Covering: up to June 2020Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging ...commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.
The locomotion of extinct secondarily aquatic tetrapods Gutarra, Susana; Rahman, Imran A.
Biological reviews of the Cambridge Philosophical Society,
February 2022, 2022-02-00, 20220201, Letnik:
97, Številka:
1
Journal Article
Recenzirano
Odprti dostop
ABSTRACT
The colonisation of freshwater and marine ecosystems by land vertebrates has repeatedly occurred in amphibians, reptiles, birds and mammals over the course of 300 million years. Functional ...interpretations of the fossil record are crucial to understanding the forces shaping these evolutionary transitions. Secondarily aquatic tetrapods have acquired a suite of anatomical, physiological and behavioural adaptations to locomotion in water. However, much of this information is lost for extinct clades, with fossil evidence often restricted to osteological data and a few extraordinary specimens with soft tissue preservation. Traditionally, functional morphology in fossil secondarily aquatic tetrapods was investigated through comparative anatomy and correlation with living functional analogues. However, in the last two decades, biomechanics in palaeobiology has experienced a remarkable methodological shift. Anatomy‐based approaches are increasingly rigorous, informed by quantitative techniques for analysing shape. Moreover, the incorporation of physics‐based methods has enabled objective tests of functional hypotheses, revealing the importance of hydrodynamic forces as drivers of evolutionary innovation and adaptation. Here, we present an overview of the latest research on the locomotion of extinct secondarily aquatic tetrapods, with a focus on amniotes, highlighting the state‐of‐the‐art experimental approaches used in this field. We discuss the suitability of these techniques for exploring different aspects of locomotory adaptation, analysing their advantages and limitations and laying out recommendations for their application, with the aim to inform future experimental strategies. Furthermore, we outline some unexplored research avenues that have been successfully deployed in other areas of palaeobiomechanical research, such as the use of dynamic models in feeding mechanics and terrestrial locomotion, thus providing a new methodological synthesis for the field of locomotory biomechanics in extinct secondarily aquatic vertebrates. Advances in imaging technology and three‐dimensional modelling software, new developments in robotics, and increased availability and awareness of numerical methods like computational fluid dynamics make this an exciting time for analysing form and function in ancient vertebrates.
Chronic liver disease due to alcohol-use disorder contributes markedly to the global burden of disease and mortality
. Alcoholic hepatitis is a severe and life-threatening form of alcohol-associated ...liver disease. The gut microbiota promotes ethanol-induced liver disease in mice
, but little is known about the microbial factors that are responsible for this process. Here we identify cytolysin-a two-subunit exotoxin that is secreted by Enterococcus faecalis
-as a cause of hepatocyte death and liver injury. Compared with non-alcoholic individuals or patients with alcohol-use disorder, patients with alcoholic hepatitis have increased faecal numbers of E. faecalis. The presence of cytolysin-positive (cytolytic) E. faecalis correlated with the severity of liver disease and with mortality in patients with alcoholic hepatitis. Using humanized mice that were colonized with bacteria from the faeces of patients with alcoholic hepatitis, we investigated the therapeutic effects of bacteriophages that target cytolytic E. faecalis. We found that these bacteriophages decrease cytolysin in the liver and abolish ethanol-induced liver disease in humanized mice. Our findings link cytolytic E. faecalis with more severe clinical outcomes and increased mortality in patients with alcoholic hepatitis. We show that bacteriophages can specifically target cytolytic E. faecalis, which provides a method for precisely editing the intestinal microbiota. A clinical trial with a larger cohort is required to validate the relevance of our findings in humans, and to test whether this therapeutic approach is effective for patients with alcoholic hepatitis.
This paper investigates economic impacts of COVID-19 on households based on differences in the socio-economic status (SES). We determine the household-level effects of the COVID-19 shock using income ...sources, types of industries, communities' resilience, household susceptibility, and relevant policy measures. For this purpose, we used primary data of 555 households collected through snowball sampling technique using an online survey questionnaire from different villages mostly located in Sichuan Province, China. Using step-wise binary logistic regression analysis, we estimated and validated the model. Results suggest the use of SES as a better measure for understanding the impacts of COVID-19 on different households. We find that households with low SES tend to depend more on farmland income and transfer payments from the government. Contrarily, high SES households focus more on business and local employment as sources of income generation. Poor households were less resilient and more likely to fall back into poverty due to COVID-19, while the opposite stands true for non-poor households with high SES. Based on the estimations, policies encouraging employment and businesses complemented with loans on lower interest rates are recommended, which may increase the SES, thus minimizing vulnerability and enhancing the households' resilience towards poverty alleviation and economic shocks.
For the consideration of environmental aspects of the personal transportation, electric vehicle (EV) and plug-in hybrid electric vehicle (PHEV) has the prospective solution nonetheless there is an ...obstacle to access the charging system plug. Additionally, the charging system delivers its own troubles when we compared it with petrol station since the participation of the different charging alternative. For the last few years, the studies associated with optimization of PHEV/EV charging infrastructure have drawn the researcher׳s consideration. New challenges and chances for the growth of smart grid technologies depend upon the recently introduced electric vehicle charging infrastructure services. In this particular review study, the literature bearing on the use of optimization methods for charging infrastructure is considered.
Techniques for virtual palaeontology Sutton, Mark D; Rahman, Imran A; Garwood, Russell J
2013., 2014/01/01, 2013, 2014, 2013-10-22, 2013-10-23
eBook
Virtual palaeontology, the use of interactive three-dimensional digital models as a supplement or alternative to physical specimens for scientific study and communication, is rapidly becoming ...important to advanced students and researchers. Using non-invasive techniques, the method allows the capture of large quantities of useful data without damaging the fossils being studied Techniques for Virtual Palaeontology guides palaeontologists through the decisions involved in designing a virtual palaeontology workflow and gives a comprehensive overview, providing discussions of underlying theory, applications, historical development, details of practical methodologies, and case studies. Techniques covered include physical-optical tomography (serial sectioning), focused ion beam tomography, all forms of X-ray CT, neutron tomography, magnetic resonance imaging, optical tomography, laser scanning, and photogrammetry. Visualization techniques and data/file formats are also discussed in detail. Readership: All palaeontologists and students interested in three-dimensional visualization and analysis. New Analytical Methods in Earth and Environmental Science Because of the plethora of analytical techniques now available, and the acceleration of technological advance, many earth scientists find it difficult to know where to turn for reliable information on the latest tools at their disposal, and may lack the expertise to assess the relative strengths or limitations of a particular technique. This new series will address these difficulties by providing accessible introductions to important new techniques, lab and field protocols, suggestions for data handling and interpretation, and useful case studies. The series represents an invaluable and trusted source of information for researchers, advanced students and applied earth scientists wishing to familiarise themselves with emerging techniques in their field. All titles in this series are available in a variety of full-colour, searchable eBook formats. Titles are also available in an enhanced eBook edition which may include additional features such as DOI linking, high resolution graphics and video.
Purpose This article examines the concepts of “deglobalization” and “decoupling” from the perspectives of developing and developed nations. It also assesses the short-term impacts of globalization, ...particularly in the context of the COVID-19 pandemic and predicts the long-term effects on global trade and cooperation between nations. Design/methodology/approach Panel data from 85 countries (2000–2022) were utilized. Poisson Pseudo-Maximum Likelihood (PPML) regression analysis was conducted to analyze pre- and post-COVID-19 globalization levels. The analysis focuses on trade patterns and trends, specifically comparing the effects on developing and developed nations. Findings First, there was a slight decline in global trade in 2020 due to COVID-19, followed by recovery in 2021–2022. Second, developing nations experienced more significant trade declines than did developed nations. Third, while US? China trade decreased slightly, China-India and US-India trade increased during the pandemic. These findings suggest that while there may be short-term disruptions, long-term trends indicate resilience in global trade patterns, with shifts in output and new partnerships emerging. Originality/value This study contributes to the understanding of deglobalization and decoupling by providing empirical evidence on pre- and post-COVID-19 trade patterns. The findings suggest that while globalization may have short-term effects, it is likely to lead to post-pandemic recovery and strengthened cooperation between developing and developed nations. This research also highlights the importance of developing strategies to manage uncertainty and external shocks in global trade, emphasizing the role of lockdown measures, national security considerations, and trade policies in shaping the future of globalization and decoupling.
Trace fossils record the interactions between organisms and their surroundings, and can therefore provide unique insights into the coevolution of trace makers and the environment. However, ...identifying the producers of trace fossils is challenging because different animals can create very similar traces and many ichnotaxa can therefore only be attributed to broad morphological grades. For example, simple horizontal traces like Gordia are generally suggested to have been produced by vermiform organisms, potentially encompassing a range of animal phyla. This uncertainty makes it difficult to decipher their palaeobiological significance through major evolutionary events and episodes of environmental change. We have developed new mathematical approaches for identifying previously unrecognized signatures left by the trace makers of simple marine locomotory traces. We calculated the deviation angle series of self‐crossing traces made by extant isopods, polychaetes, gastropods and nematodes, computing the frequency spectrum and autocorrelation function in each case. The results reveal that each of these taxa left unique markers during the trace‐making process, reflecting differences in their anatomy and locomotory behaviour. We were able to identify the possible trace makers of several early Palaeozoic Gordia specimens, demonstrating that ichnospecies within the same ichnogenus can be created by distantly related animals with very different morphologies and/or behaviours. This novel mathematical framework has great potential for identifying the possible producers of diverse trace fossils through deep time, helping to uncover the earliest evidence of certain animals or behaviours. It also has great potential for quantifying ichnotaxonomy, consolidating the link between ichnology and palaeobiology.
Computational fluid dynamics is a method for simulating fluid flows that has been widely used in engineering for decades, and which also has applications for studying function and ecology in fossil ...taxa. However, despite the possible benefits of this approach, computational fluid dynamics has been used only rarely in palaeontology to date. The theoretical basis underlying the technique is outlined and the main steps involved in carrying out computer simulations of fluid flows are detailed. I also describe previous studies that have applied the method to fossils and discuss their potential for informing future research directions in palaeontology. Computational fluid dynamics can enable large‐scale comparative analyses, as well as exacting tests of hypotheses related to the function and ecology of ancient organisms. In this way, it could transform our understanding of many extinct fossil groups.
Echinoderms are unique in being pentaradiate, having diverged from the ancestral bilaterian body plan more radically than any other animal phylum. This transformation arises during ontogeny, as ...echinoderm larvae are initially bilateral, then pass through an asymmetric phase, before giving rise to the pentaradiate adult. Many fossil echinoderms are radial and a few are asymmetric, but until now none have been described that show the original bilaterian stage in echinoderm evolution. Here we report new fossils from the early middle Cambrian of southern Europe that are the first echinoderms with a fully bilaterian body plan as adults. Morphologically they are intermediate between two of the most basal classes, the Ctenocystoidea and Cincta. This provides a root for all echinoderms and confirms that the earliest members were deposit feeders not suspension feeders.
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