Antibiotic resistance in bacteria has become a great threat to global public health. Tigecycline is a next‐generation tetracycline that is the final line of defense against severe infections by pan‐drug‐resistant bacterial pathogens. Unfortunately, this last‐resort antibiotic has been challenged by the recent emergence of the mobile Tet(X) orthologs that can confer high‐level tigecycline resistance. As it is reviewed here, these novel tetracycline destructases represent a growing threat to the next‐generation tetracyclines, and a basic framework for understanding the molecular epidemiology and (...) resistance mechanisms of them is presented. However, further large‐scale epidemiological and functional studies are urgently needed to better understand the prevalence and dissemination of these newly discovered Tet(X) orthologs among Gram‐negative bacteria in both human and veterinary medicine. (shrink)

Plasmids are a major type of mobile genetic elements (MGEs) that mediate horizontal gene transfer. The stable maintenance of plasmids plays a critical role in the functions and survival for microbial populations. However, predicting and controlling plasmid persistence and abundance in complex microbial communities remain challenging. Computationally, this challenge arises from the combinatorial explosion associated with the conventional modeling framework. Recently, a plasmid‐centric framework (PCF) has been developed to overcome this computational bottleneck. This framework enables the derivation of (...) a simple metric, the persistence potential, to predict plasmid persistence and abundance. Here, we discuss how PCF can be extended to account for plasmid interactions. We also discuss how such model‐guided predictions of plasmid fates can benefit from the development of new experimental tools and data‐driven computational methods. (shrink)

Bacterial plasmids are ubiquitous ‘minichromosomes’ that have major importance in clinical microbiology, as agents of pathogenicity and as carriers of antibiotic resistance, and in molecular genetics, through their role as vectors in gene manipulation. Plasmids carry a wide range of dispensable, transiently useful and often bizarre functions.1 Naturally occurring plasmids, in addition to modifying the host cell phenotype, carry genes involved in the control of their own vegetative replication, plasmid copy number2 and stable inheritance. They may also carry determinants (...) for the conjugal transfer of DNA between bacteria.3 Whereas low‐copy‐number plasmids must be partitioned by some active process during cell division, the evidence suggests that multicopy plasmids are distributed randomly between daughter cells. Two independent determinants are necessary for the stable inheritance of multicopy plasmids, and both of these appear to act by maximizing the number of independent plasmid molecules. (shrink)

On the brink of her sixtieth birthday, Shengold embarks on a challenge: to take the same walk along the banks of the Ashokan Reservoir, in New York's Catskill Mountain region, every day for a year and find something new every time.

DNA transfer directly from cell to cell (conjugation) is common among prokaryotes, particularly Gram‐negative bacteria like Escherichia coli. The phenomenon invariably requires a set of plasmid genes in the DNA donor cell. In addition, E. coli itself makes limited and specific contributions to the donor activity of strains carrying the conjugative plasmid F. These contributions have yet to be defined biochemically, but it is already clear that the cell envelope is an importan nexus between plasmid‐ and chromosome‐encoded (...) proteins required for the establishment and maintenance of DNA donor activity. (shrink)

Recent research has suggested that Staphylococcus epidermidis is a reservoir of genes that, after horizontal transfer, facilitate the potential of Staphylococcus aureus to colonize, survive during infection, or resist antibiotic treatment, traits that are notably manifest in methicillin‐resistant S. aureus (MRSA). S. aureus is a dangerous human pathogen and notorious for acquiring antibiotic resistance. MRSA in particular is one of the most frequent causes of morbidity and death in hospitalized patients. S. aureus is an extremely versatile pathogen with a multitude (...) of mechanisms to cause disease and circumvent immune defenses. In contrast, most other staphylococci, such as S. epidermidis, are commonly benign commensals and only occasionally cause disease. Recent findings highlight the key importance of efforts to better understand how genes of staphylococci other than S. aureus contribute to survival in the human host, how they are transferred to S. aureus, and why this exchange appears to be uni‐directional. (shrink)

Graphical AbstractThe finding that viruses with RNA and DNA genomes can recombine to produce chimeric entities provides valuable insights into the origin and evolution of viruses. It also substantiates the hypothesis that certain groups of DNA viruses could have emerged from plasmids via acquisition of capsid protein-coding genes from RNA viruses.

The soil bacteria rhizobia have the capacity to establish nitrogen‐fixing symbiosis with their leguminous host plants. In most Rhizobium species the genes for nodule development and nitrogen fixation have been localized on large indigenous plasmids that are transmissible, allowing lateral transfer of symbiotic functions. A recent paper reports on the complete sequencing of the symbiotic plasmid pNGR234a from Rhizobium species NGR234(1), revealing not only putative new symbiotic genes but also possible mechanisms for evolution and lateral dispersal of symbiotic nitrogen‐fixing (...) abilities among rhizobia. (shrink)

L'Inopos, qui constitue le principal cours d'eau de Délos, prend sa source au Sud-Ouest du Cynthe. Il coule d'abord vers le Nord puis il s'oriente vers l'Ouest pour déboucher à l'emplacement de l'Agora des Hermaïstes. Un barrage associé à un vaste bassin de retenue a été construit à l'endroit où il change d'orientation. La paroi d'amont du mur qui barre le vallon est constituée de blocs de poros dont les joints verticaux ont été remplis de plomb et dont les assises (...) successives ont été associées par des barres métalliques se développant sur toute la longueur de l'ouvrage. Des drains ménagés dans l'épaisseur du mur conduisaient vers l'aval les eaux d'infiltration. Cette construction, qui atteste une remarquable connaissance des problèmes de stabilité des barrages, est sans doute une œuvre des Athéniens réalisée vers la fin du Ve ou le début du IVe s. Le barrage et son bassin furent réaménagés au début de l'Indépendance. A l'époque impériale, le barrage fut percé en sous-œuvre et associé à un aqueduc. (shrink)

An effective approach is introduced to predict the magnitude of reservoir-triggered earthquake, based on support vector machines and fuzzy support vector machines methods. The main influence factors on RTE, including lithology, rock mass integrity, fault features, tectonic stress state, and seismic activity background in reservoir area, are categorized into 11 parameters and quantified by using analytical hierarchy process. Dataset on 100 reservoirs in China, including the 48 well-documented cases of RTE, are collected and used to train and validate the (...) prediction models established with SVM and FSVM, respectively. Through numerical tests, it is found that both the SVM and FSVM models are effective in the prediction of the magnitude of RTE with high accuracy, provided that sufficient samples are collected. While the results of FSVM which is extended from SVM by introducing a fuzzy membership to reduce the influence of noises or outliers are found to be slightly less accurate than those of SVM in the current analysis of RTE cases. The reason might be attributed to the high discreteness of the sample data in the current study. (shrink)

The discovery of a stable latent reservoir for HIV‐1 in resting memory CD4+ T cells provides a mechanism for lifelong persistence of HIV‐1. The long‐lived latently infected cells persist in spite of prolonged highly active antiretroviral therapy and present a major barrier to a cure of HIV‐1 infection. In this review, we discuss the current understanding of HIV‐1 persistence and latent viral infection in the context of effective antiretroviral therapy and the recent progress in purging latent viral reservoirs. Recent (...) studies demonstrate that reactivation of latent HIV‐1 is a promising strategy for the depletion of these viral reservoirs. A thorough evaluation of the anti‐latency activity of drug candidates should include the measurement of changes in intracellular viral RNA, plasma virus levels, and the size of latent viral reservoirs, as well as potential adverse effects. Currently, there are several technical barriers to the evaluation of anti‐latency drugs in vivo. We also discuss these challenging issues that remain unresolved. (shrink)

This paper explores the intricate relationship between the concept of “savage knowledge,” its significance during the ninteenth and twentieth centuries, and the emerging field of ethnoscience. It specifically focuses on the Amazon region as a pivotal area in the development of ethnoscience, examining the contributions of renowned naturalists Carl von Martius, Richard Spruce, and Richard Schultes, who each conducted scientific expeditions to the Amazon during this era. Their works are crucial in reevaluating the dynamic interplay between the Western perception of (...) the “savage,” the scientific principles that underpin it, and the geopolitics of knowledge exchange between countries in the global north and south. I argue that the contextual conditions which made possible the emergence of ethnoscience, including imperial assimilation, extraction, and coloniality, continue to exert influence on twentieth century political discourses concerning the integration of indigenous cultures into global politics. This influence is evident through the analysis of a UNESCO document in the second part of the paper. The study concludes that the incorporation of indigenous knowledge, systematised by ethnoscience, has often served as a pretext for controlling geographical areas historically regarded as “natural resources,” ultimately transforming them into reservoirs of indigenous epistemologies. (shrink)

This is the Professional Thesis of the DPP that was conducted from February to May 2021. The research focuses on “Illegal Fishing Management in Lower Sesan 2 Reservoir, Stung Treng Province, Cambodia” with two research objectives: to understand the illegal fishing situation and to explore solutions to address the illegal fishing issues in the Lower Sesan 2 Reservoir. The research is approached by a Conceptual Framework addressing four elements of illegal fishing in the Lower Sesan 2 reservoir. Fourth eight community (...) fishery committee members and community fishery members (36% of whom are women) joined in group discussions and 35 local fishers and stakeholders were interviewed. Two types of data were gathered in this research: secondary and primary data. The livelihoods of local fishers and migrant fishers in Lower Sesan 2 reservoir were identified: fishing, rice production, farming, animal husbandry NTFP collection. Some local fishers and all migrant fishers including men, women and youths carried out illegal fishing in Lower Sesan 2. They used illegal fishing gears, caught endangered fish species, fished in conservation area, fished with illegal fishing gears in close fishing season, trading fish without license. The causes of illegal fishing in Lower Sesan 2 reservoir were found out. The performances and challenges, opportunities of stakeholders in fishery resource management in Lower Sesan 2 were identified. The strategies of sustainable fishery resource management were found out. Some recommendations were produced. (shrink)

Acid fracturing is the most important stimulation method in the carbonate reservoir. Due to the high cost and high risk of acid fracturing, it is necessary to predict the reservoir productivity before acid fracturing, which can provide support to optimize the parameters of acid fracturing. However, the productivity of a single well is affected by various construction parameters and geological conditions. Overfitting can occur when performing productivity prediction tasks on the high-dimension, small-sized reservoir, and acid fracturing dataset. Therefore, this study (...) developed a stacking heterogeneous ensemble model with a hybrid wrapper-based feature selection strategy to forecast reservoir productivity, resolve the overfitting problem, and improve productivity prediction. Compared to other baseline models, the proposed model was found to have the best predictive performances on the test set and effectively deal with the overfitting. The results proved that the hybrid wrapper-based feature selection strategy introduced in this study reduced data acquisition costs and improved model comprehensibility without reducing model performance. (shrink)

This book encapsulates John Beebe’s influential work on the analytical psychology of consciousness. Building on C. G. Jung’s theory of psychological types and on subsequent clarifications by Marie-Louise von Franz and Isabel Briggs Myers, Beebe demonstrates the bond between the eight types of consciousness Jung named and the archetypal complexes that impart energy and purpose to our emotions, fantasies, and dreams. For this collection, Beebe has revised and updated his most influential and significant previously published papers and has introduced, in (...) a brand new chapter, a surprising theory of type and culture. Beebe’s model enables readers to take what they already know about psychological types and apply it to depth psychology. The insights contained in the fifteen chapters of this book will be especially valuable for Jungian psychotherapists, post-Jungian academics and scholars, psychological type practitioners, and type enthusiasts. (shrink)

The increasing global demand for energy necessitates devoted attention to the formulation and exploration of mechanisms of thermal heat exchangers to explore and save heat energy. Thus, innovative thermal transport fluids require to boost thermal conductivity and heat flow features to upsurge convection heat rate, and nanofluids have been effectively employed as standard heat transfer fluids. With such intention, herein, we formulated and developed the constitutive flow laws by utilizing the Rossland diffusion approximation and Stephen’s law along with the MHD (...) effect. The mathematical formulation is based on boundary layer theory pioneered by Prandtl. Governing nonlinear partial differential flow equations are changed to ODEs via the implementation of the similarity variables. A well-known computational algorithm BVPh2 has been utilized for the solution of the nonlinear system of ODEs. The consequence of innumerable physical parameters on flow field, thermal distribution, and solutal field, such as magnetic field, Lewis number, velocity parameter, Prandtl number, drag force, Nusselt number, and Sherwood number, is plotted via graphs. Finally, numerical consequences are compared with the homotopic solution as a limiting case, and an exceptional agreement is found. (shrink)

Η στήλη που δημοσιεύεται εδώ ανακαλύφθηκε το 2003 στη Δεξαμενή του Ινωπού στη Δήλο, όπου είχε επαναχρησιμοποιηθεί ως οικοδομικό υλικό, και φέρει το ψήφισμα του Ινωπού. Μπορούμε να δείξουμε, ξαναδιαβάζοντας τους λογαριασμούς των Ιεροποιών, ότι το όνομα Ινωπός αναφέρεται στην ίδια τη Δεξαμενή - η οποία από τυπολογική άποψη είναι μια κρήνη - και όχι στο ρέμα του Ινωπού. Το κείμενο παρουσιάζει άλλωστε μια δυσκολία, καθώς εμπεριέχει αντιφατικές ενδείξεις για τη χρονολόγησή του. Μπορούμε να υποθέσουμε ότι πρόκειται για ένα ελληνιστικό (...) αντίγραφο ενός αρχαιότερου κανονισμού, ο οποίος χρονολογείται στην κλασική εποχή. Στην περίπτωση αυτή πρέπει να δεχθούμε ότι οι πρώτες εργασίες διαμόρφωσης της Δεξαμενής του Ινωπού ανέρχονται σε εποχή παλαιότερη από αυτήν που πιστεύαμε μέχρι σήμερα. (shrink)

Amyloid fibril formation plays a central role in the pathogenesis of a number of neurodegenerative diseases, including Alzheimer and Parkinson diseases. Transient prefibrillar oligomers forming during the aggregation process, exhibiting a small size and a large hydrophobic surface, can aberrantly interact with a number of molecular targets on neurons, including the lipid bilayer of plasma membranes, resulting in a fatal outcome for the cells. By contrast, the mature fibrils, despite presenting generally a high hydrophobic surface, are endowed with a low (...) diffusion rate and poorly penetrate the interior of the lipid bilayer. However, increasing evidence shows that both intracellular α‐synuclein fibrils, as well and as extracellular amyloid‐β and β2‐microglobulin fibrils, can release oligomers over time that quickly diffuse to reach the membrane of the neighboring cells. The persistent leakage of harmful oligomers from fibrils triggers an ongoing cascade of events resulting in a sustained injury to neurons and glia and also provides aggregates with the ability to cross biological membranes and diffuse between cells or cellular compartments. (shrink)

The Plasmids in BioShock are essentially enhancement technologies for “healthy” individuals. Although the sea slug in BioShock is a work of fiction, in the real world researchers are investigating species‐transcending gene technology. BioShock makes apparent the usefulness of biological enhancements, but also warns us about the potential dangers of playing with biology. Not everyone is in favor of human enhancement technologies. Their opponents fear that some procedures might change what it means to be human on a fundamental level. BioShock is (...) a digital game, and the types of Plasmids you are given are adequate to the challenges you encounter. Perhaps enhancement technologies would actually lead to greater social justice and equality by benefiting those who aren't as genetically gifted as others. As things stand, we are subject to the genetic lottery, but enhancement technologies would shift our fate “from chance to choice” and level the playing field. (shrink)

The contribution of the body to cognition and control in natural and artificial agents is increasingly described as “off-loading computation from the brain to the body”, where the body is said to perform “morphological computation”. Our investigation of four characteristic cases of morphological computation in animals and robots shows that the ‘off-loading’ perspective is misleading. Actually, the contribution of body morphology to cognition and control is rarely computational, in any useful sense of the word. We thus distinguish (1) morphology that (...) facilitates control, (2) morphology that facilitates perception and the rare cases of (3) morphological computation proper, such as ‘reservoir computing.’ where the body is actually used for computation. This result contributes to the understanding of the relation between embodiment and computation: The question for robot design and cognitive science is not whether computation is offloaded to the body, but to what extent the body facilitates cognition and control – how it contributes to the overall ‘orchestration’ of intelligent behaviour. (shrink)

In Rapture some mad shit happens: there are Plasmids that allow players to fire bees out of their hands, generate electricity bolts, set enemies on fire, pick stuff up using telekinetic powers, and much more. One theory is that physical things are those that can be completely described by the vocabulary of the best possible theory of physics. Physicalism would thus be the view that this theory of physics would completely specify all the fundamental categories, all the ingredients we need (...) to make the world. Another theory is that the physical properties are the ones needed to account for the objects we accept as physical; for example, Andrew Ryan's putter. The physicalist's claim would be that these properties are the only ones we need to account for the rest of the world. (shrink)

A journal editor recently apologised for publishing a 2010 paper in which authors designated an enzyme as New Delhi metallo-β-lactamase-1 (NDM-1) and its related gene bla_NDM-1 after a city, New Delhi. This name had raised an outcry in India, with health authorities, media and medical practitioners demanding New Delhi be dropped from the name. The name was actually first given in another 2009 paper, whose corresponding author remains the same as the 2010 paper. There is a tradition of eponymous names (...) in science. But those found derogatory to races, groups, cities, and countries have been changed. For example, Mongolism was changed to Down's syndrome; Australia antigen to HBsAg; Mexican Swine flu to H1N1; GRID (Gay Related Immune Deficiency) and 4H-Disease (Haitians, Homosexuals, Haemophiliacs and Heroin Users Disease) to AIDS. It is necessary that NDM-1 also be changed to a name based on scientific characteristics. NDM-1 must be changed to PCM (plasmid-encoding carbapenem-resistant metallo-β-lactamase). It is also necessary to review the tradition of naming organisms, diseases, genes, etc. after cities, countries and races. Often, such names giving amounts to names calling. It needs to be discarded by scientists in all new names giving from now on. Geographical and racial names giving must be replaced by scientific names giving. Journal editors must ensure that such scientific names giving is laid down as standard guideline in paper submissions. All such names still in currency need to be phased out by replacing them with names based on scientific characteristics, or in honour of their pioneering scientist/s or institutions. The lead author of the above 2010 paper has said he was not consulted about the final draft and did not agree with the conclusions of the paper. To ensure that corresponding authors do not ride roughshod over co-authors, and lead and other authors do not backtrack on papers, editors must ensure written concurrence of all authors, especially the lead author, to the final draft of a paper and include this in their guidelines for paper submissions. (shrink)

The concept of “life” certainly is of some use to distinguish birds and beavers from water and stones. This pragmatic usefulness has led to its construal as a categorical predicate that can sift out living entities from non-living ones depending on their possessing specific properties—reproduction, metabolism, evolvability etc. In this paper, we argue against this binary construal of life. Using text-mining methods across over 30,000 scientific articles, we defend instead a degrees-of-life view and show how these methods can contribute to (...) experimental philosophy of science and concept explication. We apply topic-modeling algorithms to identify which specific properties are attributed to a target set of entities (bacteria, archaea, viruses, prions, plasmids, phages and the molecule of adenine). Eight major clusters of properties were identified together with their relative relevance for each target entity (two that relate to metabolism and catalysis, one to genetics, one to evolvability, one to structure, and—rather unexpectedly—three that concern interactions with the environment broadly construed). While aligning with intuitions—for instance about viruses being less alive than bacteria—these quantitative results also reveal differential degrees of performance that have so far remained elusive or overlooked. Taken together, these analyses provide a conceptual “lifeness space” that makes it possible to move away from a categorical construal of life by empirically assessing the relative lifeness of more-or-less alive entities. (shrink)

Written for non-experts, this volume introduces the mechanisms that underlie reticulate evolution. Chapters are either accompanied with glossaries that explain new terminology or timelines that position pioneering scholars and their major discoveries in their historical contexts. The contributing authors outline the history and original context of discovery of symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow, and infectious heredity. By applying key insights from the areas of molecular (phylo)genetics, microbiology, virology, ecology, systematics, immunology, epidemiology and computational science, (...) they demonstrate how reticulate evolution impacts successful survival, fitness and speciation. Reticulate evolution brings forth a challenge to the standard Neo-Darwinian framework, which defines life as the outcome of bifurcation and ramification patterns brought forth by the vertical mechanism of natural selection. Reticulate evolution puts forward a pattern in the tree of life that is characterized by horizontal mergings and lineage crossings induced by symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow, and infective heredity, making the “tree of life” look more like a “web of life.” On an epistemological level, the various means by which hereditary material can be transferred horizontally challenges our classic notions of units and levels of evolution, fitness, modes of transmission, linearity, communities, and biological individuality. The case studies presented examine topics including the origin of the eukaryotic cell and its organelles through symbiogenesis; the origin of algae through primary and secondary symbiosis and dinoflagellates through tertiary symbiosis; the superorganism and holobiont as units of evolution; how endosymbiosis induces speciation in multicellular life forms; transferrable and non-transferrable plasmids and how they symbiotically interact with their host; the means by which pro- and eukaryotic organisms transfer genes laterally (bacterial transformation, transduction and conjugation as well as transposons and other mobile genetic elements); hybridization and divergence with gene flow in sexually-reproducing individuals; current (human) microbiome and viriome studies that impact our knowledge concerning the evolution of organismal health and acquired immunity; and how symbiosis and symbiogenesis can be modelled in computational evolution. (shrink)

We address three fundamental questions: What does it mean for an entity to be living? What is the role of inter-organismic collaboration in evolution? What is a biological individual? Our central argument is that life arises when lineage-forming entities collaborate in metabolism. By conceiving of metabolism as a collaborative process performed by functional wholes, which are associations of a variety of lineage-forming entities, we avoid the standard tension between reproduction and metabolism in discussions of life – a tension particularly evident (...) in discussions of whether viruses are alive. Our perspective assumes no sharp distinction between life and non-life, and does not equate life exclusively with cellular or organismal status. We reach this conclusion through an analysis of the capabilities of a spectrum of biological entities, in which we include the pivotal case of viruses as well as prions, plasmids, organelles, intracellular and extracellular symbionts, unicellular and multicellular life-forms. The usual criterion for classifying many of the entities of our continuum as non-living is autonomy. This emphasis on autonomy is problematic, however, because even paradigmatic biological individuals, such as large animals, are dependent on symbiotic associations with many other organisms. These composite individuals constitute the metabolic wholes on which selection acts. Finally, our account treats cooperation and competition not as polar opposites but as points on a continuum of collaboration. We suggest that competitive relations are a transitional state, with multi-lineage metabolic wholes eventually outcompeting selfish competitors, and that this process sometimes leads to the emergence of new types or levels of wholes. Our view of life as a continuum of variably structured collaborative systems leaves open the possibility that a variety of forms of organized matter – from chemical systems to ecosystems – might be usefully understood as living entities. (shrink)

The 1940s and 1950s were marked by intense debates over the origin of drug resistance in microbes. Bacteriologists had traditionally invoked the notions of ‘training’ and ‘adaptation’ to account for the ability of microbes to acquire new traits. As the field of bacterial genetics emerged, however, its participants rejected ‘Lamarckian’ views of microbial heredity, and offered statistical evidence that drug resistance resulted from the selection of random resistant mutants. Antibiotic resistance became a key issue among those disputing physiological vs. genetic (...) explanations of variation in bacteria. Postwar developments connected with the Lysenko affair gave this debate a new political valence.Proponents of the neo-Darwinian synthesis weighed in with support for the genetic theory. However, certain features of drug resistance seemed inexplicable by mutation and selection, particularly the phenomenon of ‘multiple resistance’—the emergence of resistance in a single strain against several unrelated antibiotics. In the late 1950s, Tsutomu Watanabe and his collaborators solved this puzzle by determining that resistance could be conferred by cytoplasmic resistance factors rather than chromosomal mutation. These R factors could carry resistance to many antibiotics and seemed able to promote their own dissemination in bacterial populations. In the end, the vindication of the genetic view of drug resistance was accompanied by a recasting of the ‘gene’ to include extrachromosomal hereditary units carried on viruses and plasmids. (shrink)

Recently improved understanding of evolutionary processes suggests that tree-based phylogenetic analyses of evolutionary change cannot adequately explain the divergent evolutionary histories of a great many genes and gene complexes. In particular, genetic diversity in the genomes of prokaryotes, phages, and plasmids cannot be fit into classic tree-like models of evolution. These findings entail the need for fundamental reform of our understanding of molecular evolution and the need to devise alternative apparatus for integrated analysis of these genomes. We advocate the development (...) of integrative phylogenomics for analyzing these genomes and their histories, with tools suited to analyzing the importance of lateral gene transfer (LGT) and of DNA evolution in extra-cellular mobile genetic elements (e.g., viruses, plasmids). These phenomena greatly increase the complexity of relationships among interacting genetic partners, as they exchange functional genetic units. We examine the ontology of functional genetic units, interacting genetic partners, and emergent genetic associations, argue that these three categories of entities are required for a successful integrated phylogenomics. We conclude with arguments to suggest that the proposed new perspective and associated tools are suitable, and perhaps required, as a replacement for the bifurcating trees that have dominated evolutionary thinking for the last 150 years. (shrink)

This article explores and challenges notions and methodologies of conservation, including the use of blockchain technologies as a means of establishing provenance of a physical BioArtwork, of the artist’s documentation encapsulating their intentions and of the conservator’s records required for the artwork’s ongoing care. The exploration is done through a case study of an art project called ‘Unruly Objects and Biological Conservation’ created by Anna Dumitriu with support from Alex May. The artwork consists of three items containing RFID tags sealed (...) in resin – which point to the location of the artist’s documentation. Therefore, the works physically include instructions for maintaining their inherent concepts and materiality for the benefit of the conservators. Such instructions can often be difficult to track down, or become disassociated from the artwork while the digital preservation of this storage method also poses its own set of questions. The works also include biological material including mud from a bacterial ecosystem known as a Winogradsky Column, living plant material and SARS-CoV-2 (coronavirus) RNA from a plasmid construct. (shrink)

Machine-based automation has long been a key factor in the modern era. However, lately, many people have been shocked by artificial intelligence (AI) applications, such as ChatGPT (OpenAI), that can perform tasks previously thought to be human-exclusive. With recent advances in natural language processing (NLP) technologies, AI can generate written content that is similar to human-made products, and this ability has a variety of applications. As the technology of large language models continues to progress by making use of colossal (...) class='Hi'>reservoirs of digital information, AI is becoming more capable of recognizing patterns and associations within given contexts, making it especially helpful in assisting with various professional writing tasks [1]. In this paper, we will discuss several key points regarding the current state and future of AI in academia. Furthermore, since in certain aspects, acts can speak louder than words, we will also present some of our hands-on experiences of working with ChatGPT. (shrink)

This essay argues that moral self-cultivation as described in the Confucian tradition involves the cultivation of the body. Preparing the body in certain ways, perhaps by making it healthy, is a necessary part of moral self-cultivation. This claim includes: (a) nourishing the body in a proper way is a first step in moral self-cultivation, and the bodily care is instrumentally valuable to one’s flourishing life; (b) making and keeping a healthy body is partly constitutive of a moral well-being and hence (...) bodily care is also intrinsically valuable to a flourishing life. This perspective on embodied virtue is established through a discussion of qi. The body as the storehouse of qi is not only a passive reservoir of knowledge that serves as moral guidance, but also actively plays an indispensable and integral role in activities related to one’s moral transformation. A well-cared for body provides a moral agent with the temporal and spatial possibility for moral refinement and an enhanced good life. (shrink)

A recent article by Galitski and Roth(1) characterizes adaptive reversion of chromosomal lac− mutations in Salmonella typhimurium LT2. Using a classical genetic approach they show that adaptive reversion, as characterized by the appearance of late revertant colonies, is an exception rather than a general phenomenon for reversion of nonsense, missense, frameshift and insertion mutations. For certain mutations, however, the number of late revertants exceeds the predicted number. These excess revertants suggest that adaptive mutability is applicable to chromosomal genes as well (...) as to genetic changes involving F plasmids and lysogenic phages. (shrink)

Bacterial resistance mechanisms to the antibiotics known as β‐lactams, which include the penicillins and cephalosporins, can take several forms but frequently involve the production of β‐lactamases from either plasmid‐ or chromosomally‐encoded loci. Gram negative bacteria express a β‐lactamase from evolutionarily related chromosomal ampC genes. Genetic analysis of both inducible and constitutively expressed AmpC β‐lactamases provide insights into the mechanisms regulating production of the enzyme. Evolutionary relationships between the genes of different species are discussed, as well as the regulatory mechanisms (...) that in both laboratory mutants and clinical isolates lead to overproduction of β‐lactamase. (shrink)

The gut protozoan parasite, Giardia duodenalis, is the best characterized example of the most ancient eukaryotes, which are anaerobic and appear to be primitively amitochondrial. Apart from its obvious medical importance, Giardia is fascinating in its own right. Its prokaryotic-like anaerobic metabolism renders it selectively sensitive to some bacterial drugs, especially the nitroimidazoles, which are activated to form toxic radicals. Other features, including an enzyme that reduces oxygen directly to water, cysteine as the keeper of redox balance, a plasmid, (...) and toxin-like genes are also distinctly prokaryotic-like. But, unlike prokaryotes, Giardia has a sophisticated, highly developed cytoskeleton, bounded nuclei, linear chromosomes capped with telomeric repeats, and telomere positional regulation of gene expression. BioEssays 20:256–263, 1998.© 1998 John Wiley & Sons, Inc. (shrink)

Communication is defined as an interaction between at least two living agents which share a repertoire of signs. These are combined according to syntactic, semantic and context-dependent, pragmatic rules in order to coordinate behavior. This volume deals with the important roles of soil bacteria in parasitic and symbiotic interactions with viruses, plants, animals and fungi. Starting with a general overview of the key levels of communication between bacteria, further reviews examine the various aspects of intracellular as well as intercellular biocommunication (...) between soil microorganisms. This includes the various levels of biocommunication between phages and bacteria, between soil algae and bacteria, and between bacteria, fungi and plants in the rhizosphere, the role of plasmids and transposons, horizontal gene transfer, quorum sensing and quorum quenching, bacterial-host cohabitation, phage-mediated genetic exchange and soil viral ecology. (shrink)

The origin of novel traits is what draws many to evolutionary biology, yet our understanding of the mechanisms that underlie the genesis of novelty remains limited. Here I review definitions of novelty including its relationship to homology. I then discuss how ontogenetic perspectives may allow us to move beyond current roadblocks in our understanding of the mechanics of innovation. Specifically, I explore the roles of canalization, plasticity and threshold responses during development in generating a reservoir of cryptic genetic variation free (...) to drift and accumulate in natural populations. Environmental or genetic perturbations that exceed the buffering capacity of development can then release this variation, and, through evolution by genetic accommodation, result in rapid diversification, recurrence of lost phenotypes as well as the origins of novel features. I conclude that, in our quest to understand the nature of innovation, the nature of development deserves to take center stage. BioEssays 30:432–447, 2008. © 2008 Wiley Periodicals, Inc. (shrink)