Panarchy. Towards voluntary communities

An anthology on Panarchy edited by Gian Piero de Bellis for World Wide Wisdom, Saint-Imier, 2023

Interplay between non-coding rna transcription, stringent/relaxed phenotype and antibiotic production in streptomyces ambofaciens

While in recent years the key role of non-coding RNAs (ncRNAs) in the regulation of gene expression has become increasingly evident, their interaction with the global regulatory circuits is still obscure. Here we analyzed the structure and organization of the transcriptome of Streptomyces ambofaciens, the producer of spiramycin. We identified ncRNAs including 45 small-RNAs (sRNAs) and 119 antisense-RNAs (asRNAs I) that appear transcribed from dedicated promoters. Some sRNAs and asRNAs are unprecedented in Streptomyces and were predicted to target mRNAs encoding proteins involved in transcription, translation, ribosomal structure and biogenesis, and regulation of morphological and biochemical differentiation. We then compared ncRNA expression in three strains: (i) the wild-type strain; (ii) an isogenic pirA-defective mutant with central carbon metabolism imbalance, “relaxed” phenotype, and repression of antibiotic production; and (iii) a pirA-derivative strain harboring a “stringent” RNA polymerase that suppresses pirA-associated phenotypes. Data indicated that the expression of most ncRNAs was correlated to the stringent/relaxed phenotype suggesting novel effector mechanisms of the stringent response

Treatment of iatrogenic and traumatic tracheal disruptions

Background and aim. The optimal management of tracheal disruptions is still controversial. It is usually postulated that lesions wider than 1 or 2 centimetres and/or lesions of full-thickness should be treated by surgery at an early stage. Such a statement is not supported by any proven evidence. On the contrary, the conservative management of such injuries has also produced very good results according to recent reports. The aim of this study is to investigate whether conservative treatment can be safely used for wide tracheal lacerations and to assess any possible association between clinical features and modality of treatment. Methods. Records of all patients with iatrogenic and traumatic tracheal disruptions observed between January 1992 and December 2006 were collected and retrospectively reviewed. Data regarding mechanism of injury, clinical and morphological features and modalities of treatment were registered. All possible associations between clinical features and modalities of treatment were investigated. Results. 23 patients were observed overall. There were 6 males and 17 females with a median age of 58 years (range 20-84 yrs). 15 patients had undergone single tube intubation. One patient had his trachea injured during an esophagectomy. Ruptures were secondary to blunt (n=5) and open (n=2) trauma in 7 patients. Lesions varied in length between 1 and 7 centimetres (median length 3 centimetres) and all were full-thickness. The time interval until diagnosis varied between 0 and 72 hours (median 6 hours). Respiratory failure was evident in 7 patients. 16 patients (69.5%) with lacerations ranging in length between 1 and 5.5 centimetres (median length 2.75 cm) underwent conservative treatment. Seven patients (30.5%) underwent surgery. The follow up was completed for 16 patients and varied between 15 and 105 months (median 22.5). One patient died after surgical treatment. No mortality or late major sequelae were registered after conservative treatment. Female sex, absence of respiratory failure and delayed diagnosis was associated with the conservative treatment. Conclusions. Conservative treatment can play a major role even in cases of wide tracheal lacerations. Clinical rather than morphological features should be regarded as main criteria for treatment. The conservative treatment is particularly indicated in the case of stable respiratory parameters independent of the size and the depth of the lesion

The Significance of Xylem Structure and Its Chemical Components in Certain Olive Tree Genotypes with Tolerance to Xylella fastidiosa Infection

Olive quick decline syndrome (OQDS) is a devastating plant disease caused by the bacterium Xylella fastidiosa (Xf). Exploratory missions in the Salento area led to the identification of putatively Xf-resistant olive trees (putatively resistant plants, PRPs) which were pauci-symptomatic or asymptomatic infected plants belonging to different genetic clusters in orchards severely affected by OQDS. To investigate the defense strategies employed by these PRPs to contrast Xf infection, the PRPs were analyzed for the anatomy and histology of xylem vessels, patterns of Xf distribution in host tissues (by the fluorescent in situ hybridization technique—FISH) and the presence of secondary metabolites in stems. The xylem vessels of the PRPs have an average diameter significantly lower than that of susceptible plants for each annual tree ring studied. The histochemical staining of xylem vessels highlighted an increase in the lignin in the parenchyma cells of the medullary rays of the wood. The 3D images obtained from FISH-LSM (laser scanning microscope) revealed that, in the PRPs, Xf cells mostly appeared as individual cells or as small aggregates; in addition, these bacterial cells looked to be incorporated in the autofluorescence signal of gels and phenolic compounds regardless of hosts’ genotypes. In fact, the metabolomic data from asymptomatic PRP stems showed a significant increase in compounds like salicylic acid, known as a signal molecule which mediates host responses upon pathogen infection, and luteolin, a naturally derived flavonoid compound with antibacterial properties and with well-known anti-biofilm effects. Findings indicate that the xylem vessel geometry together with structural and chemical defenses are among the mechanisms operating to control Xf infection and may represent a common resistance trait among different olive genotypes

Ergogenic effect of bcaas and l-alanine supplementation: Proof-of-concept study in a murine model of physiological exercise

Background: Branched-chain amino acids (BCAAs: leucine, isoleucine, valine) account for 35% of skeletal muscle essential amino acids (AAs). As such, they must be provided in the diet to support peptide synthesis and inhibit protein breakdown. Although substantial evidence has been collected about the potential usefulness of BCAAs in supporting muscle function and structure, dietary supplements containing BCAAs alone may not be effective in controlling muscle protein turnover, due to the rate-limiting bioavailability of other AAs involved in BCAAs metabolism. Methods: We aimed to evaluate the in vivo/ex vivo effects of a 4-week treatment with an oral formulation containing BCAAs alone (2:1:1) on muscle function, structure, and metabolism in a murine model of physiological exercise, which was compared to three modified formulations combining BCAAs with increasing concentrations of L-Alanine (ALA), an AA controlling BCAAs catabolism. Results: A preliminary pharmacokinetic study confirmed the ability of ALA to boost up BCAAs bioavailability. After 4 weeks, mix 2 (BCAAs + 2ALA) had the best protective effect on mice force and fatigability, as well as on muscle morphology and metabolic indices. Conclusion: Our study corroborates the use of BCAAs + ALA to support muscle health during physiological exercise, underlining how the relative BCAAs/ALA ratio is important to control BCAAs distribution

Neuropsychological findings in childhood neglect and their relationships to pediatric PTSD

Although child neglect is the most prevalent form of child maltreatment, the neurocognitive effects of neglect is understudied

Cardiac surgery practice during the COVID-19 outbreak: A regionwide survey

Background: Health systems worldwide have been overburdened by the "COVID-19 surge". Consequently, strategies to remodulate non-COVID medical and surgical care had to be developed. Knowledge of the impact of COVID surge on cardiac surgery practice is mainstem. Present study aims to evaluate the regional practice pattern during lockdown in Campania. Methods: A multicenter regional observational 26-question survey was conducted, including all adult cardiac surgery units in Campania, Italy, to assess how surgical practice has changed during COVID-19 national lockdown. Results: All centers adopted specific protocols for screening patients and personnel. A significant reduction in the number of dedicated intensive care unit (ICU) beds (-30.0%±38.1%, range: 0-100%) and cardiac operating rooms (-22.2%±26.4%, range: 0-50%) along with personnel relocation to other departments was disclosed (anesthesiologists -5.8%±11.1%, range: 0-33.3%; perfusionists -5.6%±16.7%, range: 0-50%; nurses -4.8%±13.2%, range: 0-40%; cardiologists -3.2%±9.5%, range: 0-28.6%). Cardiac surgeons were never reallocated to other services. Globally, we witnessed dramatically lower adult cardiac surgery case volumes (335 vs. 667 procedures, P<0.001), as institutions and surgeons followed guidelines to curtail non-urgent operations. Conclusions: This regional survey demonstrates major changes in practice as a response to the COVID-19 pandemic. In this respect, this experience might lead to the development of permanent systems-based plans for future pandemic and may effectively help policy decision making when prioritizing healthcare resource reallocation during and after the pandemic

Gigwa v2—Extended and improved genotype investigator

The study of genetic variations is the basis of many research domains in biology. From genome structure to population dynamics, many applications involve the use of genetic variants. The advent of next-generation sequencing technologies led to such a flood of data that the daily work of scientists is often more focused on data management than data analysis. This mass of genotyping data poses several computational challenges in terms of storage, search, sharing, analysis, and visualization. While existing tools try to solve these challenges, few of them offer a comprehensive and scalable solution. Gigwa v2 is an easy-to-use, species-agnostic web application for managing and exploring high-density genotyping data. It can handle multiple databases and may be installed on a local computer or deployed as an online data portal. It supports various standard import and export formats, provides advanced filtering options, and offers means to visualize density charts or push selected data into various stand-alone or online tools. It implements 2 standard RESTful application programming interfaces, GA4GH, which is health-oriented, and BrAPI, which is breeding-oriented, thus offering wide possibilities of interaction with third-party applications. The project home page provides a list of live instances allowing users to test the system on public data (or reasonably sized user-provided data). This new version of Gigwa provides a more intuitive and more powerful way to explore large amounts of genotyping data by offering a scalable solution to search for genotype patterns, functional annotations, or more complex filtering. Furthermore, its user-friendliness and interoperability make it widely accessible to the life science community

Gene and protein expression in response to different growth temperatures and oxygen availability in Burkholderia thailandensis.

Published onlineJournal ArticleResearch Support, Non-U.S. Gov'tThis is the final version of the article. Available from Public Library of Science via the DOI in this record.Burkholderia thailandensis, although normally avirulent for mammals, can infect macrophages in vitro and has occasionally been reported to cause pneumonia in humans. It is therefore used as a model organism for the human pathogen B. pseudomallei, to which it is closely related phylogenetically. We characterized the B. thailandensis clinical isolate CDC2721121 (BtCDC272) at the genome level and studied its response to environmental cues associated with human host colonization, namely, temperature and oxygen limitation. Effects of the different growth conditions on BtCDC272 were studied through whole genome transcription studies and analysis of proteins associated with the bacterial cell surface. We found that growth at 37°C, compared to 28°C, negatively affected cell motility and flagella production through a mechanism involving regulation of the flagellin-encoding fliC gene at the mRNA stability level. Growth in oxygen-limiting conditions, in contrast, stimulated various processes linked to virulence, such as lipopolysaccharide production and expression of genes encoding protein secretion systems. Consistent with these observations, BtCDC272 grown in oxygen limitation was more resistant to phagocytosis and strongly induced the production of inflammatory cytokines from murine macrophages. Our results suggest that, while temperature sensing is important for regulation of B. thailandensis cell motility, oxygen limitation has a deeper impact on its physiology and constitutes a crucial environmental signal for the production of virulence factors.This work was supported by Fondazione CARIPLO (Progetto Vaccini, contract number 2009–3577) and by Ministero dell’Istruzione, dell’Università e della Ricerca (MIUR) (project FIRB RBLA039LSF). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript