Diverging Entanglement Length in Gapped Quantum Spin Systems

We prove the existence of gapped quantum Hamiltonians whose ground states exhibit an infinite entanglement length, as opposed to their finite correlation length. Using the concept of entanglement swapping, the localizable entanglement is calculated exactly for valence bond and finitely correlated states, and the existence of the so--called string-order parameter is discussed. We also report on evidence that the ground state of an antiferromagnetic chain can be used as a perfect quantum channel if local measurements on the individual spins can be implemented.Comment: 4 page

The metIC operon involved in methionine biosynthesis in Bacillus subtilis is controlled by transcription antitermination

There are two major pathways for methionine biosynthesis in micro-organisms. Little is known about these pathways in Bacillus subtilis. The authors assigned a function to the metI (formerly yjcI) and metC (formerly yjcJ) genes of B. subtilis by complementing Escherichia coli metB and metC mutants, analysing the phenotype of B. subtilis metI and metC mutants, and carrying out enzyme activity assays. These genes encode polypeptides belonging to the cystathionine -synthase family of proteins. Interestingly, the MetI protein has both cystathionine -synthase and O-acetylhomoserine thiolyase activities, whereas the MetC protein is a cystathionine ß-lyase. In B. subtilis, the transsulfuration and the thiolation pathways are functional in vivo. Due to its dual activity, the MetI protein participates in both pathways. The metI and metC genes form an operon, the expression of which is subject to sulfur-dependent regulation. When the sulfur source is sulfate or cysteine the transcription of this operon is high. Conversely, when the sulfur source is methionine its transcription is low. An S-box sequence, which is located upstream of the metI gene, is involved in the regulation of the metIC operon. Northern blot experiments demonstrated the existence of two transcripts: a small transcript corresponding to the premature transcription termination at the terminator present in the S-box and a large one corresponding to transcription of the complete metIC operon. When methionine levels were limiting, the amount of the full-length transcript increased. These results substantiate a model of regulation by transcription antitermination.published_or_final_versio

Complete-Graph Tensor Network States: A New Fermionic Wave Function Ansatz for Molecules

We present a new class of tensor network states that are specifically designed to capture the electron correlation of a molecule of arbitrary structure. In this ansatz, the electronic wave function is represented by a Complete-Graph Tensor Network (CGTN) ansatz which implements an efficient reduction of the number of variational parameters by breaking down the complexity of the high-dimensional coefficient tensor of a full-configuration-interaction (FCI) wave function. We demonstrate that CGTN states approximate ground states of molecules accurately by comparison of the CGTN and FCI expansion coefficients. The CGTN parametrization is not biased towards any reference configuration in contrast to many standard quantum chemical methods. This feature allows one to obtain accurate relative energies between CGTN states which is central to molecular physics and chemistry. We discuss the implications for quantum chemistry and focus on the spin-state problem. Our CGTN approach is applied to the energy splitting of states of different spin for methylene and the strongly correlated ozone molecule at a transition state structure. The parameters of the tensor network ansatz are variationally optimized by means of a parallel-tempering Monte Carlo algorithm

PlcRa, a new quorum-sensing regulator from Bacillus cereus, plays a role in oxidative stress responses and cysteine metabolism in stationary phase

We characterized a new quorum-sensing regulator, PlcRa, which is present in various members of the B. cereus group and identified a signaling heptapeptide for PlcRa activity: PapRa7. We demonstrated that PlcRa is a 3D structural paralog of PlcR using sequence analysis and homology modeling. A comparison of the transcriptomes at the onset of stationary phase of a ¿plcRa mutant and the wild-type B. cereus ATCC 14579 strain showed that 68 genes were upregulated and 49 genes were downregulated in the ¿plcRa mutant strain (>3-fold change). Genes involved in the cysteine metabolism (putative CymR regulon) were downregulated in the ¿plcRa mutant strain. We focused on the gene with the largest difference in expression level between the two conditions, which encoded -AbrB2- a new regulator of the AbrB family. We demonstrated that purified PlcRa bound specifically to the abrB2 promoter in the presence of synthetic PapRa7, in an electrophoretic mobility shift assay. We further showed that the AbrB2 regulator controlled the expression of the yrrT operon involved in methionine to cysteine conversion. We found that the ¿plcRa mutant strain was more sensitive to hydrogen peroxide- and disulfide-induced stresses than the wild type. When cystine was added to the culture of the ¿plcRa mutant, challenged with hydrogen peroxide, growth inhibition was abolished. In conclusion, we identified a new RNPP transcriptional regulator in B. cereus that activated the oxidative stress response and cysteine metabolism in transition state cells

Photoelectric Emission from Interstellar Dust: Grain Charging and Gas Heating

We model the photoelectric emission from and charging of interstellar dust and obtain photoelectric gas heating efficiencies as a function of grain size and the relevant ambient conditions. Using realistic grain size distributions, we evaluate the net gas heating rate for various interstellar environments, and find less heating for dense regions characterized by R_V=5.5 than for diffuse regions with R_V=3.1. We provide fitting functions which reproduce our numerical results for photoelectric heating and recombination cooling for a wide range of interstellar conditions. In a separate paper we will examine the implications of these results for the thermal structure of the interstellar medium. Finally, we investigate the potential importance of photoelectric heating in H II regions, including the warm ionized medium. We find that photoelectric heating could be comparable to or exceed heating due to photoionization of H for high ratios of the radiation intensity to the gas density. We also find that photoelectric heating by dust can account for the observed variation of temperature with distance from the galactic midplane in the warm ionized medium.Comment: 50 pages, including 18 figures; corrected title and abstract field

Obscured Activity: AGN, Quasars, Starbursts and ULIGs observed by the Infrared Space Observatory

Some of the most active galaxies in the Universe are obscured by large quantities of dust and emit a substantial fraction of their bolometric luminosity in the infrared. Observations of these infrared luminous galaxies with the Infrared Space Observatory (ISO) have provided a relatively unabsorbed view to the sources fuelling this active emission. The improved sensitivity, spatial resolution and spectroscopic capability of ISO over its predecessor Infrared Astronomical Satellite (IRAS), has enabled significant advances in the understanding of the infrared properties of active galaxies. ISO surveyed a wide range of active galaxies which, in the context of this review, includes those powered by intense bursts of star-formation as well as those containing a dominant active galactic nucleus (AGN). Mid infrared imaging resolved for the first time the dust enshrouded nuclei in many nearby galaxies, while a new era in infrared spectroscopy was opened by probing a wealth of atomic, ionic and molecular lines as well as broad band features in the mid and far infrared. This was particularly useful since it resulted in the understanding of the power production, excitation and fuelling mechanisms in the nuclei of active galaxies including the intriguing but so far elusive ultraluminous infrared galaxies. Detailed studies of various classes of AGN and quasars greatly improved our understanding of the unification scenario. Far-infrared imaging and photometry also revealed the presence of a new very cold dust component in galaxies and furthered our knowledge of the far-infrared properties of faint starbursts, ULIGs and quasars. We summarise almost nine years of key results based upon ISO data spanning the full range of luminosity and type of active galaxies.Comment: Accepted for publication in 'ISO science legacy - a compact review of ISO major achievements', Space Science Reviews - dedicated ISO issue. To be published by Springer in 2005. 62 pages (low resolution figures version). Higher resolution PDFs available from http://users.physics.uoc.gr/~vassilis/papers/VermaA.pdf or http://www.iso.vilspa.esa.es/science/SSR/Verma.pd

Increased sporulation underpins adaptation of Clostridium difficile strain 630 to a biologically–relevant faecal environment, with implications for pathogenicity

Abstract Clostridium difficile virulence is driven primarily by the processes of toxinogenesis and sporulation, however many in vitro experimental systems for studying C. difficile physiology have arguably limited relevance to the human colonic environment. We therefore created a more physiologically–relevant model of the colonic milieu to study gut pathogen biology, incorporating human faecal water (FW) into growth media and assessing the physiological effects of this on C. difficile strain 630. We identified a novel set of C. difficile–derived metabolites in culture supernatants, including hexanoyl– and pentanoyl–amino acid derivatives by LC-MSn. Growth of C. difficile strain 630 in FW media resulted in increased cell length without altering growth rate and RNA sequencing identified 889 transcripts as differentially expressed (p < 0.001). Significantly, up to 300–fold increases in the expression of sporulation–associated genes were observed in FW media–grown cells, along with reductions in motility and toxin genes’ expression. Moreover, the expression of classical stress–response genes did not change, showing that C. difficile is well–adapted to this faecal milieu. Using our novel approach we have shown that interaction with FW causes fundamental changes in C. difficile biology that will lead to increased disease transmissibility

A concept for international societally relevant microbiology education and microbiology knowledge promulgation in society

Executive summary Microbes are all pervasive in their distribution and influence on the functioning and well-being of humans, life in general and the planet. Microbially-based technologies contribute hugely to the supply of important goods and services we depend upon, such as the provision of food, medicines and clean water. They also offer mechanisms and strategies to mitigate and solve a wide range of problems and crises facing humanity at all levels, including those encapsulated in the sustainable development goals (SDGs) formulated by the United Nations. For example, microbial technologies can contribute in multiple ways to decarbonisation and hence confronting global warming, provide sanitation and clean water to the billions of people lacking them, improve soil fertility and hence food production and develop vaccines and other medicines to reduce and in some cases eliminate deadly infections. They are the foundation of biotechnology, an increasingly important and growing business sector and source of employment, and the centre of the bioeconomy, Green Deal, etc. But, because microbes are largely invisible, they are not familiar to most people, so opportunities they offer to effectively prevent and solve problems are often missed by decision-makers, with the negative consequences this entrains. To correct this lack of vital knowledge, the International Microbiology Literacy Initiative–the IMiLI–is recruiting from the global microbiology community and making freely available, teaching resources for a curriculum in societally relevant microbiology that can be used at all levels of learning. Its goal is the development of a society that is literate in relevant microbiology and, as a consequence, able to take full advantage of the potential of microbes and minimise the consequences of their negative activities. In addition to teaching about microbes, almost every lesson discusses the influence they have on sustainability and the SDGs and their ability to solve pressing problems of societal inequalities. The curriculum thus teaches about sustainability, societal needs and global citizenship. The lessons also reveal the impacts microbes and their activities have on our daily lives at the personal, family, community, national and global levels and their relevance for decisions at all levels. And, because effective, evidence-based decisions require not only relevant information but also critical and systems thinking, the resources also teach about these key generic aspects of deliberation. The IMiLI teaching resources are learner-centric, not academic microbiology-centric and deal with the microbiology of everyday issues. These span topics as diverse as owning and caring for a companion animal, the vast range of everyday foods that are produced via microbial processes, impressive geological formations created by microbes, childhood illnesses and how they are managed and how to reduce waste and pollution. They also leverage the exceptional excitement of exploration and discovery that typifies much progress in microbiology to capture the interest, inspire and motivate educators and learners alike. The IMiLI is establishing Regional Centres to translate the teaching resources into regional languages and adapt them to regional cultures, and to promote their use and assist educators employing them. Two of these are now operational. The Regional Centres constitute the interface between resource creators and educators–learners. As such, they will collect and analyse feedback from the end-users and transmit this to the resource creators so that teaching materials can be improved and refined, and new resources added in response to demand: educators and learners will thereby be directly involved in evolution of the teaching resources. The interactions between educators–learners and resource creators mediated by the Regional Centres will establish dynamic and synergistic relationships–a global societally relevant microbiology education ecosystem–in which creators also become learners, teaching resources are optimised and all players/stakeholders are empowered and their motivation increased. The IMiLI concept thus embraces the principle of teaching societally relevant microbiology embedded in the wider context of societal, biosphere and planetary needs, inequalities, the range of crises that confront us and the need for improved decisioning, which should ultimately lead to better citizenship and a humanity that is more sustainable and resilient. AbstractThe biosphere of planet Earth is a microbial world: a vast reactor of countless microbially driven chemical transformations and energy transfers that push and pull many planetary geochemical processes, including the cycling of the elements of life, mitigate or amplify climate change (e.g., Nature Reviews Microbiology, 2019, 17, 569) and impact the well-being and activities of all organisms, including humans. Microbes are both our ancestors and creators of the planetary chemistry that allowed us to evolve (e.g., Life's engines: How microbes made earth habitable, 2023). To understand how the biosphere functions, how humans can influence its development and live more sustainably with the other organisms sharing it, we need to understand the microbes. In a recent editorial (Environmental Microbiology, 2019, 21, 1513), we advocated for improved microbiology literacy in society. Our concept of microbiology literacy is not based on knowledge of the academic subject of microbiology, with its multitude of component topics, plus the growing number of additional topics from other disciplines that become vitally important elements of current microbiology. Rather it is focused on microbial activities that impact us–individuals/communities/nations/the human world–and the biosphere and that are key to reaching informed decisions on a multitude of issues that regularly confront us, ranging from personal issues to crises of global importance. In other words, it is knowledge and understanding essential for adulthood and the transition to it, knowledge and understanding that must be acquired early in life in school. The 2019 Editorial marked the launch of the International Microbiology Literacy Initiative, the IMiLI. Here, we present - our concept of how microbiology literacy may be achieved and the rationale underpinning it; - the type of teaching resources being created to realise the concept and the framing of microbial activities treated in these resources in the context of sustainability, societal needs and responsibilities and decision-making; and - the key role of Regional Centres that will translate the teaching resources into local languages, adapt them according to local cultural needs, interface with regional educators and develop and serve as hubs of microbiology literacy education networks. The topics featuring in teaching resources are learner-centric and have been selected for their inherent relevance, interest and ability to excite and engage. Importantly, the resources coherently integrate and emphasise the overarching issues of sustainability, stewardship and critical thinking and the pervasive interdependencies of processes. More broadly, the concept emphasises how the multifarious applications of microbial activities can be leveraged to promote human/animal, plant, environmental and planetary health, improve social equity, alleviate humanitarian deficits and causes of conflicts among peoples and increase understanding between peoples (Microbial Biotechnology, 2023, 16(6), 1091–1111). Importantly, although the primary target of the freely available (CC BY-NC 4.0) IMiLI teaching resources is schoolchildren and their educators, they and the teaching philosophy are intended for all ages, abilities and cultural spectra of learners worldwide: in university education, lifelong learning, curiosity-driven, web-based knowledge acquisition and public outreach. The IMiLI teaching resources aim to promote development of a global microbiology education ecosystem that democratises microbiology knowledge

The Pleiotropic CymR Regulator of Staphylococcus aureus Plays an Important Role in Virulence and Stress Response

We have characterized a novel pleiotropic role for CymR, the master regulator of cysteine metabolism. We show here that CymR plays an important role both in stress response and virulence of Staphylococcus aureus. Genes involved in detoxification processes, including oxidative stress response and metal ion homeostasis, were differentially expressed in a ΔcymR mutant. Deletion of cymR resulted in increased sensitivity to hydrogen peroxide-, disulfide-, tellurite- and copper-induced stresses. Estimation of metabolite pools suggests that this heightened sensitivity could be the result of profound metabolic changes in the ΔcymR mutant, with an increase in the intracellular cysteine pool and hydrogen sulfide formation. Since resistance to oxidative stress within the host organism is important for pathogen survival, we investigated the role of CymR during the infectious process. Our results indicate that the deletion of cymR promotes survival of S. aureus inside macrophages, whereas virulence of the ΔcymR mutant is highly impaired in mice. These data indicate that CymR plays a major role in virulence and adaptation of S. aureus for survival within the host