Avoidance of apoptosis is critical for the development and sustained growth of tumours. The pro-survival protein myeloid cell leukemia 1 (MCL1) is overexpressed in many cancers, but the development ...of small molecules targeting this protein that are amenable for clinical testing has been challenging. Here we describe S63845, a small molecule that specifically binds with high affinity to the BH3-binding groove of MCL1. Our mechanistic studies demonstrate that S63845 potently kills MCL1-dependent cancer cells, including multiple myeloma, leukaemia and lymphoma cells, by activating the BAX/BAK-dependent mitochondrial apoptotic pathway. In vivo, S63845 shows potent anti-tumour activity with an acceptable safety margin as a single agent in several cancers. Moreover, MCL1 inhibition, either alone or in combination with other anti-cancer drugs, proved effective against several solid cancer-derived cell lines. These results point towards MCL1 as a target for the treatment of a wide range of tumours.
Currently available tools for multiplex bacterial genome engineering are optimized for a few laboratory model strains, demand extensive prior modification of the host strain, and lead to the ...accumulation of numerous off-target modifications. Building on prior development of multiplex automated genome engineering (MAGE), our work addresses these problems in a single framework. Using a dominant-negative mutant protein of the methyl-directed mismatch repair (MMR) system, we achieved a transient suppression of DNA repair in Escherichia coli, which is necessary for efficient oligonucleotide integration. By integrating all necessary components into a broad-host vector, we developed a new workflow we term pORTMAGE. It allows efficient modification of multiple loci, without any observable off-target mutagenesis and prior modification of the host genome. Because of the conserved nature of the bacterial MMR system, pORTMAGE simultaneously allows genome editing and mutant library generation in other biotechnologically and clinically relevant bacterial species. Finally, we applied pORTMAGE to study a set of antibiotic resistance-conferring mutations in Salmonella enterica and E. coli. Despite over 100 million y of divergence between the two species, mutational effects remained generally conserved. In sum, a single transformation of a pORTMAGE plasmid allows bacterial species of interest to become an efficient host for genome engineering. These advances pave the way toward biotechnological and therapeutic applications. Finally, pORTMAGE allows systematic comparison of mutational effects and epistasis across a wide range of bacterial species.
To capture highly dynamic biological processes at cellular resolution is a recurring challenge in biology. Here we show that combining selective-volume illumination with simultaneous acquisition of ...orthogonal light fields yields three-dimensional images with high, isotropic spatial resolution and a significant reduction of reconstruction artefacts, thereby overcoming current limitations of light-field microscopy implementations. We demonstrate medaka heart and blood flow imaging at single-cell resolution and free of motion artefacts at volume rates of up to 200 Hz.
Drawing on our long-term research experiences, in this deliberately provocative but also reflexive paper we argue that international food and agriculture studies constitute a research area that would ...particularly benefit from insights obtained from research conducted in the world's peripheries—in this case, specifically from insights on East European food systems. Instead of seeing them as textbook case studies of undeveloped, traditional and hence uninspiring systems, we propose to study them from the East European perspective. This enables us to move away from a unidirectional development path and to acknowledge the diversity, resilience and unintended but real sustainability of the melange of East European formal and informal food systems. Such endeavour reveals food practices that cannot easily be reduced to ‘food chains’, ‘food initiatives’ or diets. It recognises meanings that go beyond the conventional food system terminology and are rooted in surrounding contexts. Evidence from Eastern Europe reveals a rich diversity of food practices challenging normative assumptions and neatly structured explanatory models underlying Western food system scholarship.
•Food practices which are marginal in the West are widespread in Eastern Europe.•These practices located at the intersection of the formal market and non-market economies.•They are based on the entangling of binaries considered to stand in opposition.•This makes Eastern Europe a source of critical and innovative thinking about AFNs.
•We discuss how Citizen Science (CS) can contribute to sustainability transitions.•Pathways include shaping research agendas; mobilizing resources; facilitating socio-technical co-evolution.•Several ...challenges arise for CS particularly in the context of sustainability transitions.•We substantiate our arguments using a wide range of case examples.•We discuss implications for future research, citizens and scientists, as well as policy makers.
Citizen Science (CS) projects involve members of the general public as active participants in research. While some advocates hope that CS can increase scientific knowledge production (“productivity view”), others emphasize that it may bridge a perceived gap between science and the broader society (“democratization view”). We discuss how an integration of both views can allow Citizen Science to support complex sustainability transitions in areas such as renewable energy, public health, or environmental conservation. We first identify three pathways through which such impacts can occur: (1) Problem identification and agenda setting; (2) Resource mobilization; and (3) Facilitating socio-technical co-evolution. To realize this potential, however, CS needs to address important challenges that emerge especially in the context of sustainability transitions: Increasing the diversity, level, and intensity of participation; addressing the social as well as technical nature of sustainability problems; and reducing tensions between CS and the traditional institution of academic science. Grounded in a review of academic literature and policy reports as well as a broad range of case examples, this article contributes to scholarship on science, innovation, and sustainability transitions. We also offer insights for actors involved in initiating or institutionalizing Citizen Science efforts, including project organizers, funding agencies, and policy makers.
Antimicrobial peptides are promising alternative antimicrobial agents. However, little is known about whether resistance to small-molecule antibiotics leads to cross-resistance (decreased ...sensitivity) or collateral sensitivity (increased sensitivity) to antimicrobial peptides. We systematically addressed this question by studying the susceptibilities of a comprehensive set of 60 antibiotic-resistant Escherichia coli strains towards 24 antimicrobial peptides. Strikingly, antibiotic-resistant bacteria show a high frequency of collateral sensitivity to antimicrobial peptides, whereas cross-resistance is relatively rare. We identify clinically relevant multidrug-resistance mutations that increase bacterial sensitivity to antimicrobial peptides. Collateral sensitivity in multidrug-resistant bacteria arises partly through regulatory changes shaping the lipopolysaccharide composition of the bacterial outer membrane. These advances allow the identification of antimicrobial peptide-antibiotic combinations that enhance antibiotic activity against multidrug-resistant bacteria and slow down de novo evolution of resistance. In particular, when co-administered as an adjuvant, the antimicrobial peptide glycine-leucine-amide caused up to 30-fold decrease in the antibiotic resistance level of resistant bacteria. Our work provides guidelines for the development of efficient peptide-based therapies of antibiotic-resistant infections.
The number of collaborative initiatives between scientists and volunteers (i.e., citizen science) is increasing across many research fields. The promise of societal transformation together with ...scientific breakthroughs contributes to the current popularity of citizen science (CS) in the policy domain. We examined the transformative capacity of citizen science in particular learning through environmental CS as conservation tool. We reviewed the CS and social-learning literature and examined 14 conservation projects across Europe that involved collaborative CS. We also developed a template that can be used to explore learning arrangements (i.e., learning events and materials) in CS projects and to explain how the desired outcomes can be achieved through CS learning. We found that recent studies aiming to define CS for analytical purposes often fail to improve the conceptual clarity of CS; CS programs may have transformative potential, especially for the development of individual skills, but such transformation is not necessarily occurring at the organizational and institutional levels; empirical evidence on simple learning outcomes, but the assertion of transformative effects of CS learning is often based on assumptions rather than empirical observation; and it is unanimous that learning in CS is considered important, but in practice it often goes unreported or unevaluated. In conclusion, we point to the need for reliable and transparent measurement of transformative effects for democratization of knowledge production. El número de iniciativas colaborativas entre los científicos y los voluntarios (es decir, ciencia ciudadana) está incrementando en muchas áreas de investigación. La promesa de una transformación social junto con avances científicos contribuye a la popularidad actual de la ciencia ciudadana (CC) en el dominio político. Examinamos la capacidad transformativa de la ciencia ciudadana, en particular del aprendizaje por medio de CC ambiental como herramienta de conservación. Revisamos la literatura sobre CC y aprendizaje social y examinamos 14 proyectos de conservación en Europa que involucraban CC colaborativa. También desarrollamos un patrón que puede usarse para explorar los arreglos de aprendizaje (es decir, los materiales y eventos de aprendizaje) en los proyectos de CC y para explicar cómo los desarrollos deseados pueden obtenerse mediante el aprendizaje de CC. Encontramos que los estudios recientes que buscan definir a la CC por propósitos analíticos fallan continuamente en la mejora de la claridad conceptual de la CC; que los programas de CC pueden tener potencial transformativo, especialmente para el desarrollo de las habilidades individuales, pero dicha transformación no está ocurriendo necesariamente en los niveles institucionales y de organización; que existe evidencia empírica de los resultados simples de aprendizaje, pero la aseveración de los efectos transformativos del aprendizaje de CC está basada continuamente en suposiciones en lugar de observaciones empíricas; y que es unánime que el aprendizaje en la CC está considerado como importante, pero en la práctica continuamente sigue sin ser reportado o evaluado. En conclusión, señalamos la necesidad de una medida confiable y transparente de los efectos transformadores para la democratización de la producción del conocimiento.
In the last decades, several gene expression-based predictors of clinical behavior were developed for breast cancer. A common feature of these is the use of multiple genes to predict hormone receptor ...status and the probability of tumor recurrence, survival or response to chemotherapy. We developed an online analysis tool to compute ER and HER2 status, Oncotype DX 21-gene recurrence score and an independent recurrence risk classification using gene expression data obtained by interrogation of Affymetrix microarray profiles. We implemented rigorous quality control algorithms to promptly exclude any biases related to sample processing, hybridization and scanning. After uploading the raw microarray data, the system performs the complete evaluation automatically and provides a report summarizing the results. The system is accessible online at
http://www.recurrenceonline.com
. We validated the system using data from 2,472 publicly available microarrays. The validation of the prediction of the 21-gene recurrence score was significant in lymph node negative patients (Cox-Mantel,
P
= 5.6E-16, HR = 0.4, CI = 0.32–0.5). A correct classification was obtained for 88.5% of ER- and 90.5% of ER + tumors (
n
= 1,894). The prediction of recurrence risk in all patients by using the mean of the independent six strongest genes (
P
< 1E-16, HR = 2.9, CI = 2.5–3.3), of the four strongest genes in lymph node negative ER positive patients (
P
< 1E-16, HR = 2.8, CI = 2.2–3.5) and of the three genes in lymph node positive patients (
P
= 3.2E-9, HR = 2.5, CI = 1.8–3.4) was highly significant. In summary, we integrated available knowledge in one platform to validate currently used predictors and to provide a global tool for the online determination of different prognostic parameters simultaneously using genome-wide microarrays.
A central challenge in evolutionary biology concerns the mechanisms by which complex metabolic innovations requiring multiple mutations arise. Here, we propose that metabolic innovations accessible ...through the addition of a single reaction serve as stepping stones towards the later establishment of complex metabolic features in another environment. We demonstrate the feasibility of this hypothesis through three complementary analyses. First, using genome-scale metabolic modelling, we show that complex metabolic innovations in Escherichia coli can arise via changing nutrient conditions. Second, using phylogenetic approaches, we demonstrate that the acquisition patterns of complex metabolic pathways during the evolutionary history of bacterial genomes support the hypothesis. Third, we show how adaptation of laboratory populations of E. coli to one carbon source facilitates the later adaptation to another carbon source. Our work demonstrates how complex innovations can evolve through series of adaptive steps without the need to invoke non-adaptive processes.
Antibiotic development is frequently plagued by the rapid emergence of drug resistance. However, assessing the risk of resistance development in the preclinical stage is difficult. Standard ...laboratory evolution approaches explore only a small fraction of the sequence space and fail to identify exceedingly rare resistance mutations and combinations thereof. Therefore, new rapid and exhaustive methods are needed to accurately assess the potential of resistance evolution and uncover the underlying mutational mechanisms. Here, we introduce directed evolution with random genomic mutations (DIvERGE), a method that allows an up to million-fold increase in mutation rate along the full lengths of multiple predefined loci in a range of bacterial species. In a single day, DIvERGE generated specific mutation combinations, yielding clinically significant resistance against trimethoprim and ciprofloxacin. Many of these mutations have remained previously undetected or provide resistance in a species-specific manner. These results indicate pathogen-specific resistance mechanisms and the necessity of future narrow-spectrum antibacterial treatments. In contrast to prior claims, we detected the rapid emergence of resistance against gepotidacin, a novel antibiotic currently in clinical trials. Based on these properties, DIvERGE could be applicable to identify less resistance-prone antibiotics at an early stage of drug development. Finally, we discuss potential future applications of DIvERGE in synthetic and evolutionary biology.
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