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Abstract We investigate the emergence, mutation profile, and dissemination of SARS-CoV-2 lineage B.1.214.2, first identified in Belgium in January 2021. This variant, featuring a 3-amino acid insertion in the spike protein similar to the Omicron variant, was speculated to enhance transmissibility or immune evasion. Initially detected in international travelers, it substantially transmitted in Central Africa, Belgium, Switzerland, and France, peaking in April 2021. Our travel-aware phylogeographic analysis, incorporating travel history, estimated the origin to the Republic of the Congo, with primary European entry through France and Belgium, and multiple smaller introductions during the epidemic. We correlate its spread with human travel patterns and air passenger data. Further, upon reviewing national reports of SARS-CoV-2 outbreaks in Belgian nursing homes, we found this strain caused moderately severe outcomes (8.7% case fatality ratio). A distinct nasopharyngeal immune response was observed in elderly patients, characterized by 80% unique signatures, higher B- and T-cell activation, increased type I IFN signaling, and reduced NK, Th17, and complement system activation, compared to similar outbreaks. This unique immune response may explain the variant's epidemiological behavior and underscores the need for nasal vaccine strategies against emerging variants.

Abstract Alternative splicing is crucial for cancer progression and can be targeted pharmacologically, yet identifying driver exons genome-wide remains challenging. We propose identifying such exons by associating statistically gene-level cancer dependencies from knockdown viability screens with splicing profiles and gene expression. Our models predict the effects of splicing perturbations on cell proliferation from transcriptomic data, enabling in silico RNA screening and prioritizing targets for splicing-based therapies. We identified 1,073 exons impacting cell proliferation, many from genes not previously linked to cancer. Experimental validation confirms their influence on proliferation, especially in highly proliferative cancer cell lines. Integrating pharmacological screens with splicing dependencies highlights the potential driver exons affecting drug sensitivity. Our models also allow predicting treatment outcomes from tumor transcriptomes, suggesting applications in precision oncology. This study presents an approach to identifying cancer driver exon and their therapeutic potential, emphasizing alternative splicing as a cancer target.

Abstract Proteins are often referred to as the workhorses of cells, and their interactions are necessary to facilitate specific cellular functions. Despite the recognition that protein-protein interactions, and thus protein functions, are determined by proteoform states, such as mutations and post-translational modifications (PTMs), methods for determining the differential abundance of proteoforms across conditions are very limited. Classically, immunoprecipitation coupled with mass spectrometry (IP-MS) has been used to understand how the interactome (preys) of a given protein (bait) changes between conditions to elicit specific cellular functions. Reversing this concept, we present here a new workflow for IP-MS data analysis that focuses on identifying the differential peptidoforms of the bait protein between conditions. This method can provide detailed information about specific bait proteoforms, potentially revealing pathogenic protein states that can be exploited for the development of targeted therapies.

Abstract Background Having a simple and fast dividing organism capable of producing and exposing at its surface or secreting functional complex biomolecules with disulphide bridges is of great interest. The mycoplasma bacterial genus offers a set of relevant properties that make it an interesting chassis for such purposes, the main one being the absence of a cell wall. However, due to their slow growth, they have rarely been considered as a potential platform in this respect. This notion may be challenged with the recent discovery of Mycoplasma feriruminatoris, a species with a dividing time close to that of common microbial workhorses. So far, no tools for heterologous protein expression nor secretion have been described for it. Results The work presented here develops the fast-dividing M. feriruminatoris as a tool for secreting functional biomolecules of therapeutic interest that could be used for screening functional mutants as well as potentially for protein-protein interactions. Based on RNAseq, quantitative proteomics and promoter sequence comparison we have rationally designed optimal promoter sequences. Then, using in silico analysis, we have identified putative secretion signals that we validated using a luminescent reporter. The potential of the resulting secretion cassette has been shown with set of active clinically relevant proteins (interleukins and nanobodies). Conclusions We have engineered Mycoplasma feriruminatoris for producing and secreting functional proteins of medical interest.

Despite the location (Earth or Space), surgical simulation is a vital part of improving technical skills and ensuring patients' safety in the real procedure. The purpose of this study is to describe the Space System for Minimally Invasive Surgery (SY-MIS©) project, which started in 2016 under the supervision of the Center for Space Systems (C-SET). The process connects the best features of the following machines: Biomedik Surgeon, Space Biosurgeon, SP-LAP 1, and SP-LAP 2, which were defined using the VDI 2221 guidelines. This research uses methods based on 3 standards: i) Biomedical design: ISO 9001-13485 / FDA 21 CFR 820.30 / ASTM F1744-96(2016); ii) Aerospace human factors: HF-STD-001; iii) Mechatronics design: VDI 2206. The results depict the conceptual biomedical design of a novel training system named Surgical Engineering and Mechatronic System (SETY©), which integrates the use of 2 laparoscopic tools and 2 anthropomorphic mini-robotic arms (6 DOF). It has been validated by the Evaluation of Technical Criteria, getting a total score of 90% related to clinical assessment, machine adaptability, and robustness. The novelty of the research lies in the introduction of a new procedure that covers the simultaneous use of laparoscopic and robotic systems, named Hybrid Cyber-Physical Surgery (HYS©). In conclusion, the development of SY-MIS© promotes the use of advanced technologies to improve surgical procedures and human-machine medical cooperation for the next frontier of habitability on other planets. Doi: 10.28991/ESJ-2024-08-02-01 Full Text: PDF

Abstract Alternative Splicing (AS) programs serve as instructive signals of cell type specificity, particularly within the brain, which comprises dozens of molecularly and functionally distinct cell types. Among them, retinal photoreceptors stand out due to their unique transcriptome, making them a particularly well-suited system for studying how AS shapes cell type-specific molecular functions. Here, we use the Splicing Regulatory State (SRS) as a novel framework to discuss the splicing factors governing the unique AS pattern of photoreceptors, and how this pattern may aid in the specification of their highly specialized sensory cilia. In addition, we discuss how other sensory cells with ciliated structures, for which data is much scarcer, also rely on specific SRSs to implement a proteome specialized in the detection of sensory stimuli. By reviewing the general rules of cell type- and tissue-specific AS programs, firstly in the brain and subsequently in specialized sensory neurons, we propose a novel paradigm on how SRSs are established and how they can diversify. Finally, we illustrate how SRSs shape the outcome of mutations in splicing factors to produce cell type-specific phenotypes that can lead to various human diseases.

Abstract Identifying open reading frames (ORFs) being translated is not a trivial task. ProTInSeq is a technique designed to characterize proteomes by sequencing transposon insertions engineered to express a selection marker when they occur in-frame within a protein-coding gene. In the bacterium Mycoplasma pneumoniae, ProTInSeq identifies 83% of its annotated proteins, along with 5 proteins and 153 small ORF-encoded proteins (SEPs; ≤100 aa) that were not previously annotated. Moreover, ProTInSeq can be utilized for detecting translational noise, as well as for relative quantification and transmembrane topology estimation of fitness and non-essential proteins. By integrating various identification approaches, the number of initially annotated SEPs in this bacterium increases from 27 to 329, with a quarter of them predicted to possess antimicrobial potential. Herein, we describe a methodology complementary to Ribo-Seq and mass spectroscopy that can identify SEPs while providing other insights in a proteome with a flexible and cost-effective DNA ultra-deep sequencing approach.

Individuals with Parkinson’s disease (PD) have a higher risk of developing dementia compared to age-matched controls. Rapid eye movement sleep behavior disorder (RBD) and hyposmia can influence symptoms severity. We report associations between polysomnography-assessed sleep architecture, olfactory identification, and cognition. Twenty adults with early-stage PD (mean age 69 ± 7.9; 25% female) completed cognitive assessments, the Brief Smell Identification Test (BSIT), and overnight in-clinic polysomnography. A global cognitive score was derived from principal component analysis. Linear regression models examined associations between sleep variables, BSIT performance, and cognition. Cognitive performance was compared between participants with and without RBD. Deep sleep attainment (β ± SE: 1.18 ± 0.45, p = .02) and olfactory identification (0.37 ± 0.12, p = .01) were associated with better cognition. Light sleep, REM sleep, arousal index, and sleep efficiency were not (all p > .05). Participants with RBD had significantly worse cognition ( t -test = −1.06 ± 0.44, p = .03) compared to those without RBD; none entered deep sleep. Deep sleep attainment was associated with better memory (1.20 ± 0.41, p = .01) and executive function (2.94 ± 1.13, p = .02); sleep efficiency was associated with executive function (0.05 ± 0.02, p = .02). These findings suggest interrelationships between lack of deep sleep, hyposmia, and poorer cognition in PD, particularly among individuals with RBD. Assessing these markers together may improve early identification of high-risk individuals and access to interventions.

The International Consensus Classification of Myeloid Neoplasms and Acute Leukemias (ICC) and the 5th edition of the WHO classification (WHO 2022) have refined the diagnosis of myelodysplastic syndromes (MDS). Both classifications segregate MDS subtypes based on molecular or cytogenetic findings but rely on the subjective assessment of blast cell percentage and dysplasia in hematopoietic cell lineages. This study aimed to evaluate interobserver concordance among 13 cytomorphologists from eight hospitals in assessing blast percentages and dysplastic features in 44 MDS patients. The study found fair interobserver agreement for the PB blast percentage and moderate agreement for the BM blast percentage, with the best concordance in cases with 10% BM blasts. Monocyte count agreement was fair, and dysplasia assessment showed moderate concordance for megakaryocytic lineage but lower concordance for erythroid and granulocytic lineages. Overall, interobserver concordance for MDS subtypes was moderate across all classifications, with slightly better results for WHO 2022. These findings highlight the ongoing need for morphological evaluation in MDS diagnosis despite advances in genetic and molecular techniques. The study supports the blast percentage ranges established by the ICC but suggests refining BM blast cutoffs. Given the moderate interobserver concordance, a unified classification approach for MDS is recommended.

In the context of isolated photovoltaic (PV) installations, selecting the optimal combination of modules and batteries is crucial for ensuring efficient and reliable energy supply. This paper presents a Decision Support System (DSS) designed to aid in the selection process of the development of new PV isolated installations. Two different multi-criteria decision-making (MCDM) approaches are employed and compared: AHP (Analytic Hierarchy Process) combined with TOPSIS (technique for order of preference by similarity to ideal solution) and Entropy combined with TOPSIS. AHP and Entropy are used to weight the technical and economic criteria considered, and TOPSIS ranks the alternatives. A comparative analysis of the AHP + TOPSIS and Entropy + TOPSIS methods was conducted to determine their effectiveness and applicability in real-world scenarios. The results show that AHP and Entropy produce contrasting criteria weights, yet TOPSIS converges on similar top-ranked alternatives using either set of weights, with the combination of lithium-ion batteries with the copper indium gallium selenide PV module as optimal. AHP allows for the incorporation of expert subjectivity, prioritising costs and an energy yield intuitive to PV projects. Entropy’s objectivity elevates criteria with limited data variability, potentially misrepresenting their true significance. Despite these discrepancies, this study highlights the practical implications of using structured decision support methodologies in optimising renewable energy systems. Even though the proposed methodology is applied to a PV isolated system, it can effectively support decision making for optimising other stand-alone or grid-connected installations, contributing to the advancement of sustainable energy solutions.

Abstract Triple‐negative breast cancer (TNBC) often develops resistance to single‐agent treatment, which can be circumvented using targeted combinatorial approaches. Here, we demonstrate that the simultaneous inhibition of LOXL2 and BRD4 synergistically limits TNBC proliferation in vitro and in vivo. Mechanistically, LOXL2 interacts in the nucleus with the short isoform of BRD4 (BRD4S), MED1, and the cell cycle transcriptional regulator B‐MyB. These interactions sustain the formation of BRD4 and MED1 nuclear transcriptional foci and control cell cycle progression at the gene expression level. The pharmacological co‐inhibition of LOXL2 and BRD4 reduces BRD4 nuclear foci, BRD4‐MED1 colocalization, and the transcription of cell cycle genes, thus suppressing TNBC cell proliferation. Targeting the interaction between BRD4S and LOXL2 could be a starting point for the development of new anticancer strategies for the treatment of TNBC.

Abstract Background Codon usage and nucleotide composition of coding sequences have profound effects on protein expression. However, while it is recognized that different tissues have distinct tRNA profiles and codon usages in their transcriptomes, the effect of tissue-specific codon optimality on protein synthesis remains elusive. Results We leverage existing state-of-the-art transcriptomics and proteomics datasets from the GTEx project and the Human Protein Atlas to compute the protein-to-mRNA ratios of 36 human tissues. Using this as a proxy of translational efficiency, we build a machine learning model that identifies codons enriched or depleted in specific tissues. We detect two clusters of tissues with an opposite pattern of codon preferences. We then use these identified patterns for the development of CUSTOM, a codon optimizer algorithm which suggests a synonymous codon design in order to optimize protein production in a tissue-specific manner. In human cell-line models, we provide evidence that codon optimization should take into account particularities of the translational machinery of the tissues in which the target proteins are expressed and that our approach can design genes with tissue-optimized expression profiles. Conclusions We provide proof-of-concept evidence that codon preferences exist in tissue-specific protein synthesis and demonstrate its application to synthetic gene design. We show that CUSTOM can be of benefit in biological and biotechnological applications, such as in the design of tissue-targeted therapies and vaccines.

Abstract Translation efficiency has been mainly studied by ribosome profiling, which only provides an incomplete picture of translation kinetics. Here, we integrated the absolute quantifications of tRNAs, mRNAs, RNA half‐lives, proteins, and protein half‐lives with ribosome densities and derived the initiation and elongation rates for 475 genes (67% of all genes), 73 with high precision, in the bacterium Mycoplasma pneumoniae (Mpn). We found that, although the initiation rate varied over 160‐fold among genes, most of the known factors had little impact on translation efficiency. Local codon elongation rates could not be fully explained by the adaptation to tRNA abundances, which varied over 100‐fold among tRNA isoacceptors. We provide a comprehensive quantitative view of translation efficiency, which suggests the existence of unidentified mechanisms of translational regulation in Mpn.

Abstract Background Independent Component Analysis (ICA) allows the dissection of omic datasets into modules that help to interpret global molecular signatures. The inherent randomness of this algorithm can be overcome by clustering many iterations of ICA together to obtain robust components. Existing algorithms for robust ICA are dependent on the choice of clustering method and on computing a potentially biased and large Pearson distance matrix. Results We present robustica, a Python-based package to compute robust independent components with a fully customizable clustering algorithm and distance metric. Here, we exploited its customizability to revisit and optimize robust ICA systematically. Of the 6 popular clustering algorithms considered, DBSCAN performed the best at clustering independent components across ICA iterations. To enable using Euclidean distances, we created a subroutine that infers and corrects the components’ signs across ICA iterations. Our subroutine increased the resolution, robustness, and computational efficiency of the algorithm. Finally, we show the applicability of robustica by dissecting over 500 tumor samples from low-grade glioma (LGG) patients, where we define two new gene expression modules with key modulators of tumor progression upon IDH1 and TP53 mutagenesis. Conclusion robustica brings precise, efficient, and customizable robust ICA into the Python toolbox. Through its customizability, we explored how different clustering algorithms and distance metrics can further optimize robust ICA. Then, we showcased how robustica can be used to discover gene modules associated with combinations of features of biological interest. Taken together, given the broad applicability of ICA for omic data analysis, we envision robustica will facilitate the seamless computation and integration of robust independent components in large pipelines.

The authors show that polyglutamylation of spindle microtubules is essential for error-free chromosome segregation and is mediated through Tubulin Tyrosine Ligase Like 11 (TTLL11), which is found to be frequently downregulated in cancer.

Nanocellulose (NC) has recently emerged as of high interest in water purification because of its high surface area, aspect ratio, and versatile surface chemistry. In the present study, nanocellulose has been isolated from cellulose pulp, extracted from barley straw residues via a mechanical pulping treatment, through a combination of chemical and mechanical refining treatments. The obtained cellulose pulp and (ligno)cellulose nanofibrils (L)CNFs, in the form of papers and nanopapers, respectively, were characterized in terms of mechanical properties. Finally, (L)CNFs-based aerogels were developed, and adsorption tests at 25 °C using 0.1 g of aerogels in 50 mL of methylene blue (MB) dye solution at 10 mg/L were studied. The results revealed that CNF-based aerogels can be exploited as an effective eco-adsorbent for the removal of methylene blue dye and provide a new platform for dye removal.

ABSTRACT To assist in the advancement of the large-scale production of safe Mycoplasma vaccines and other Mycoplasma-based therapies, we developed a culture medium free of animal serum and other animal components for Mycoplasma pneumoniae growth. By establishing a workflow method to systematically test different compounds and concentrations, we provide optimized formulations capable of supporting serial passaging and robust growth reaching 60 to 70% of the biomass obtained in rich medium. Global transcriptomic and proteomic analysis showed minor physiological changes upon cell culture in the animal component-free medium, supporting its suitability for the production of M. pneumoniae-based therapies. The major contributors to growth performance were found to be glucose as a carbon source, glycerol, cholesterol, and phospholipids as a source of fatty acids. Bovine serum albumin or cyclodextrin (in the animal component-free medium) were required as lipid carriers to prevent lipid toxicity. Connaught Medical Research Laboratories medium (CMRL) used to simplify medium preparation as a source of amino acids, nucleotide precursors, vitamins, and other cofactors could be substituted by cysteine. In fact, the presence of protein hydrolysates such as yeastolate or peptones was found to be essential and preferred over free amino acids, except for the cysteine. Supplementation of nucleotide precursors and vitamins is not strictly necessary in the presence of yeastolate, suggesting that this animal origin-free hydrolysate serves as an efficient source for these compounds. Finally, we adapted the serum-free medium formulation to support growth of Mycoplasma hyopneumoniae, a swine pathogen for which inactivated whole-cell vaccines are available. IMPORTANCE Mycoplasma infections have a significant negative impact on both livestock production and human health. Vaccination is often the first option to control disease and alleviate the economic impact that some Mycoplasma infections cause on milk production, weight gain, and animal health. The fastidious nutrient requirements of these bacteria, however, challenges the industrial production of attenuated or inactivated whole-cell vaccines, which depends on the use of animal serum and other animal raw materials. Apart from their clinical relevance, some Mycoplasma species have become cellular models for systems and synthetic biology, owing to the small size of their genomes and the absence of a cell wall, which offers unique opportunities for the secretion and delivery of biotherapeutics. This study proposes medium formulations free of serum and animal components with the potential of supporting large-scale production upon industrial optimization, thus contributing to the development of safe vaccines and other Mycoplasma-based therapies.

(1) Background: Nanostructured cellulose has emerged as an efficient bio-adsorbent aerogel material, offering biocompatibility and renewable sourcing advantages. This study focuses on isolating (ligno)cellulose nanofibers ((L)CNFs) from barley straw and producing aerogels to develop sustainable and highly efficient decontamination systems. (2) Methods: (Ligno)cellulose pulp has been isolated from barley straw through a pulping process, and was subsequently deconstructed into nanofibers employing various pre-treatment methods (TEMPO-mediated oxidation process or PFI beater mechanical treatment) followed by the high-pressure homogenization (HPH) process. (3) Results: The aerogels made by (L)CNFs, with a higher crystallinity degree, larger aspect ratio, lower shrinkage rate, and higher Young’s modulus than cellulose aerogels, successfully adsorb and remove organic dye pollutants from wastewater. (L)CNF-based aerogels, with a quality index (determined using four characterization parameters) above 70%, exhibited outstanding contaminant removal capacity over 80%. The high specific surface area of nanocellulose isolated using the TEMPO oxidation process significantly enhanced the affinity and interactions between hydroxyl and carboxyl groups of nanofibers and cationic groups of contaminants. The efficacy in adsorbing cationic dyes in wastewater onto the aerogels was verified by the Langmuir adsorption isotherm model. (4) Conclusions: This study offers insights into designing and applying advanced (L)CNF-based aerogels as efficient wastewater decontamination and environmental remediation platforms.

O objetivo desta investigação é verificar as necessidades dos utilizadores de bibliotecas de imigrantes, bem como a existência, eficácia e eficiência dos serviços de biblioteca para este grupo, dado que, como tem sido observado nos últimos anos, a imigração está a aumentar de forma constante. Em primeiro lugar, começamos com uma revisão bibliográfica, através da qual são delineadas a utilização e as necessidades dos imigrantes no que diz respeito aos serviços da biblioteca. Segue-se um estudo que consiste numa análise dos serviços de 26 bibliotecas nacionais em termos de IDH, número de bibliotecas por habitante e número de imigrantes no país (originalmente o ponto de partida era 30 países, 10 por indicador, mas devido às repetições e à existência de um como protetorado, este foi reduzido para 26). Para este efeito, foi efetuada uma análise dos sítios Web das bibliotecas nacionais dos países selecionados acima mencionados, em busca de serviços específicos para este grupo (em Abril de 2020). Esta investigação mostra-nos a falta de serviços e/ou de serviços eficazes para os utilizadores imigrantes. Uma vez recolhidos estes dados, e acrescentados à pesquisa bibliográfica anteriormente realizada, conclui-se que existe a necessidade de implementar, melhorar e atualizar os serviços acima mencionados para os migrantes.

La wifala es un personaje tradicional en los carnavales de la comunidad campesina de Ccoyllorpuquio. Este es un ser ambiguo, ya que es interpretado por un varón vestido con ropas de mujer. El concepto de lo liminal permite definir a priori la ambigüedad de las wifalas, ya que existe una coincidencia de contrarios en la significación del personaje. Así, lo liminal en la cultura es definido por aquello que no se encuentra ni en un sitio ni en otro; en el ámbito ritual, está representado por símbolos que representan transiciones como la muerte, la bisexualidad o los tiempos de orto y ocaso. Sin embargo, el objetivo principal de este artículo es dar a comprender la wifala —y su aparente condición liminal— desde la perspectiva de los propios protagonistas de la costumbre y de la comunidad que los representa. Siguiendo esa pauta, se estableció un corpus a partir de la revisión bibliográfica y etnográfica sobre el significado de la wifala. Desde la perspectiva de los comuneros de Ccoyllorpuquio, wifala es “el costumbre” de sus antepasados; de modo que otros términos y conceptos académicos no son suficientes para explicar el fenómeno, ya que es necesario entenderlo desde “el costumbre”, es decir, como una lógica ontológica que se aprende haciendo. Así, el principal fenómeno en la diferencia de estas perspectivas será la traducción, ya que el problema se presta al régimen del poder de la colonialidad, en cuanto no permite generar un ambiente de pertinencia cultural. De esta forma, esta investigación aporta a la negación de un constructivismo intelectual en un único sentido y permite una apertura a la re-creación intelectual en comunidad.

Ethanolic extracts of bay leaves were obtained using the Soxhlet method (extraction yield of 22.3 ± 1.2%) and further analyzed through different methods, thus determining the chemical composition with gas chromatography, phenolic content with the Folin–Ciocalteu technique (11.8 ± 0.4% wt.) and antioxidant power with the radical 2,2′-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) method (75.06%). Furthermore, its effect on the growth of two bacteria, Escherichia coli and Bacillus cereus, and on two yeasts, Candida glabrata and Saccharomyces cerevisiae, was determined, showing a minimum inhibitory concentration of 0.65 mg/mL on the growth of B. cereus. Finally, edible films were prepared using different polymers (carboxymethyl cellulose, gum Arabic, polyvinyl pyrrolidone, and polyvinyl alcohol) containing 0, 5, 10, or 15% wt. of bay leaf extract as troubleshooting for perishable fruits, specifically for cultivated strawberry. The prepared composites presented reduced water vapor permeabilities (up to 4.3 × 10−7 g·Pa−1·m−1·h−1), high specific transparencies (≈30%/mm), as well as the effective blocking of ultraviolet radiation (>99.9%). In vivo tests showed that the most suitable treatment for strawberry protection was the impregnation with a composite comprising polyvinyl alcohol and a 15% wt. bay leaf extract, resulting in a noteworthy reduction in mass loss (22% after 6 days). It can be asserted that food packaging with the designed composites would be an effective alternative for the reduction in postharvest losses.

Abstract Interleukin‐10 (IL‐10) is an anti‐inflammatory cytokine that is active as a swapped domain dimer and is used in bacterial therapy of gut inflammation. IL‐10 can be used as treatment of a wide range of pulmonary diseases. Here we have developed a non‐pathogenic chassis (CV8) of the human lung bacterium Mycoplasma pneumoniae (MPN) to treat lung diseases. We find that IL‐10 expression by MPN has a limited impact on the lung inflammatory response in mice. To solve these issues, we rationally designed a single‐chain IL‐10 (SC‐IL10) with or without surface mutations, using our protein design software (ModelX and FoldX). As compared to the IL‐10 WT, the designed SC‐IL10 molecules increase the effective expression in MPN four‐fold, and the activity in mouse and human cell lines between 10 and 60 times, depending on the cell line. The SC‐IL10 molecules expressed in the mouse lung by CV8 in vivo have a powerful anti‐inflammatory effect on Pseudomonas aeruginosa lung infection. This rational design strategy could be used to other molecules with immunomodulatory properties used in bacterial therapy.

Summary The removal of unwanted genetic material is a key aspect in many synthetic biology efforts and often requires preliminary knowledge of which genomic regions are dispensable. Typically, these efforts are guided by transposon mutagenesis studies, coupled to deepsequencing (TnSeq) to identify insertion points and gene essentiality. However, epistatic interactions can cause unforeseen changes in essentiality after the deletion of a gene, leading to the redundancy of these essentiality maps. Here, we present LoxTnSeq, a new methodology to generate and catalogue libraries of genome reduction mutants. LoxTnSeq combines random integration of lox sites by transposon mutagenesis, and the generation of mutants via Cre recombinase, catalogued via deep sequencing. When LoxTnSeq was applied to the naturally genome reduced bacterium Mycoplasma pneumoniae, we obtained a mutant pool containing 285 unique deletions. These deletions spanned from > 50 bp to 28 Kb, which represents 21% of the total genome. LoxTnSeq also highlighted large regions of non‐essential genes that could be removed simultaneously, and other non‐essential regions that could not, providing a guide for future genome reductions.

The use of biofuels in vehicles becomes more advantageous than the consumption of fossil fuels, mainly because it uses renewable sources of energy. Recently there are some concerns about biodiesel sources, and hydrotreated vegetable oils (HVO) appear as a possible advanced solution. To understand the effect that the implementation of the new and old European type-approval test cycles (NEDC e WLTP) has on the results of these fuels considering pollutant emissions and fuel consumption results, a EURO V vehicle was subject to these cycles and also to engine performance evaluation tests. For this analysis, the fuels considered were: B0 (pure diesel), B7 (7% of biodiesel), B15 (15% of biodiesel), B100 (pure biodiesel), and HVO15 (15% of HVO). The findings lead to the conclusion that completely replacing fossil fuels with biofuels is not the most cost-effective approach. No significant differences were observed considering the two homologation cycles, the oldest (NEDC) and the actual (WLTP) and the use of HVO also does not present any relevant differences concerning the fuel consumption differences to B0 (+0.58% NEDC and +0.05%WLTP), comparing well with biodiesel behavior (−1.74% NEDC and −0.69%WLTP for B7 and +1.48% NEDC and 1.89% WLTP for B15). Considering the power of the engine obtained with the fuels, the differences are almost negligible, revealing variations smaller than 2% for B7, B15, and HVO15.

Abstract Background Open streets events, where roads are temporarily closed to motorized vehicles, can provide safe spaces for physical activity (PA) and become sustainable community infrastructure. Since 2016, we have collaborated with a rural community to implement an open streets event, named ciclovía. In 2019, ciclovía was adopted as a community-wide program. This paper describes the process of building and progressing a ciclovía from a research intervention to a community-adopted program and participation of a rural community in ciclovía. Methods We used community-based participatory research to foster bidirectional learning on how to optimize the content and implementation of ciclovía to be feasible and acceptable for rural communities. The community-academic partnership focused on: 1) understanding the science of ciclovía; 2) learning the implementation process; 3) creating tools to facilitate planning, implementation, and evaluation of ciclovía; and 4) developing transition steps from a research intervention to a community-adopted program. Results The progression of the research intervention to community adoption spanned 2 years. First, the partnership met quarterly to discuss the science of ciclovía, its utility, and its adaptation for rural communities. Second, the partnership studied processes that facilitated ciclovía implementation. Third, the partnership created the ciclovía planning guide and tools for communities to establish their own ciclovía. The guide included forming a planning committee, setting meeting and communication plans, marketing and promotion, and selecting evaluation tools. Fourth, the transition steps from research intervention to community adoption included creating roles and responsibilities, implementing ciclovía using the planning guide, and convening listening sessions for improvement on implementation. Community attendance at ciclovía doubled from 189 individuals (126 children and 63 adults) when it was a research intervention to 394 individuals (277 children and 117 adults) when it was a community program. Conclusions The progression from a research intervention to a community-adopted program encompasses multiple steps that involve bidirectional learning and partnership with the community. Lessons learned from this study are integrated into a disseminatable ciclovía planning guide.

The human pathogen Mycoplasma pneumoniae is viable independently from host cells or organisms, despite its strongly reduced genome with only about 700 protein-coding genes. The investigation of M. pneumoniae can therefore help to obtain general insights concerning the basic requirements for cellular life. Accordingly, M. pneumoniae has become a model organism for systems biology in the past decade. To support the investigation of the components of this minimal bacterium, we have generated the database MycoWiki. (http://mycowiki.uni-goettingen.de) MycoWiki organizes data under a relational database and provides access to curated and state-of-the-art information on the genes and proteins of M. pneumoniae. Interestingly, M. pneumoniae has undergone an evolution that resulted in the limited similarity of many proteins to proteins of model organisms. To facilitate the analysis of the functions of M. pneumoniae proteins, we have integrated structure predictions from the AlphaFold Protein Structure Database for most proteins, structural information resulting from in vivo cross-linking, and protein-protein interactions based on a global in vivo study. MycoWiki is an important tool for the systems and synthetic biology community that will support the comprehensive understanding of a minimal organism and the functional annotation of so far uncharacterized proteins.

As a transition strategy towards sustainability, food packaging plays a crucial role in the current era. This, carried out in a biorefinery context of agricultural residues, involves not only obtaining desirable products but a comprehensive utilization of biomass that contributes to the circular bioeconomy. The present work proposes the preparation of bioactive absorbent food pads through a multi-product biorefinery approach from bay tree pruning waste (BTPW). In a first step, chitosan aerogels reinforced with lignocellulose and cellulose micro/nanofibers from BTPW were prepared, studying the effect of residual lignin on the material’s properties. The presence of micro/nanofibers improved the mechanical performance (up to 60%) in addition to increasing the water uptake (42%) when lignin was present. The second step was to make them bioactive by incorporating bay leaf extract. The residual lignin in the micro/nanofibers was decisive, since when present, the release profiles of the extract were faster, reaching an antioxidant power of more than 85% after only 30 min. Finally, these bioactive aerogels were used as absorbent pads for fresh meat. With the use of the bioactive aerogels (with ≥2% extract), the meat remained fresh for 10 days as a result of delayed oxidation of the food during storage (20% metmyoglobin proportion).

La impresión por hilo fundido (FDM, por sus siglas en inglés) tiene una gran cantidad de parámetros que influyen directamente sobre la calidad y las propiedades mecánicas de la pieza final. Actualmente, la manufactura aditiva por FDM ha presentado un gran auge para desarrollos de prótesis por su bajo costo respecto a otros procesos de manufactura; además, esta tecnología es de gran interés para el área de la medicina, dada su capacidad de crear soluciones personalizadas para cada paciente, debido a la variedad de materiales que se pueden emplear, ya que hay una amplia oferta de empresas que fabrican y suministran impresoras y materiales para la impresión. En este trabajo se investigó la influencia de la densidad y de la geometría de los patrones de relleno sobre el esfuerzo máximo, el esfuerzo de fluencia y el módulo de elasticidad a la compresión, en probetas de PLA elaboradas mediante manufactura aditiva con la técnica modelado por FDM. Se emplearon densidades de 10 %, 25 %, 50 %, 75 % y 100 %, y los parámetros de relleno utilizados fueron trihexagonal, subdivisión cúbica y giroide. Todas las probetas se sometieron a ensayos de compresión para calcular sus propiedades mecánicas, y en términos generales se observó que, al aumentar la densidad de relleno, se presenta un aumento en las propiedades a la compresión del material, y la geometría del patrón de relleno puede alterar estas propiedades.

Abstract Age-related macular degeneration (AMD) is one of the commonest causes of sight loss in the elderly population and to date there is no intervention that slows or prevents early AMD disease progressing to blinding neovascularization or geographic atrophy. AMD is a complex disease and factors proposed to contribute to the development and progression of disease include aging, genetics, epigenetics, oxidative stress, pro-inflammatory state, and life-style factors such as smoking, alcohol, and high fat diet. Here, we generate a knowledge repository of pathways and protein–protein interaction (PPI) networks likely to be implicated in AMD pathogenesis, such as complement activation, lipid trafficking and metabolism, vitamin A cycle, oxidative stress, proteostasis, bioenergetics, autophagy/mitophagy, extracellular matrix (ECM) turnover, and choroidal vascular dropout. Two disctinct clusters ermerged from the networks for parainflamation and ECM homeostasis, which may represent two different disease modules underlying AMD pathology. Our analyses also suggest that the disease manifests primarily in RPE/choroid and less in neural retina. The use of standardized syntax when generating maps of these biological processes (SBGN standard) and networks (PSI standard) enables visualization of complex information in graphical programs such as CellDesigner and Cytoscape and enhances reusability and extension of data. The ability to focus onto subnetworks, multiple visualizations and simulation options will enable the AMD research community to computationally model subnetworks or to test experimentally new hypotheses arising from connectivities in the AMD pathway map.

Kras is often mutated in colorectal cancer but how this oncogenic mutation alters signalling pathways globally is undetermined. Here, the authors analyse how this mutation affects protein interaction networks and signal flow showing an extensive re‐wiring of signalling in response to KRas mutation

Abstract Bacteria present a promising delivery system for treating human diseases. Here, we engineered the genome‐reduced human lung pathogen Mycoplasma pneumoniae as a live biotherapeutic to treat biofilm‐associated bacterial infections. This strain has a unique genetic code, which hinders gene transfer to most other bacterial genera, and it lacks a cell wall, which allows it to express proteins that target peptidoglycans of pathogenic bacteria. We first determined that removal of the pathogenic factors fully attenuated the chassis strain in vivo. We then designed synthetic promoters and identified an endogenous peptide signal sequence that, when fused to heterologous proteins, promotes efficient secretion. Based on this, we equipped the chassis strain with a genetic platform designed to secrete antibiofilm and bactericidal enzymes, resulting in a strain capable of dissolving Staphylococcus aureus biofilms preformed on catheters in vitro, ex vivo, and in vivo. To our knowledge, this is the first engineered genome‐reduced bacterium that can fight against clinically relevant biofilm‐associated bacterial infections.

It is well-established that FtsZ drives peptidoglycan synthesis at the division site in walled bacteria. However, the function and conservation of FtsZ in wall-less prokaryotes such as mycoplasmas are less clear. In the genome-reduced bacterium Mycoplasma genitalium, the cell division gene cluster is limited to four genes: mraZ, mraW, MG_223, and ftsZ. In a previous study, we demonstrated that ftsZ was dispensable for growth of M. genitalium under laboratory culture conditions. Herein, we show that the entire cell division gene cluster of M. genitalium is non-essential for growth in vitro. Our analyses indicate that loss of the mraZ gene alone is more detrimental for growth of M. genitalium than deletion of ftsZ or the entire cell division gene cluster. Transcriptional analysis revealed a marked upregulation of ftsZ in the mraZ mutant. Stable isotope labeling by amino acids in cell culture (SILAC)-based proteomics confirmed the overexpression of FtsZ in MraZ-deprived cells. Of note, we found that ftsZ expression was upregulated in non-adherent cells of M. genitalium, which arise spontaneously at relatively high rates. Single cell analysis using fluorescent markers showed that FtsZ localization varied throughout the cell cycle of M. genitalium in a coordinated manner with the chromosome and the terminal organelle (TMO). In addition, our results indicate a possible role for the RNA methyltransferase MraW in the regulation of FtsZ expression at the post-transcriptional level. Altogether, this study provides an extensive characterization of the cell division gene cluster of M. genitalium and demonstrates the existence of regulatory elements controlling FtsZ expression at the temporal and spatial level in mycoplasmas.

Summary: Trans-translation is a ubiquitous bacterial mechanism of ribosome rescue mediated by a transfer-messenger RNA (tmRNA) that adds a degradation tag to the truncated nascent polypeptide. Here, we characterize this quality control system in a genome-reduced bacterium, Mycoplasma pneumoniae (MPN), and perform a comparative analysis of protein quality control components in slow and fast-growing prokaryotes. We show in vivo that in MPN the sole quality control cytoplasmic protease (Lon) degrades efficiently tmRNA-tagged proteins. Analysis of tmRNA-mutants encoding a tag resistant to proteolysis reveals extensive tagging activity under normal growth. Unlike knockout strains, these mutants are viable demonstrating the requirement of tmRNA-mediated ribosome recycling. Chaperone and Lon steady-state levels maintain proteostasis in these mutants suggesting a model in which co-evolution of Lon and their substrates offer simple mechanisms of regulation without specialized degradation machineries. Finally, comparative analysis shows relative increase in Lon/Chaperone levels in slow-growing bacteria suggesting physiological adaptation to growth demand.

Abstract Background Cancer is a rapidly evolving, multifactorial disease that accumulates numerous genetic and epigenetic alterations. This results in molecular and phenotypic heterogeneity within the tumor, the complexity of which is further amplified through specific interactions between cancer cells. We aimed to dissect the molecular mechanisms underlying the cooperation between different clones. Methods We produced clonal cell lines derived from the MDA-MB-231 breast cancer cell line, using the UbC-StarTrack system, which allowed tracking of multiple clones by color: GFP C3, mKO E10 and Sapphire D7. Characterization of these clones was performed by growth rate, cell metabolic activity, wound healing, invasion assays and genetic and epigenetic arrays. Tumorigenicity was tested by orthotopic and intravenous injections. Clonal cooperation was evaluated by medium complementation, co-culture and co-injection assays. Results Characterization of these clones in vitro revealed clear genetic and epigenetic differences that affected growth rate, cell metabolic activity, morphology and cytokine expression among cell lines. In vivo, all clonal cell lines were able to form tumors; however, injection of an equal mix of the different clones led to tumors with very few mKO E10 cells. Additionally, the mKO E10 clonal cell line showed a significant inability to form lung metastases. These results confirm that even in stable cell lines heterogeneity is present. In vitro, the complementation of growth medium with medium or exosomes from parental or clonal cell lines increased the growth rate of the other clones. Complementation assays, co-growth and co-injection of mKO E10 and GFP C3 clonal cell lines increased the efficiency of invasion and migration. Conclusions These findings support a model where interplay between clones confers aggressiveness, and which may allow identification of the factors involved in cellular communication that could play a role in clonal cooperation and thus represent new targets for preventing tumor progression.

Las fiestas patronales se realizan durante todo el año en las parroquias de la ciudad del Cusco y, comprenden diversas expresiones culturales autóctonas, que conforman un atractivo cultural de gran potencial; sin embargo, no forman parte activa de la oferta turística, lo cual no permite promocionar ni diversificar el producto turístico. El objetivo de esta investigación fue describir y categorizar las características de las fiestas patronales de la ciudad del Cusco como producto turístico cultural en potencia. La muestra de estudio consideró 35 fiestas patronales del calendario festivo y el análisis de la información fue recolectado en la ficha de categorización del patrimonio inmaterial del Ministerio de Cultura. El tipo de investigación fue cualitativa, de nivel exploratorio/descriptivo y la metodología de investigación fue inductiva. El análisis demostró que las fiestas patronales del Cusco, al ser categorizadas como atractivo turístico cultural, permiten su incorporación a la oferta turística actual. Junto con ello, se recomendó la jerarquización y promoción turística de las festividades y la sensibilización y capacitación de las personas involucradas en dicha actividad turística.

RNA splicing is widely dysregulated in cancer, frequently due to altered expression or activity of splicing factors (SFs). Microexons are extremely small exons (3-27 nucleotides long) that are highly evolutionarily conserved and play critical roles in promoting neuronal differentiation and development. Inclusion of microexons in mRNA transcripts is mediated by the SF Serine/Arginine Repetitive Matrix 4 (SRRM4), whose expression is largely restricted to neural tissues. However, microexons have been largely overlooked in prior analyses of splicing in cancer, as their small size necessitates specialized computational approaches for their detection. Here, we demonstrate that despite having low expression in normal nonneural tissues, SRRM4 is further silenced in tumors, resulting in the suppression of normal microexon inclusion. Remarkably, SRRM4 is the most consistently silenced SF across all tumor types analyzed, implying a general advantage of microexon down-regulation in cancer independent of its tissue of origin. We show that this silencing is favorable for tumor growth, as decreased SRRM4 expression in tumors is correlated with an increase in mitotic gene expression, and up-regulation of SRRM4 in cancer cell lines dose-dependently inhibits proliferation in vitro and in a mouse xenograft model. Further, this proliferation inhibition is accompanied by induction of neural-like expression and splicing patterns in cancer cells, suggesting that SRRM4 expression shifts the cell state away from proliferation and toward differentiation. We therefore conclude that SRRM4 acts as a proliferation brake, and tumors gain a selective advantage by cutting off this brake.

Abstract Protein degradation is a crucial cellular process in all‐living systems. Here, using Mycoplasma pneumoniae as a model organism, we defined the minimal protein degradation machinery required to maintain proteome homeostasis. Then, we conditionally depleted the two essential ATP‐dependent proteases. Whereas depletion of Lon results in increased protein aggregation and decreased heat tolerance, FtsH depletion induces cell membrane damage, suggesting a role in quality control of membrane proteins. An integrative comparative study combining shotgun proteomics and RNA‐seq revealed 62 and 34 candidate substrates, respectively. Cellular localization of substrates and epistasis studies supports separate functions for Lon and FtsH. Protein half‐life measurements also suggest a role for Lon‐modulated protein decay. Lon plays a key role in protein quality control, degrading misfolded proteins and those not assembled into functional complexes. We propose that regulating complex assembly and degradation of isolated proteins is a mechanism that coordinates important cellular processes like cell division. Finally, by considering the entire set of proteases and chaperones, we provide a fully integrated view of how a minimal cell regulates protein folding and degradation.

The coronavirus disease COVID-19 constitutes the most severe pandemic of the last decades having caused more than 1 million deaths worldwide. The SARS-CoV-2 virus recognizes the angiotensin converting enzyme 2 (ACE2) on the surface of human cells through its spike protein. It has been reported that the coronavirus can mildly infect cats, and ferrets, and perhaps dogs while not pigs, mice, chicken and ducks. Differences in viral infectivity among different species or individuals could be due to amino acid differences at key positions of the host proteins that interact with the virus, the immune response, expression levels of host proteins and translation efficiency of the viral proteins among other factors. Here, first we have addressed the importance that sequence variants of different animal species, human individuals and virus isolates have on the interaction between the RBD domain of the SARS-CoV-2 spike S protein and human angiotensin converting enzyme 2 (ACE2). Second, we have looked at viral translation efficiency by using the tRNA adaptation index. We find that integration of both interaction energy with ACE2 and translational efficiency explains animal infectivity. Humans are the top species in which SARS-CoV-2 is both efficiently translated as well as optimally interacting with ACE2. We have found some viral mutations that increase affinity for hACE and some hACE2 variants affecting ACE2 stability and virus binding. These variants suggest that different sensitivities to coronavirus infection in humans could arise in some cases from allelic variability affecting ACE2 stability and virus binding.

Summary: Here, we propose an approach to identify active metabolic pathways by integrating gene essentiality analysis and protein abundance. We use two bacterial species (Mycoplasma pneumoniae and Mycoplasma agalactiae) that share a high gene content similarity yet show significant metabolic differences. First, we build detailed metabolic maps of their carbon metabolism, the most striking difference being the absence of two key enzymes for glucose metabolism in M. agalactiae. We then determine carbon sources that allow growth in M. agalactiae, and we introduce glucose-dependent growth to show the functionality of its remaining glycolytic enzymes. By analyzing gene essentiality and performing quantitative proteomics, we can predict the active metabolic pathways connected to carbon metabolism and show significant differences in use and direction of key pathways despite sharing the large majority of genes. Gene essentiality combined with quantitative proteomics and metabolic maps can be used to determine activity and directionality of metabolic pathways.

Abstract The C‐terminal sequence of a protein is involved in processes such as efficiency of translation termination and protein degradation. However, the general relationship between features of this C‐terminal sequence and levels of protein expression remains unknown. Here, we identified C‐terminal amino acid biases that are ubiquitous across the bacterial taxonomy (1,582 genomes). We showed that the frequency is higher for positively charged amino acids (lysine, arginine), while hydrophobic amino acids and threonine are lower. We then studied the impact of C‐terminal composition on protein levels in a library of Mycoplasma pneumoniae mutants, covering all possible combinations of the two last codons. We found that charged and polar residues, in particular lysine, led to higher expression, while hydrophobic and aromatic residues led to lower expression, with a difference in protein levels up to fourfold. We further showed that modulation of protein degradation rate could be one of the main mechanisms driving these differences. Our results demonstrate that the identity of the last amino acids has a strong influence on protein expression levels.

Abstract Different tissues express genes with particular codon usage and anticodon tRNA repertoires. However, the codon–anticodon co‐adaptation in humans is not completely understood, nor is its effect on tissue‐specific protein levels. Here, we first validated the accuracy of small RNA‐seq for tRNA quantification across five human cell lines. We then analyzed the tRNA abundance of more than 8,000 tumor samples from TCGA, together with their paired mRNA‐seq and proteomics data, to determine the Supply‐to‐Demand Adaptation. We thereby elucidate that the dynamic adaptation of the tRNA pool is largely related to the proliferative state across tissues. The distribution of such tRNA pools over the whole cellular translatome affects the subsequent translational efficiency, which functionally determines a condition‐specific expression program both in healthy and tumor states. Furthermore, the aberrant translational efficiency of some codons in cancer, exemplified by ArgAGA, is associated with poor patient survival†. The regulation of these tRNA profiles is partly explained by the tRNA gene copy numbers and their promoter DNA methylation.

The efficient and selective detection of volatile organic compounds (VOCs) provides key information for various purposes ranging from the toxicological analysis of indoor/outdoor environments to the diagnosis of diseases or to the investigation of biological processes. In the last decade, different sensors and biosensors providing reliable, rapid, and economic responses in the detection of VOCs have been successfully conceived and applied in numerous practical cases; however, the global necessity of a sustainable development, has driven the design of devices for the detection of VOCs to greener methods. In this review, the most recent and innovative VOC sensors and biosensors with sustainable features are presented. The sensors are grouped into three of the main industrial sectors of daily life, including environmental analysis, highly important for toxicity issues, food packaging tools, especially aimed at avoiding the spoilage of meat and fish, and the diagnosis of diseases, crucial for the early detection of relevant pathological conditions such as cancer and diabetes. The research outcomes presented in the review underly the necessity of preparing sensors with higher efficiency, lower detection limits, improved selectivity, and enhanced sustainable characteristics to fully address the sustainable manufacturing of VOC sensors and biosensors.

Current methods to unveil protein–protein and protein–RNA interactions often involve long, costly procedures. Here the authors present a rapid yeast 2- and 3-hybrid screening pipeline to detect interactions within protein libraries or between protein libraries and RNA fragment pools.

Abstract Background Proteins of the ubiquitously expressed core proteome are quantitatively correlated across multiple eukaryotic species. In addition, it was found that many protein paralogues exhibit expression anticorrelation, suggesting that the total level of protein with a given functionality must be kept constant. Methods We performed Spearman’s rank correlation analyses of gene expression levels for the RAS GTPase subfamily and their regulatory GEF and GAP proteins across tissues and across individuals for each tissue. A large set of published data for normal tissues from a wide range of species, human cancer tissues and human cell lines was analysed. Results We show that although the multidomain regulatory proteins of Ras GTPases exhibit considerable tissue and individual gene expression variability, their total amounts are balanced in normal tissues. In a given tissue, the sum of activating (GEFs) and deactivating (GAPs) domains of Ras GTPases can vary considerably, but each person has balanced GEF and GAP levels. This balance is impaired in cell lines and in cancer tissues for some individuals. Conclusions Our results are relevant for critical considerations of knock out experiments, where functionally related homologs may compensate for the down regulation of a protein.

Abstract Background Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments.

The monolithic materials of reduced graphene oxide (rGO) can be used successfully in CO2 adsorption. Here, the incorporation of CeO2 particles with and without polymer brushes grafted from the particles showed that the structural properties could be changed, affecting the adsorption of CO2. Polymer brushes of (1) poly(acrylic acid) (PAA), (2) poly(vinyl caprolactam) (PVCL) and (3) poly[(2-(methacryloyloxy)ethyl) trimethylammonium chloride] (PMETAC) were grafted from CeO2 via reversible addition−fragmentation chain transfer (RAFT) polymerization. The preparation of monoliths of rGO with different modified CeO2 particles led to different thermal properties (TGA), structural changes (BET isotherms) and CO2 adsorption. The responsive character of the CeO2@polymer was proven by the DLS and UV results. The responsive character of the particles incorporated into the rGO monolith affected not only the adsorption capacity but also the microstructure and values of the surface volume of the pores of the monolith. Monoliths with porosity values for better adsorption were affected by the responsive character of the polymer.