the ubiquitination levels of cellular proteins. Conversely, in Maps ^-/- pachytene cells, protein ubiquitination was dramatically increased, likely contributing to the large-scale disruption in gene expression in pachytene cells. Thus, MAPS is a protein essential for pachynema progression in male mice, possibly in mammals in general.

MDMA to Treat PTSD in Adults

Post-traumatic stress disorder (PTSD) has become one of the most common psychiatric diagnosis in the United States specifically within the veteran population. The current treatment options for this debilitating diagnosis include trauma-focused psychotherapies along with selective serotonin reuptake inhibitors (SSRI) and serotonin-norepinephrine reuptake inhibitors (SNRI).¹ MDMA has recently been shown as a novel therapeutic agent with promisingly results in the treatment of PTSD. MDMA is a psychoactive compound traditionally categorized as a psychedelic amphetamine that deemed a Schedule I controlled substance in the 1980s. Prior to its status as a controlled substance, it was used by psychotherapists for an array of psychiatric issues. In more recent times, MDMA has resurfaced as a potential therapy for PTSD and the data produced from randomized, controlled trials back the desire for MDMA to be utilized as an effective pharmacologic therapy in conjunction with psychotherapy.².

Design and Characterization of Backside Termination Structures for Thick Fully-Depleted MAPS

Fully Depleted Monolithic Active Pixel Sensors (FD-MAPS) represent an appealing alternative to hybrid detectors for radiation imaging applications. We have recently demonstrated the feasibility of FD-MAPS based on a commercial 110 nm CMOS technology, adapted using high-resistivity substrates and backside post-processing. A p/n junction diode, fabricated on the detector backside using low-temperature processing steps after the completion of the front-side Back End of Line (BEOL), is reverse-biased to achieve the full depletion of the substrate and thus fast charge collection by drift. Test diodes including termination structures with different numbers of floating guard rings and different pitches were fabricated together with other Process Control Monitor structures. In this paper, we present the design of the backside diodes, together with results from the electrical characterization of the test devices, aiming to improve understanding of the strengths and limitations of the proposed approach. Characterization results obtained on several wafers demonstrate the effectiveness of the termination rings in increasing the breakdown voltage of the backside diodes and in coping with the variability of the passivation layer characteristics. A breakdown voltage exceeding 400 V in the worst case was demonstrated in devices with 30 guard rings with 6 μm pitch, thus enabling the full depletion of high-resistivity substrates with a thickness larger than or equal to 300 μm. Additionally, we show the first direct comparison for this technology of measured pixel characteristics with 3D TCAD simulations, proving a good agreement in the extracted operating voltages.

Endoscopic surveillance at 3 years after diagnosis, according to European guidelines, seems safe in patients with atrophic gastritis in a low-risk region

BACKGROUND

Autoimmune and multifocal atrophic gastritis (AG) are at risk for gastric neoplastic lesions. European guidelines recommend surveillance with high-quality endoscopy every 3 years.

AIM

To prospectively investigate the occurrence of gastric neoplastic lesions at the 3-year follow-up in patients with autoimmune and multifocal AG.

METHODS

Longitudinal cohort study conducted between 2011 and 2019: consecutive patients with histological diagnosis of autoimmune or multifocal AG underwent follow-up gastroscopy 3 years after diagnosis with high-resolution-narrow-band-imaging endoscopes.

RESULTS

Overall, 160 patients were included(F117(73.0%);median age 66(35-87)years). Autoimmune and multifocal AG were present in 122(76.3%) and 38(23.7%) patients, respectively. At the 3-year follow-up, 16(10.0%) patients presented 16 gastric neoplastic lesions: 3(18.7%) gastric cancers, 4(25.0%) low-grade dysplasia, 2(12.5%) low-grade dysplasia adenomas, 7(43.7%) type-1 neuroendocrine tumours. In these patients, OLGA and OLGIM III/IV stages were present in 4(25.0)% and 1(6.3%), respectively; 11(69.0%) presented autoimmune AG, and all but one(93.7%) had parietal cells antibodies positivity (p = 0.026 vs patients without lesions). All lesions were endoscopically(87.5%) or surgically(12.5%) treated with favourable outcome. Age>70 years was associated with a 9-fold higher probability of developing gastric epithelial neoplastic lesions (OR 9.6,95CI% 1.2-79.4,p = 0.0359).

CONCLUSIONS

The first endoscopic surveillance 3 years after diagnosis seems safe for autoimmune and multifocal AG patients and should be offered to elderly patients who are at higher risk for gastric neoplasia.

Trajectories of Depressive Symptoms among Multicultural Adolescents in Korea: Longitudinal Analysis Using Latent Class Growth Model

The purpose of this study was to investigate the trajectory of depressive symptoms in multicultural adolescents using longitudinal data, and to identify predictive factors related to depressive symptoms of multicultural adolescents using latent class analysis. We used six time-point data derived from the 2012 to 2017 Multicultural Adolescents Panel Study (MAPS). Latent growth curve modeling was used to assess the overall features of depressive symptom trajectories in multicultural adolescents, and latent class growth modeling was used to determine the number and shape of trajectories. We applied multinomial logistic regression analysis to each class to explore predictive factors. We found that the overall slope of depressive symptoms in multicultural adolescents increased. Latent class analysis demonstrated three classes: (1) high-increasing class (i.e., high intercept, significantly increasing slope), (2) moderate-increasing class (i.e., moderate intercept, significantly increasing slope), and (3) low-stable class (i.e., low intercept, no significant slope). In particular, we found that the difference in the initial intercept of depressive symptoms determined the subsequent trajectory. There is a need for early screening for depressive symptoms in multicultural adolescents and preparing individual mental health care plans.

Biopsy Sampling in Upper Gastrointestinal Endoscopy: A Survey from 10 Tertiary Referral Centres Across Europe

BACKGROUND

Guidelines give robust recommendations on which biopsies should be taken when there is endoscopic suggestion of gastric inflammation. Adherence to these guidelines often seems arbitrary. This study aimed to give an overview on current practice in tertiary referral centres across Europe.

METHODS

Data were collected at 10 tertiary referral centres. Demographic data, the indication for each procedure, endoscopic findings, and the number and sampling site of biopsies were recorded. Findings were compared between centres, and factors influencing the decision to take biopsies were explored.

RESULTS

Biopsies were taken in 56.6% of 9,425 procedures, with significant variation between centres (p < 0.001). Gastric biopsies were taken in 43.8% of all procedures. Sampling location varied with the procedure indication (p < 0.001) without consistent pattern across the centres. Fewer biopsies were taken in centres which routinely applied the updated Sydney classification for gastritis assessment (46.0%), compared to centres where this was done only upon request (75.3%, p < 0.001). This was the same for centres stratifying patients according to the OLGA system (51.8 vs. 73.0%, p < 0.001). More biopsies were taken in centres following the MAPS guidelines on stomach surveillance (68.1 vs. 37.1%, p < 0.001). Biopsy sampling was more likely in younger patients in 8 centres (p < 0.05), but this was not true for the whole cohort (p = 0.537). The percentage of procedures with biopsies correlated directly with additional costs charged in case of biopsies (r = 0.709, p = 0.022).

CONCLUSION

Adherence to guideline recommendations for biopsy sampling at gastroscopy was inconsistent across the participating centres. Our data suggest that centre-specific policies are applied instead.

Using a TRAPS upstream transmission detector to verify multileaf collimator positions during dynamic radiotherapy delivery

With the advancement of high-precision radiotherapy and the increasing use of higher intensity beams, the risk to the patient increases should the radiotherapy machine malfunction. Hence more accurate treatment verification is required. In this paper we provide a solution for real-time monitoring of X-ray beams from radiotherapy linear accelerators using monolithic active pixel sensors. We show that leaf errors can be detected with high precision in static fields and IMRT step and shoot, and accurate leaf tracking is possible in Volumetric Modulated Arc Therapy. The prototype MAPS detector meets the criteria of 1% attenuation acceptable for clinical use.

The power of cooperation: Experimental and computational approaches in the functional characterization of bacterial sRNAs

Trans‐acting small regulatory RNAs (sRNAs) are key players in the regulation of gene expression in bacteria. There are hundreds of different sRNAs in a typical bacterium, which in contrast to eukaryotic microRNAs are more heterogeneous in length, sequence composition, and secondary structure. The vast majority of sRNAs function post‐transcriptionally by binding to other RNAs (mRNAs, sRNAs) through rather short regions of imperfect sequence complementarity. Besides, every single sRNA may interact with dozens of different target RNAs and impact gene expression either negatively or positively. These facts contributed to the view that the entirety of the regulatory targets of a given sRNA, its targetome, is challenging to identify. However, recent developments show that a more comprehensive sRNAs targetome can be achieved through the combination of experimental and computational approaches. Here, we give a short introduction into these methods followed by a description of two sRNAs, RyhB, and RsaA, to illustrate the particular strengths and weaknesses of these approaches in more details. RyhB is an sRNA involved in iron homeostasis in Enterobacteriaceae, while RsaA is a modulator of virulence in Staphylococcus aureus. Using such a combined strategy, a better appreciation of the sRNA‐dependent regulatory networks is now attainable.

On the Prowl: An In Vivo Method to Identify RNA Partners of a sRNA

Bacterial cells dispose of numerous strategies to regulate gene expression. Small regulatory RNAs (sRNA) are pervasive molecules that allow gene expression regulation with exquisite precision. These molecules can bind mRNAs and negatively or positively modify their stability and interfere with translation. However, many features of sRNAs render identification of new targets or RNA interacting partners increasingly complex. In this chapter, we present a detailed procedure of MAPS, an in vivo technique based on the copurification of any type of RNA bound to an MS2-tagged sRNA. By focusing on the interaction between two RNAs rather than the outcome of this interaction, MAPS has proven useful in identifying unprecedented sRNA-RNA interactions. Below, we describe how to prepare MAPS samples and how to analyze RNA sequencing data files to determine enrichment ratios of different RNAs in an experimental condition vs a control condition. MAPS can be applied to most sRNAs of Escherichia coli and Salmonella spp., and can be easily optimized to more distant bacterial species.

Identification of New Bacterial Small RNA Targets Using MS2 Affinity Purification Coupled to RNA Sequencing

Small regulatory RNAs (sRNAs) are ubiquitous regulatory molecules expressed in living cells. In prokaryotes, sRNAs usually bind to target mRNAs to either promote their degradation or interfere with translation initiation. Because a single sRNA can regulate a considerable number of target mRNAs, we seek to identify those targets rapidly and reliably. Here, we present a robust method based on the co-purification of target mRNAs bound to MS2-tagged sRNAs expressed in vivo. After purification of the tagged-sRNA, we use RNAseq to determine the identity of all RNA interacting partners and their enrichment level. We describe how to analyze the RNAseq data through the Galaxy Project Platform bioinformatics tools to identify new mRNA targets. This technique is applicable to most sRNAs of E. coli and Salmonella.

Ethanol impairs microtubule formation via interactions at a microtubule associated protein-sensitive site

Prolonged ethanol abuse has been associated with brain injury caused by impaired synaptogenesis, cellular migration, neurogenesis, and cell signaling, all of which require proper microtubule functioning. However, the means by which ethanol may impair microtubule formation or function and the role that microtubule-associated proteins (MAPs) have in mediating such effects are not clear. In the present studies, purified MAP-deficient (2 mg/mL) and MAP-rich (pre-conjugated; 1 mg/mL) bovine α/β tubulin dimer was allowed to polymerize at 37 °C, forming microtubules in the presence or absence of ethanol (25-500 mM). Microtubule formation was assessed in a 96-well format using a turbidity assay, with absorption measured at 340 nm for 45 min. Additional studies co-exposed α/β tubulin dimers to 50 mM ethanol and purified MAPs (0.1 mg/mL) for 45 min. Polymerization of MAP-deficient tubulin was significantly decreased (at 15-45 min of polymerization) during exposure to ethanol (>25 mM). In contrast, ethanol exposure did not alter polymerization of α/β tubulin dimers pre-conjugated to MAPs, at any concentration. Concurrent exposure of MAP-deficient tubulin with purified MAPs and ethanol resulted in significant and time-dependent decreases in tubulin polymerization, with recovery from inhibition at later time points. The present results suggest that ethanol disrupts MAP-independent microtubule formation and MAP-dependent microtubule formation via direct actions at an MAP-sensitive microtubule residue, indicating that disruption of neuronal microtubule formation and function may contribute to the neurodegenerative effects of binge-like ethanol intake.