Reconstructing the evolution of the mitochondrial ribosomal proteome

For production of proteins that are encoded by the mitochondrial genome, mitochondria rely on their own mitochondrial translation system, with the mitoribosome as its central component. Using extensive homology searches, we have reconstructed the evolutionary history of the mitoribosomal proteome that is encoded by a diverse subset of eukaryotic genomes, revealing an ancestral ribosome of alpha-proteobacterial descent that more than doubled its protein content in most eukaryotic lineages. We observe large variations in the protein content of mitoribosomes between different eukaryotes, with mammalian mitoribosomes sharing only 74 and 43% of its proteins with yeast and Leishmania mitoribosomes, respectively. We detected many previously unidentified mitochondrial ribosomal proteins (MRPs) and found that several have increased in size compared to their bacterial ancestral counterparts by addition of functional domains. Several new MRPs have originated via duplication of existing MRPs as well as by recruitment from outside of the mitoribosomal proteome. Using sensitive profile–profile homology searches, we found hitherto undetected homology between bacterial and eukaryotic ribosomal proteins, as well as between fungal and mammalian ribosomal proteins, detecting two novel human MRPs. These newly detected MRPs constitute, along with evolutionary conserved MRPs, excellent new screening targets for human patients with unresolved mitochondrial oxidative phosphorylation disorders

Call for emergency action to restore dietary diversity and protect global food systems in times of COVID-19 and beyond: Results from a cross-sectional study in 38 countries

Background: The COVID-19 pandemic has revealed the fragility of the global food system, sending shockwaves across countries\u27 societies and economy. This has presented formidable challenges to sustaining a healthy and resilient lifestyle. The objective of this study is to examine the food consumption patterns and assess diet diversity indicators, primarily focusing on the food consumption score (FCS), among households in 38 countries both before and during the first wave of the COVID-19 pandemic. Methods: A cross-sectional study with 37 207 participants (mean age: 36.70 ± 14.79, with 77 % women) was conducted in 38 countries through an online survey administered between April and June 2020. The study utilized a pre-tested food frequency questionnaire to explore food consumption patterns both before and during the COVID-19 periods. Additionally, the study computed Food Consumption Score (FCS) as a proxy indicator for assessing the dietary diversity of households. Findings: This quantification of global, regional and national dietary diversity across 38 countries showed an increment in the consumption of all food groups but a drop in the intake of vegetables and in the dietary diversity. The household\u27s food consumption scores indicating dietary diversity varied across regions. It decreased in the Middle East and North Africa (MENA) countries, including Lebanon (p \u3c 0.001) and increased in the Gulf Cooperation Council countries including Bahrain (p = 0.003), Egypt (p \u3c 0.001) and United Arab Emirates (p = 0.013). A decline in the household\u27s dietary diversity was observed in Australia (p \u3c 0.001), in South Africa including Uganda (p \u3c 0.001), in Europe including Belgium (p \u3c 0.001), Denmark (p = 0.002), Finland (p \u3c 0.001) and Netherland (p = 0.027) and in South America including Ecuador (p \u3c 0.001), Brazil (p \u3c 0.001), Mexico (p \u3c 0.0001) and Peru (p \u3c 0.001). Middle and older ages [OR = 1.2; 95 % CI = [1.125–1.426] [OR = 2.5; 95 % CI = [1.951–3.064], being a woman [OR = 1.2; 95 % CI = [1.117–1.367], having a high education (p \u3c 0.001), and showing amelioration in food-related behaviors [OR = 1.4; 95 % CI = [1.292–1.709] were all linked to having a higher dietary diversity. Conclusion: The minor to moderate changes in food consumption patterns observed across the 38 countries within relatively short time frames could become lasting, leading to a significant and prolonged reduction in dietary diversity, as demonstrated by our findings

Considerations in designing and testing plasma devices for medical applications

Cold atmospheric plasma has been shown to have great potential for many applications on or in the human body, such as disinfection, wound healing, and cancer treatment. Several medical plasma devices have been developed and have obtained CE certification. However, the route there and into clinical practice is not straightforward. Already during the design stage, many matters need to be taken into account: (1) application and user requirements, (2) medical device regulations, e.g. on electrical safety and electromagnetic compatibility, and (3) production-related issues. Subsequent research should be conducted using a setup that resembles the clinical situation as closely as possible, since seemingly insignificant factors can have a large influence on the plasma and its effects. To ensure that the CE marked device will actually be adopted in clinical practice requires further actions during the research and development process: the demands and concerns of all parties directly and indirectly involved in its use should be identified and at least the crucial parties should be acquainted with plasma medicine and the specific medical device. Some examples will be given from the R&D process of a new flexible volume Dielectric Barrier Discharge (vDBD)

A new flexible DBD device for treating infected wounds: in vitro and ex vivo evaluation and comparison with a RF argon plasma jet

Cold plasma has been shown to provide a promising alternative antimicrobial treatment for wound healing. We developed and tested a flexible surface dielectric barrier discharge (DBD) and compared it to an argon gas based plasma jet operated remotely with a distance between plasma plume and sample of 8 mm. Tests were conducted using different models: on cultured cells, on ex vivo human skin and on bacteria (Pseudomonas aeruginosa) (on agar, in suspension, in collagen/elastin matrix or on ex vivo human skin), allowing us to directly compare bactericidal with safety aspects under identical conditions.\u3cbr/\u3eBoth plasma devices were highly efficient when used on bacteria in non-buffered solutions, but DBD was faster in reaching the maximum bacterial reduction. Treatment of bacteria on intact skin with DBD resulted in up to 6 log reductions in 3 min. The jet was far less efficient on intact skin. Even after 8 min treatment no more than 2 log reductions were obtained with the jet. Treatment of bacteria in burn wound models with DBD for 6 min resulted in a 4.5 log reduction. Even when using DBD for 6 min on infected burn wound models with colonizing or biofilm phase bacteria, the log reductions were 3.8 or 3.2 respectively.\u3cbr/\u3eDBD plasma treatment for 6 min did not affect fibroblast viability, whereas a treatment for 8 min was detrimental. Similarly, treatment with DBD or plasma jet for 6 min did also not affect the metabolic activity of skin biopsies. After treatment for 8 min with DBD or plasma jet, 78% or 60% of activity in skin biopsies remained, respectively. Multiple treatments of in vitro burn wound models with surface DBD for 6 min or with plasma jet for 8 min did not affect re-epithelialization.\u3cbr/\u3eWith the flexible surface DBD plasma strip we were able to quickly inactivate large numbers of bacteria on and in skin. Under the same conditions, viability of skin cells or re-epithelialization was not affected. The DBD source has potential for treating larger wound areas

Genome-wide analysis of FOXO3 mediated transcription regulation through RNA polymerase II profiling

<p>Forkhead box O (FOXO) transcription factors are key players in diverse cellular processes affecting tumorigenesis, stem cell maintenance and lifespan. To gain insight into the mechanisms of FOXO-regulated target gene expression, we studied genome-wide effects of FOXO3 activation. Profiling RNA polymerase II changes shows that FOXO3 regulates gene expression through transcription initiation. Correlative analysis of FOXO3 and RNA polymerase II ChIP-seq profiles demonstrates FOXO3 to act as a transcriptional activator. Furthermore, this analysis reveals a significant part of FOXO3 gene regulation proceeds through enhancer regions. FOXO3 binds to pre-existing enhancers and further activates these enhancers as shown by changes in histone acetylation and RNA polymerase II recruitment. In addition, FOXO3-mediated enhancer activation correlates with regulation of adjacent genes and pre-existence of chromatin loops between FOXO3 bound enhancers and target genes. Combined, our data elucidate how FOXOs regulate gene transcription and provide insight into mechanisms by which FOXOs can induce different gene expression programs depending on chromatin architecture. Molecular Systems Biology 9: 638; published online 22 January 2013; doi:10.1038/msb.2012.74</p>

Mutation in mitochondrial ribosomal protein MRPS22 leads to Cornelia de Lange-like phenotype, brain abnormalities and hypertrophic cardiomyopathy

The oxidative phosphorylation (OXPHOS) system is under control of both the mitochondrial and the nuclear genomes; 13 subunits are synthesized by the mitochondrial translation machinery. We report a patient with Cornelia de Lange-like dysmorphic features, brain abnormalities and hypertrophic cardiomyopathy, and studied the genetic defect responsible for the combined OXPHOS complex I, III and IV deficiency observed in fibroblasts. The combination of deficiencies suggested a primary defect associated with the synthesis of mitochondrially encoded OXPHOS subunits. Analysis of mitochondrial protein synthesis revealed a marked impairment in mitochondrial translation. Homozygosity mapping and sequence analysis of candidate genes revealed a homozygous mutation in MRPS22, a gene encoding a mitochondrial ribosomal small subunit protein. The mutation predicts a Leu215Pro substitution at an evolutionary conserved site. Mutations in genes implicated in Cornelia de Lange syndrome or copy number variations were not found. Transfection of patient fibroblasts, in which MRPS22 was undetectable, with the wild-type MRPS22 cDNA restored the amount and activity of OXPHOS complex IV, as well as the 12S rRNA transcript level to normal values. These findings demonstrate the pathogenicity of the MRPS22 mutation and stress the significance of mutations in nuclear genes, including genes that have no counterparts in lower species like bacteria and yeast, for mitochondrial translation defects