BBF RFC 105: The Intein standard - a universal way to modify proteins after translation

This Request for Comments (RFC) proposes a new standard that allows for easy and flexible cloning of intein constructs and thus makes this technology accessible to the synthetic biology community

Loss and damage livelihood resilience

Climate change Loss and Damage has emerged as a key challenge of the 21st century. This Policy Brief first frames the challenge and then introduces the Resilience Academy, highlighting 5 key insights that both feed the debate and inform action. Finally, it provides 5 recommendations to the Executive Committee of the Warsaw International Mechanism (WIM ExCom) for its 5-year work plan

Privacy-By-Design Constrained Traffic Video Surveillance

V tej diplomski nalogi je opisan postopek izdelave baze označenih zamegljenih slik cestnega prometa, ki je zasnovana za prihodnje treniranje algoritmov za detekcijo prometa z vgrajeno zasebnostjo. Zameglitev slik je namenjena prikrivanju identitete posameznikov in drugih identifikacijskih podatkov, kar zagotavlja varovanje zasebnosti. Postopek vključuje izdelavo sistema za snemanje prometa z uporabo dveh kamer za Raspberry Pi, ki sta simultano snemali promet – ena je zagotavljala zamegljene in druga ostre posnetke. Slike smo nato poravnali s pomočjo algoritma SIFT. Jasne slike smo označili s pomočjo algoritma DETR, pri čemer so oznake enake tudi za zamegljene slike, saj smo snemanje opravljali z dvema kamerama. Končni rezultat je baza več kot tisoč zamegljenih slik z označbami v formatu COCO. Ta baza je pripravljena za uporabo v nadaljnjih raziskavah in razvoju algoritmov za detekcijo prometa z vgrajeno zasebnostjo.This thesis describes the process of creating a dataset of labeled blurred traffic images, designed for the future training of traffic detection algorithms with built-in privacy. The blurring of images is intended to obscure the identity of individuals and other identifying data, thus ensuring privacy protection. The process includes the development of a traffic recording system using two Raspberry Pi cameras, which simultaneously recorded traffic - one providing blurred and the other sharp images. The images were then aligned using the SIFT algorithm. Clear images were labeled using the DETR algorithm, with the labels being the same for blurred images as we recorded with two cameras. The final result is a database of over a thousand blurred images with labels in COCO format. This dataset is prepared for use in further research and development of traffic detection algorithms with built-in privacy

When does risk become residual? A systematic review of research on flood risk management in West Africa

Flood events in West Africa have devastating impacts on the lives of people. Additionally, developments such as climate change, settlement expansion into flood-prone areas, and modification of rivers are expected to increase flood risk in the future. Policy documents have issued calls for conducting local risk assessments and understanding disaster risk in diverse aspects, leading to an increase in such research. Similarly, in a shift from flood protection to flood risk management, the consideration of various dimensions of flood risk, the necessity of addressing flood risk through an integrated strategy containing structural and non-structural measures, and the presence of residual risk are critical perspectives raised. However, the notion of “residual risk” remains yet to be taken up in flood risk management-related academic literature. This systematic review seeks to approach the notion of residual risk by reviewing information on flood impacts, common measures, and recommendations in academic literature. The review reveals various dimensions of impacts from residual flood risk aside from material damage, in particular, health impacts and economic losses. Infrastructural measures were a dominant category of measures before and after flood events and in recommendations, despite their shortcomings. Also, spatial planning interventions, a more participatory and inclusive governance approach, including local knowledge, sensitisation, and early warning systems, were deemed critical. In the absence of widespread access to insurance schemes, support from social networks after flood events emerged as the most frequent measure. This finding calls for in-depth assessments of those networks and research on potential complementary formal risk transfer mechanisms.Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347Munich Climate Insurance Initiative (MCII)Rheinische Friedrich-Wilhelms-Universität Bonn (1040

When does risk become residual? A systematic review of research on flood risk management in West Africa

Flood events in West Africa have devastating impacts on the lives of people. Additionally, developments such as climate change, settlement expansion into flood-prone areas, and modification of rivers are expected to increase flood risk in the future. Policy documents have issued calls for conducting local risk assessments and understanding disaster risk in diverse aspects, leading to an increase in such research. Similarly, in a shift from flood protection to flood risk management, the consideration of various dimensions of flood risk, the necessity of addressing flood risk through an integrated strategy containing structural and non-structural measures, and the presence of residual risk are critical perspectives raised. However, the notion of “residual risk” remains yet to be taken up in flood risk management-related academic literature. This systematic review seeks to approach the notion of residual risk by reviewing information on flood impacts, common measures, and recommendations in academic literature. The review reveals various dimensions of impacts from residual flood risk aside from material damage, in particular, health impacts and economic losses. Infrastructural measures were a dominant category of measures before and after flood events and in recommendations, despite their shortcomings. Also, spatial planning interventions, a more participatory and inclusive governance approach, including local knowledge, sensitisation, and early warning systems, were deemed critical. In the absence of widespread access to insurance schemes, support from social networks after flood events emerged as the most frequent measure. This finding calls for in-depth assessments of those networks and research on potential complementary formal risk transfer mechanisms

Flagellar interference with plasmid uptake in biofilms:a joint experimental and modeling study

Plasmid conjugation is a key facilitator of horizontal gene transfer (HGT), and plasmids encoding antibiotic resistance drive the increasing prevalence of antibiotic resistance. In natural, engineered, and clinical environments, bacteria often grow in protective biofilms. Therefore, a better understanding of plasmid transfer in biofilms is needed. Our aim was to investigate plasmid transfer in a biofilm-adapted wrinkly colony mutant of Xanthomonas retroflexus (XRw) with enhanced matrix production and reduced motility. We found that XRw biofilms had an increased uptake of the broad host-range IncP-1ϵ plasmid pKJK5 compared to the wild type (WT). Proteomics revealed fewer flagellar-associated proteins in XRw, suggesting that flagella were responsible for reducing plasmid uptake. This was confirmed by the higher plasmid uptake of non-flagellated fliM mutants of the X. retroflexus wrinkly mutant as well as the wild type. Moreover, testing several flagellar mutants of Pseudomonas putida suggested that the flagellar effect was more general. We identified seven mechanisms with the potential to explain the flagellar effect and simulated them in an individual-based model. Two mechanisms could thus be eliminated (increased distances between cells and increased lag times due to flagella). Another mechanism identified as viable in the modeling was eliminated by further experiments. The possibility of steric hindrance of pilus movement and binding by flagella, reducing the frequency of contact and thus plasmid uptake, proved viable, and the three other viable mechanisms had a reduced probability of plasmid transfer in common. Our findings highlight the important yet complex effects of flagella during bacterial conjugation in biofilms.IMPORTANCEBiofilms are the dominant form of microbial life and bacteria living in biofilms are markedly different from their planktonic counterparts, yet the impact of the biofilm lifestyle on horizontal gene transfer (HGT) is still poorly understood. Horizontal gene transfer by conjugative plasmids is a major driver in bacterial evolution and adaptation, as exemplified by the troubling spread of antibiotic resistance. To either limit or promote plasmid prevalence and dissemination, we need a better understanding of plasmid transfer between bacterial cells, especially in biofilms. Here, we identified a new factor impacting the transfer of plasmids, flagella, which are required for many types of bacterial motility. We show that their absence or altered activity can lead to enhanced plasmid uptake in two bacterial species, Xanthomonas retroflexus and Pseudomonas putida. Moreover, we demonstrate the utility of mathematical modeling to eliminate hypothetical mechanisms

Flagellar interference with plasmid uptake in biofilms:a joint experimental and modeling study

Plasmid conjugation is a key facilitator of horizontal gene transfer (HGT), and plasmids encoding antibiotic resistance drive the increasing prevalence of antibiotic resistance. In natural, engineered, and clinical environments, bacteria often grow in protective biofilms. Therefore, a better understanding of plasmid transfer in biofilms is needed. Our aim was to investigate plasmid transfer in a biofilm-adapted wrinkly colony mutant of Xanthomonas retroflexus (XRw) with enhanced matrix production and reduced motility. We found that XRw biofilms had an increased uptake of the broad host-range IncP-1ϵ plasmid pKJK5 compared to the wild type (WT). Proteomics revealed fewer flagellar-associated proteins in XRw, suggesting that flagella were responsible for reducing plasmid uptake. This was confirmed by the higher plasmid uptake of non-flagellated fliM mutants of the X. retroflexus wrinkly mutant as well as the wild type. Moreover, testing several flagellar mutants of Pseudomonas putida suggested that the flagellar effect was more general. We identified seven mechanisms with the potential to explain the flagellar effect and simulated them in an individual-based model. Two mechanisms could thus be eliminated (increased distances between cells and increased lag times due to flagella). Another mechanism identified as viable in the modeling was eliminated by further experiments. The possibility of steric hindrance of pilus movement and binding by flagella, reducing the frequency of contact and thus plasmid uptake, proved viable, and the three other viable mechanisms had a reduced probability of plasmid transfer in common. Our findings highlight the important yet complex effects of flagella during bacterial conjugation in biofilms