Dynamic mimicry in an Indo-Malayan octopus

During research dives in Indonesia (Sulawesi and Bali), we filmed a distinctive long-armed octopus, which is new to science. Diving over 24 h periods revealed that the 'mimic octopus' emerges during daylight hours to forage on sand substrates in full view of pelagic fish predators. We observed nine individuals of this species displaying a repertoire of postures and body patterns, several of which are clearly impersonations of venomous animals co-occurring in this habitat. This 'dynamic mimicry' avoids the genetic constraints that may limit the diversity of genetically polymorphic mimics but has the same effect of decreasing the frequency with which predators encounter particular mimics. Additionally, our observations suggest that the octopus makes decisions about the most appropriate form of mimicry to use, allowing it to enhance further the benefits of mimicking toxic models by employing mimicry according to the nature of perceived threats

Accurate reconstruction of bacterial pan- and core genomes with PEPPAN

Bacterial genomes can contain traces of a complex evolutionary history, including extensive homologous recombination, gene loss, gene duplications and horizontal gene transfer. In order to reconstruct the phylogenetic and population history of a set of multiple bacteria, it is necessary to examine their pangenome, the composite of all the genes in the set. Here we introduce PEPPAN, a novel pipeline that can reliably construct pangenomes from thousands of genetically diverse bacterial genomes that represent the diversity of an entire genus. PEPPAN outperforms existing pangenome methods by providing consistent gene and pseudogene annotations extended by similarity-based gene predictions, and identifying and excluding paralogs by combining tree- and synteny-based approaches. The PEPPAN package additionally includes PEPPAN_parser, which implements additional downstream analyses including the calculation of trees based on accessory gene content or allelic differences between core genes. In order to test the accuracy of PEPPAN, we implemented SimPan, a novel pipeline for simulating the evolution of bacterial pangenomes. We compared the accuracy and speed of PEPPAN with four state-of-the-art pangenome pipelines using both empirical and simulated datasets. PEPPAN was more accurate and more specific than any of the other pipelines and was almost as fast as any of them. As a case study, we used PEPPAN to construct a pangenome of ~40,000 genes from 3052 representative genomes spanning at least 80 species of Streptococcus. The resulting gene and allelic trees provide an unprecedented overview of the genomic diversity of the entire Streptococcus genus

Preclinical evaluation of the Versius surgical system: A next‐generation surgical robot for use in minimal access prostate surgery

© 2023 The Authors. BJUI Compass published by John Wiley & Sons Ltd on behalf of BJU International Company. This is an open access article under the terms of the Creative Commons Attribution License, https://creativecommons.org/licenses/by/4.0/Objectives: To evaluate the Versius surgical system for robot‐assisted prostatectomy in a preclinical cadaveric model using varying system setups and collect surgeon feedback on the performance of the system and instruments, in line with IDEAL‐D recommendations. Materials and methods: Procedures were performed in cadaveric specimens by consultant urological surgeons to evaluate system performance in completing the surgical steps required for a prostatectomy. Procedures were conducted using either a 3‐arm or 4‐arm bedside unit (BSU) setup. Optimal port placements and BSU layouts were determined and surgeon feedback collected. Procedure success was defined as the satisfactory completion of all steps of the procedure, according to the operating surgeon. Results: All four prostatectomies were successfully completed; two were completed with a 3‐arm BSU setup and two using a 4‐arm BSU setup. Small adjustments were made to the port and BSU positioning, according to surgeon preference, in order to complete the surgical steps. The surgeons noted some instrument difficulties with the Monopolar Curved Scissor tip and the Needle Holders, which were subsequently refined between the first and second sessions of the study, in line with surgeon feedback. Three cystectomies were also successfully completed, demonstrating the capability of the system to perform additional urological procedures. Conclusions: This study provides a preclinical assessment of a next‐generation surgical robot for prostatectomies. All procedures were completed successfully, and port and BSU positions were validated, thus supporting the progression of the system to further clinical development according to the IDEAL‐D framework.Peer reviewe

Universal Mortality Law, Life Expectancy and Immortality

Well protected human and laboratory animal populations with abundant resources are evolutionary unprecedented, and their survival far beyond reproductive age may be a byproduct rather than tool of evolution. Physical approach, which takes advantage of their extensively quantified mortality, establishes that its dominant fraction yields the exact law, and suggests its unusual mechanism. The law is universal for all animals, from yeast to humans, despite their drastically different biology and evolution. It predicts that the universal mortality has short memory of the life history, at any age may be reset to its value at a significantly younger age, and mean life expectancy extended (by biologically unprecedented small changes) from its current maximal value to immortality. Mortality change is rapid and stepwise. Demographic data and recent experiments verify these predictions for humans, rats, flies, nematodes and yeast. In particular, mean life expectancy increased 6-fold (to "human" 430 years), with no apparent loss in health and vitality, in nematodes with a small number of perturbed genes and tissues. Universality allows one to study unusual mortality mechanism and the ways to immortality

EnteroBase : Hierarchical clustering of 100,000s of bacterial genomes into species/sub-species and populations

The definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCC’s ability to correctly assign 100,000s of genomes to the species/subspecies and population levels for Salmonella, Escherichia, Clostridoides, Yersinia, Vibrio and Streptococcus. HierCC assignments were more consistent with maximum-likelihood super-trees of core SNPs or presence/absence of accessory genes than classical taxonomic assignments or 95% ANI. However, neither HierCC nor ANI were uniformly consistent with classical taxonomy of Streptococcus. HierCC was also consistent with legacy eBGs/ST Complexes in Salmonella or Escherichia and with O serogroups in Salmonella. Thus, EnteroBase HierCC supports the automated 36 identification of and assignment to species/subspecies and populations for multiple genera

No Accumulation of Transposable Elements in Asexual Arthropods.

Transposable elements (TEs) and other repetitive DNA can accumulate in the absence of recombination, a process contributing to the degeneration of Y-chromosomes and other nonrecombining genome portions. A similar accumulation of repetitive DNA is expected for asexually reproducing species, given their entire genome is effectively nonrecombining. We tested this expectation by comparing the whole-genome TE loads of five asexual arthropod lineages and their sexual relatives, including asexual and sexual lineages of crustaceans (Daphnia water fleas), insects (Leptopilina wasps), and mites (Oribatida). Surprisingly, there was no evidence for increased TE load in genomes of asexual as compared to sexual lineages, neither for all classes of repetitive elements combined nor for specific TE families. Our study therefore suggests that nonrecombining genomes do not accumulate TEs like nonrecombining genomic regions of sexual lineages. Even if a slight but undetected increase of TEs were caused by asexual reproduction, it appears to be negligible compared to variance between species caused by processes unrelated to reproductive mode. It remains to be determined if molecular mechanisms underlying genome regulation in asexuals hamper TE activity. Alternatively, the differences in TE dynamics between nonrecombining genomes in asexual lineages versus nonrecombining genome portions in sexual species might stem from selection for benign TEs in asexual lineages because of the lack of genetic conflict between TEs and their hosts and/or because asexual lineages may only arise from sexual ancestors with particularly low TE loads

Analysis of Nkx3.1:Cre-driven Erk5 deletion reveals a profound spinal deformity which is linked to increased osteoclast activity

Extracellular signal-regulated protein kinase 5 (ERK5) has been implicated during development and carcinogenesis. Nkx3.1-mediated Cre expression is a useful strategy to genetically manipulate the mouse prostate. While grossly normal at birth, we observed an unexpected phenotype of spinal protrusion in Nkx3.1:Cre;Erk5fl/fl (Erk5fl/fl) mice by ~6–8 weeks of age. X-ray, histological and micro CT (µCT) analyses showed that 100% of male and female Erk5fl/fl mice had a severely deformed curved thoracic spine, with an associated loss of trabecular bone volume. Although sex-specific differences were observed, histomorphometry measurements revealed that both bone resorption and bone formation parameters were increased in male Erk5fl/fl mice compared to wild type (WT) littermates. Osteopenia occurs where the rate of bone resorption exceeds that of bone formation, so we investigated the role of the osteoclast compartment. We found that treatment of RANKL-stimulated primary bone marrow-derived macrophage (BMDM) cultures with small molecule ERK5 pathway inhibitors increased osteoclast numbers. Furthermore, osteoclast numbers and expression of osteoclast marker genes were increased in parallel with reduced Erk5 expression in cultures generated from Erk5fl/fl mice compared to WT mice. Collectively, these results reveal a novel role for Erk5 during bone maturation and homeostasis in vivo

Assessment of the domestic energy use impacts of unplanned refugee settlements on the forest ecology of Cox’s Bazar, Bangladesh

This study monitors the forest ecology in Himchari National Park, Teknaf Wildlife Sanctuary, and between the areas in Cox's Bazar district, Bangladesh. The area has a rich biodiversity, including globally endangered species such as Asian Elephants (Elephas maximus) and Boilam Trees (Anisoptera scaphula), which are threatened by anthropogenic development, newly refugees’ unplanned settlements and their use of domestic energy. Geographic Information System (GIS) and Landsat satellite images are used to monitor forest coverage for 1995–2018. The Normalized Difference Vegetation Index (NDVI) is applied to quantify forest area. Focus group discussions and questionnaire surveys were conducted to reveal stakeholder perceptions about their dependency on forest resources as ecosystem services. Close to the refugee camp areas, the forest coverage changes to grassland due to the unsustainable forest resource extraction. Despite the free of charge supply of Liquefied Petroleum Gas, the refugees burn 2,380 metric tons of firewood every month to satisfy energy for cooking. Besides, 200,000 households frequently use bamboo, small trees, and shrubs to maintain their dwellings' structure. Thus, deforestation caused by immigration between 2017–2018 is similar to that caused by the effect of climate change, including severe tropical cyclones in 1994–1995. This research identifies domestic energy supply deficiency and impacts, and the need for comparatively durable housing materials to reduce stress on forest resources and health hazards

Spatial transition dynamics of urbanization and Rohingya refugees’ settlements in Bangladesh

Urbanization needs to conceptualize land use policy beyond the city boundaries. It might be explained by exploring complex and interconnected interdependencies in regional key driving factors that can have tele-coupling effects during sudden shocks. Over one million Rohingya have settled in the rural/forest area in Cox’s Bazar for locational proximity and comparatively easy escape from Myanmar after domestic conflicts. This study aims to explore the spatial dimension of urbanization in a regional transition context focusing on the newly built refugee settlements in the south-eastern coastal area of Bangladesh. Additional, we also identify further research scopes and gaps in the context of the case study. Analysis of openly available global data products from historical built-up expansion from 1975 to 2021 suggests that refugee settlements impact spatial development intensity (annual rate ⁓2.55 ha/year) and population density (annual rate ⁓9431 person/year) dimensions, which have a transition (rural-to-urban) of a greater regional scale than local urbanization. Our results from the expert-based key informant interviews have a broad agreement with the quantitative findings; however, the environmental: deforestation, economic: increasing business and employment opportunities and daily living expenses; and socio-cultural impacts: increasing conflict between host and refugee communities due to prostitution, drug dealing, and insecurity, are more local than findings from the geospatial analysis. Therefore, the local development policies need an urgent adjustment to comply with the local and regional balances in the above factors, along with that international development actors may also need attentive measures in the policy formulation. Further investigations in scenario-based urbanization dynamics are required to avoid an urban desert initiated in the absence or relocation of refugee settlement. Similar kinds of studies may also be replicated even in prosperous global North countries in order to conceptualize the spatial transformative process of rapid migration influx on urbanization with innovative open data in the absence of up-to-date official datasets and adoptions of mixed methods approaches with related actors including policymakers