bluuebunny/crossref_metadata_2025 huggingface dataset:
The complete general secretory pathway in gram-negative bacteria
Authors: Pugsley A P
Published: December 2020

The unifying feature of all proteins that are transported out of the cytoplasm of gram-negative bacteria by the general secretory pathway (GSP) is the presence of a long stretch of predominantly hydrophobic amino acids, the signal sequence. The interaction between signal sequence-bearing proteins and the cytoplasmic membrane may be a spontaneous event driven by the electrochemical energy potential across the cytoplasmic membrane, leading to membrane integration. The translocation of large, hydrophilic polypeptide segments to the periplasmic side of this membrane almost always requires at least six different proteins encoded by the sec genes and is dependent on both ATP hydrolysis and the electrochemical energy potential. Signal peptidases process precursors with a single, amino-terminal signal sequence, allowing them to be released into the periplasm, where they may remain or whence they may be inserted into the outer membrane. Selected proteins may also be transported across this membrane for assembly into cell surface appendages or for release into the extracellular medium. Many bacteria secrete a variety of structurally different proteins by a common pathway, referred to here as the main terminal branch of the GSP. This recently discovered branch pathway comprises at least 14 gene products. Other, simpler terminal branches of the GSP are also used by gram-negative bacteria to secrete a more limited range of extracellular proteins.
Stationary phase in the yeast Saccharomyces cerevisiae
Authors: Werner-Washburne M , Braun E , Johnston G C , Singer R A
Published: December 2020

Growth and proliferation of microorganisms such as the yeast Saccharomyces cerevisiae are controlled in part by the availability of nutrients. When proliferating yeast cells exhaust available nutrients, they enter a stationary phase characterized by cell cycle arrest and specific physiological, biochemical, and morphological changes. These changes include thickening of the cell wall, accumulation of reserve carbohydrates, and acquisition of thermotolerance. Recent characterization of mutant cells that are conditionally defective only for the resumption of proliferation from stationary phase provides evidence that stationary phase is a unique developmental state. Strains with mutations affecting entry into and survival during stationary phase have also been isolated, and the mutations have been shown to affect at least seven different cellular processes: (i) signal transduction, (ii) protein synthesis, (iii) protein N-terminal acetylation, (iv) protein turnover, (v) protein secretion, (vi) membrane biosynthesis, and (vii) cell polarity. The exact nature of the relationship between these processes and survival during stationary phase remains to be elucidated. We propose that cell cycle arrest coordinated with the ability to remain viable in the absence of additional nutrients provides a good operational definition of starvation-induced stationary phase.
Micrasterias cells as a model system for research on morphogenesis
Authors: Meindl U
Published: December 2020

Micrasterias species have been the subject of numerous experimental studies on cell shape formation in the last 40 years. Chemical and physical treatment during different developmental stages, as well as investigations of ultrastructure by means of various different preparation methods, have yielded information about some principles of morphogenesis in the symmetric, highly ornamented Micrasterias cell. The basic symmetry of a Micrasterias cell is determined prior to mitosis and is established without nuclear control thereafter. Normal cell development, however, may occur only under the conditions of continuous protein synthesis throughout the cell cycle. A prepattern for the later cell shape seems to be present at the plasma membrane at the early stages of septum formation. It is realized by a local, patterned distributed incorporation of cell wall material that is delivered by Golgi-produced vesicles. The areas where fusions take place between the primary wall material containing vesicles and the plasma membrane are defined by inward ionic currents that are carried at least in part by calcium. These areas develop into lobes during the following course of cell growth. Cell shaping in Micrasterias cells is thus mediated by both an enhanced extension of the cell wall and an additional incorporation of wall material in the areas of the lobes. Numerous studies have indicated that actin plays an important role in morphogenesis, whereas microtubules do not participate in this process but are involved mainly in nuclear migration. The present review shows that although a wealth of details concerning Micrasterias morphogenesis has already been elucidated, two main questions, i.e., the method of septum formation and the splitting of the lobes, remain to be answered.
Trichothecene biosynthesis in Fusarium species: chemistry, genetics, and significance
Authors: Desjardins A E , Hohn T M , McCormick S P
Published: December 2020

Several species of the genus Fusarium and related fungi produce trichothecenes which are sesquiterpenoid epoxides that act as potent inhibitors of eukaryotic protein synthesis. Interest in the trichothecenes is due primarily to their widespread contamination of agricultural commodities and their adverse effects on human and animal health. In this review, we describe the trichothecene biosynthetic pathway in Fusarium species and discuss genetic evidence that several trichothecene biosynthetic genes are organized in a gene cluster. Trichothecenes are highly toxic to a wide range of eukaryotes, but their specific function, if any, in the survival of the fungi that produce them is not obvious. Trichothecene gene disruption experiments indicate that production of trichothecenes can enhance the severity of disease caused by Fusarium species on some plant hosts. Understanding the regulation and function of trichothecene biosynthesis may aid in development of new strategies for controlling their production in food and feed products.
Mosquitocidal toxins of bacilli and their genetic manipulation for effective biological control of mosquitoes
Authors: Porter A G , Davidson E W , Liu J W
Published: December 2020

The identification, cloning, and characterization of protein toxins from various species of bacilli have demonstrated the existence of mosquitocidal toxins with different structures, mechanisms of action, and host ranges. A start has been made in understanding the polypeptide determinants of toxicity and insecticidal activity, and the purification of toxins from recombinant organisms may lead to the elucidation of their X-ray crystal structures and the cloning of brush border membrane receptors. The results of cloning mosquitocidal toxins in heterologous microorganisms show the potential of expanding the range of susceptible mosquito species by combining several toxins of different host specificity in one cell. Toxins have been expressed in new microorganisms with the potential for increasing potency by persisting at the larval feeding zone. The powerful tools of bacterial genetics are being applied to engineer genetically stable, persistent toxin expression and expand the insecticidal host ranges of Bacillus sphaericus and Bacillus thuringiensis strains. These techniques, together with modern formulation technology, should eventually lead to the construction of mosquitocidal microorganisms which are effective enough to have a real impact on mosquito-borne diseases.
Molecular genetics of Thiobacillus ferrooxidans
Authors: Rawlings D E , Kusano T
Published: December 2020

Thiobacillus ferrooxidans is a gram-negative, highly acidophilic (pH 1.5 to 2.0), autotrophic bacterium that obtains its energy through the oxidation of ferrous iron or reduced inorganic sulfur compounds. It is usually dominant in the mixed bacterial populations that are used industrially for the extraction of metals such as copper and uranium from their ores. More recently, these bacterial consortia have been used for the biooxidation of refractory gold-bearing arsenopyrite ores prior to the recovery of gold by cyanidation. The commercial use of T. ferrooxidans has led to an increasing interest in the genetics and molecular biology of the bacterium. Initial investigations were aimed at determining whether the unique physiology and specialized habitat of T. ferrooxidans had been accompanied by a high degree of genetic drift from other gram-negative bacteria. Early genetic studies were comparative in nature and concerned the isolation of genes such as nifHDK, glnA, and recA, which are widespread among bacteria. From a molecular biology viewpoint, T. ferrooxidans appears to be a typical member of the proteobacteria. In most instances, cloned gene promoters and protein products have been functional in Escherichia coli. Although T. ferrooxidans has proved difficult to transform with DNA, research on indigenous plasmids and the isolation of the T. ferrooxidans merA gene have resulted in the development of a low-efficiency electroporation system for one strain of T. ferrooxidans. The most recent studies have focused on the molecular genetics of the pathways associated with nitrogen metabolism, carbon dioxide fixation, and components of the energy-producing mechanisms.
Computer-aided analyses of transport protein sequences: gleaning evidence concerning function, structure, biogenesis, and evolution
Authors: Saier M H
Published: December 2020

Three-dimensional structures have been elucidated for very few integral membrane proteins. Computer methods can be used as guides for estimation of solute transport protein structure, function, biogenesis, and evolution. In this paper the application of currently available computer programs to over a dozen distinct families of transport proteins is reviewed. The reliability of sequence-based topological and localization analyses and the importance of sequence and residue conservation to structure and function are evaluated. Evidence concerning the nature and frequency of occurrence of domain shuffling, splicing, fusion, deletion, and duplication during evolution of specific transport protein families is also evaluated. Channel proteins are proposed to be functionally related to carriers. It is argued that energy coupling to transport was a late occurrence, superimposed on preexisting mechanisms of solute facilitation. It is shown that several transport protein families have evolved independently of each other, employing different routes, at different times in evolutionary history, to give topologically similar transmembrane protein complexes. The possible significance of this apparent topological convergence is discussed.
Developmental decisions in Dictyostelium discoideum
Authors: Gross J D
Published: December 2020

A few hours after the onset of starvation, amoebae of Dictyostelium discoideum start to form multicellular aggregates by chemotaxis to centers that emit periodic cyclic AMP signals. There are two major developmental decisions: first, the aggregates either construct fruiting bodies directly, in a process known as culmination, or they migrate for a period as "slugs." Second, the amoebae differentiate into either prestalk or prespore cells. These are at first randomly distributed within aggregates and then sort out from each other to form polarized structures with the prestalk cells at the apex, before eventually maturing into the stalk cells and spores of fruiting bodies. Developmental gene expression seems to be driven primarily by cyclic AMP signaling between cells, and this review summarizes what is known of the cyclic AMP-based signaling mechanism and of the signal transduction pathways leading from cell surface cyclic AMP receptors to gene expression. Current understanding of the factors controlling the two major developmental choices is emphasized. The weak base ammonia appears to play a key role in preventing culmination by inhibiting activation of cyclic AMP-dependent protein kinase, whereas the prestalk cell-inducing factor DIF-1 is central to the choice of cell differentiation pathway. The mode of action of DIF-1 and of ammonia in the developmental choices is discussed.
The alphaviruses: gene expression, replication, and evolution
Authors: Strauss J H , Strauss E G
Published: December 2020

The alphaviruses are a genus of 26 enveloped viruses that cause disease in humans and domestic animals. Mosquitoes or other hematophagous arthropods serve as vectors for these viruses. The complete sequences of the +/- 11.7-kb plus-strand RNA genomes of eight alphaviruses have been determined, and partial sequences are known for several others; this has made possible evolutionary comparisons between different alphaviruses as well as comparisons of this group of viruses with other animal and plant viruses. Full-length cDNA clones from which infectious RNA can be recovered have been constructed for four alphaviruses; these clones have facilitated many molecular genetic studies as well as the development of these viruses as expression vectors. From these and studies involving biochemical approaches, many details of the replication cycle of the alphaviruses are known. The interactions of the viruses with host cells and host organisms have been exclusively studied, and the molecular basis of virulence and recovery from viral infection have been addressed in a large number of recent papers. The structure of the viruses has been determined to about 2.5 nm, making them the best-characterized enveloped virus to date. Because of the wealth of data that has appeared, these viruses represent a well-characterized system that tell us much about the evolution of RNA viruses, their replication, and their interactions with their hosts. This review summarizes our current knowledge of this group of viruses.
Chemostat cultivation as a tool for studies on sugar transport in yeasts
Authors: Weusthuis R A , Pronk J T , van den Broek P J , van Dijken J P
Published: December 2020

Chemostat cultivation enables investigations into the effects of individual environmental parameters on sugar transport in yeasts. Various means are available to manipulate the specific rate of sugar uptake (qs) in sugar-limited chemostat cultures. A straightforward way to manipulate qs is variation of the dilution rate, which, in substrate-limited chemostat cultures, is equal to the specific growth rate. Alternatively, qs can be varied independently of the growth rate by mixed-substrate cultivation or by variation of the biomass yield on sugar. The latter can be achieved, for example, by addition of nonmetabolizable weak acids to the growth medium or by variation of the oxygen supply. Such controlled manipulation of metabolic fluxes cannot be achieved in batch cultures, in which various parameters that are essential for the kinetics of sugar transport cannot be controlled. In sugar-limited chemostat cultures, yeasts adapt their sugar transport systems to cope with the low residual sugar concentrations, which are often in the micromolar range. Under the conditions, yeasts with high-affinity proton symport carriers have a competitive advantage over yeasts that transport sugars via facilitated-diffusion carriers. Chemostat cultivation offers unique possibilities to study the energetic consequences of sugar transport in growing cells. For example, anaerobic, sugar-limited chemostat cultivation has been used to quantify the energy requirement for maltose-proton symport in Saccharomyces cerevisiae. Controlled variation of growth conditions in chemostat cultures can be used to study the differential expression of genes involved in sugar transport and as such can make an important contribution to the ongoing studies on the molecular biology of sugar transport in yeasts.
Persistent chlamydiae: from cell culture to a paradigm for chlamydial pathogenesis
Authors: Beatty W L , Morrison R P , Byrne G I
Published: December 2020

Chlamydiae are medically important bacteria responsible for a wide range of human infections and diseases. Repeated episodes of infection promote chronic inflammation associated with detrimental immune system-mediated pathologic changes. However, the true nature of chlamydial pathogenesis may encompass repeated infection superimposed upon persistent infection, which would allow for heightened immune reactivity. During the course of chlamydial infection, numerous host elaborated factors with inhibitory or modifying effects may cause alterations in the chlamydia-host cell relationship such that the organism is maintained in a nonproductive stage of growth. Abnormal or persistent chlamydiae have been recognized under a variety of cell culture systems. The numerous factors associated with altered growth suggest an innate flexibility in the developmental cycle of chlamydiae. This review evaluates in vitro studies of chlamydial persistence and correlates these model systems to features of natural chlamydial disease.
The sigma factors of Bacillus subtilis
Authors: Haldenwang W G
Published: December 2020

The specificity of DNA-dependent RNA polymerase for target promotes is largely due to the replaceable sigma subunit that it carries. Multiple sigma proteins, each conferring a unique promoter preference on RNA polymerase, are likely to be present in all bacteria; however, their abundance and diversity have been best characterized in Bacillus subtilis, the bacterium in which multiple sigma factors were first discovered. The 10 sigma factors thus far identified in B. subtilis directly contribute to the bacterium's ability to control gene expression. These proteins are not merely necessary for the expression of those operons whose promoters they recognize; in many instances, their appearance within the cell is sufficient to activate these operons. This review describes the discovery of each of the known B. subtilis sigma factors, their characteristics, the regulons they direct, and the complex restrictions placed on their synthesis and activities. These controls include the anticipated transcriptional regulation that modulates the expression of the sigma factor structural genes but, in the case of several of the B. subtilis sigma factors, go beyond this, adding novel posttranslational restraints on sigma factor activity. Two of the sigma factors (sigma E and sigma K) are, for example, synthesized as inactive precursor proteins. Their activities are kept in check by "pro-protein" sequences which are cleaved from the precursor molecules in response to intercellular cues. Other sigma factors (sigma B, sigma F, and sigma G) are inhibited by "anti-sigma factor" proteins that sequester them into complexes which block their ability to form RNA polymerase holoenzymes. The anti-sigma factors are, in turn, opposed by additional proteins which participate in the sigma factors' release. The devices used to control sigma factor activity in B, subtilis may prove to be as widespread as multiple sigma factors themselves, providing ways of coupling sigma factor activation to environmental or physiological signals that cannot be readily joined to other regulatory mechanisms.
Phylogenetic identification and in situ detection of individual microbial cells without cultivation
Authors: Amann R I , Ludwig W , Schleifer K H
Published: December 2020

The frequent discrepancy between direct microscopic counts and numbers of culturable bacteria from environmental samples is just one of several indications that we currently know only a minor part of the diversity of microorganisms in nature. A combination of direct retrieval of rRNA sequences and whole-cell oligonucleotide probing can be used to detect specific rRNA sequences of uncultured bacteria in natural samples and to microscopically identify individual cells. Studies have been performed with microbial assemblages of various complexities ranging from simple two-component bacterial endosymbiotic associations to multispecies enrichments containing magnetotactic bacteria to highly complex marine and soil communities. Phylogenetic analysis of the retrieved rRNA sequence of an uncultured microorganism reveals its closest culturable relatives and may, together with information on the physicochemical conditions of its natural habitat, facilitate more directed cultivation attempts. For the analysis of complex communities such as multispecies biofilms and activated-sludge flocs, a different approach has proven advantageous. Sets of probes specific to different taxonomic levels are applied consecutively beginning with the more general and ending with the more specific (a hierarchical top-to-bottom approach), thereby generating increasingly precise information on the structure of the community. Not only do rRNA-targeted whole-cell hybridizations yield data on cell morphology, specific cell counts, and in situ distributions of defined phylogenetic groups, but also the strength of the hybridization signal reflects the cellular rRNA content of individual cells. From the signal strength conferred by a specific probe, in situ growth rates and activities of individual cells might be estimated for known species. In many ecosystems, low cellular rRNA content and/or limited cell permeability, combined with background fluorescence, hinders in situ identification of autochthonous populations. Approaches to circumvent these problems are discussed in detail.
Mechanisms of membrane toxicity of hydrocarbons
Authors: Sikkema J , de Bont J A , Poolman B
Published: December 2020

Microbial transformations of cyclic hydrocarbons have received much attention during the past three decades. Interest in the degradation of environmental pollutants as well as in applications of microorganisms in the catalysis of chemical reactions has stimulated research in this area. The metabolic pathways of various aromatics, cycloalkanes, and terpenes in different microorganisms have been elucidated, and the genetics of several of these routes have been clarified. The toxicity of these compounds to microorganisms is very important in the microbial degradation of hydrocarbons, but not many researchers have studied the mechanism of this toxic action. In this review, we present general ideas derived from the various reports mentioning toxic effects. Most importantly, lipophilic hydrocarbons accumulate in the membrane lipid bilayer, affecting the structural and functional properties of these membranes. As a result of accumulated hydrocarbon molecules, the membrane loses its integrity, and an increase in permeability to protons and ions has been observed in several instances. Consequently, dissipation of the proton motive force and impairment of intracellular pH homeostasis occur. In addition to the effects of lipophilic compounds on the lipid part of the membrane, proteins embedded in the membrane are affected. The effects on the membrane-embedded proteins probably result to a large extent from changes in the lipid environment; however, direct effects of lipophilic compounds on membrane proteins have also been observed. Finally, the effectiveness of changes in membrane lipid composition, modification of outer membrane lipopolysaccharide, altered cell wall constituents, and active excretion systems in reducing the membrane concentrations of lipophilic compounds is discussed. Also, the adaptations (e.g., increase in lipid ordering, change in lipid/protein ratio) that compensate for the changes in membrane structure are treated.
Genetic map of Salmonella typhimurium, edition VIII
Authors: Sanderson K E , Hessel A , Rudd K E
Published: December 2020

We present edition VIII of the genetic map of Salmonella typhimurium LT2. We list a total of 1,159 genes, 1,080 of which have been located on the circular chromosome and 29 of which are on pSLT, the 90-kb plasmid usually found in LT2 lines. The remaining 50 genes are not yet mapped. The coordinate system used in this edition is neither minutes of transfer time in conjugation crosses nor units representing "phage lengths" of DNA of the transducing phage P22, as used in earlier editions, but centisomes and kilobases based on physical analysis of the lengths of DNA segments between genes. Some of these lengths have been determined by digestion of DNA by rare-cutting endonucleases and separation of fragments by pulsed-field gel electrophoresis. Other lengths have been determined by analysis of DNA sequences in GenBank. We have constructed StySeq1, which incorporates all Salmonella DNA sequence data known to us. StySeq1 comprises over 548 kb of nonredundant chromosomal genomic sequences, representing 11.4% of the chromosome, which is estimated to be just over 4,800 kb in length. Most of these sequences were assigned locations on the chromosome, in some cases by analogy with mapped Escherichia coli sequences.
mRNA stability in mammalian cells
Authors: Ross J
Published: December 2020

This review concerns how cytoplasmic mRNA half-lives are regulated and how mRNA decay rates influence gene expression. mRNA stability influences gene expression in virtually all organisms, from bacteria to mammals, and the abundance of a particular mRNA can fluctuate manyfold following a change in the mRNA half-life, without any change in transcription. The processes that regulate mRNA half-lives can, in turn, affect how cells grow, differentiate, and respond to their environment. Three major questions are addressed. Which sequences in mRNAs determine their half-lives? Which enzymes degrade mRNAs? Which (trans-acting) factors regulate mRNA stability, and how do they function? The following specific topics are discussed: techniques for measuring eukaryotic mRNA stability and for calculating decay constants, mRNA decay pathways, mRNases, proteins that bind to sequences shared among many mRNAs [like poly(A)- and AU-rich-binding proteins] and proteins that bind to specific mRNAs (like the c-myc coding-region determinant-binding protein), how environmental factors like hormones and growth factors affect mRNA stability, and how translation and mRNA stability are linked. Some perspectives and predictions for future research directions are summarized at the end.
Role of nitric oxide in parasitic infections
Authors: James S L
Published: December 2020

Nitric oxide is produced by a number of different cell types in response to cytokine stimulation and thus has been found to play a role in immunologically mediated protection against a growing list of protozoan and helminth parasites in vitro and in animal models. The biochemical basis of its effects on the parasite targets appears to involve primarily inactivation of enzymes crucial to energy metabolism and growth, although it has other biologic activities as well. NO is produced not only by macrophages and macrophage-like cells commonly associated with the effector arm of cell-mediated immune reactivity but also by cells commonly considered to lie outside the immunologic network, such as hepatocytes and endothelial cells, which are intimately involved in the life cycle of a number of parasites. NO production is stimulated by gamma interferon in combination with tumor necrosis factor alpha or other secondary activation signals and is regulated by a number of cytokines (especially interleukin-4, interleukin-10, and transforming growth factor beta) and other mediators, as well as through its own inherent inhibitory activity. The potential for design of prevention and/or intervention approaches against parasitic infection (e.g., vaccination or combination chemo- and immunotherapy strategies) on the basis of induction of cell-mediated immunity and NO production appears to be great, but the possible pathogenic consequences of overproduction of NO must be taken into account. Moreover, more research on the role and regulation of NO in human parasitic infection is needed before its possible clinical relevance can be determined.
Conjugative transposons: an unusual and diverse set of integrated gene transfer elements
Authors: Salyers A A , Shoemaker N B , Stevens A M , Li L Y
Published: December 2020

Conjugative transposons are integrated DNA elements that excise themselves to form a covalently closed circular intermediate. This circular intermediate can either reintegrate in the same cell (intracellular transposition) or transfer by conjugation to a recipient and integrate into the recipient's genome (intercellular transposition). Conjugative transposons were first found in gram-positive cocci but are now known to be present in a variety of gram-positive and gram-negative bacteria also. Conjugative transposons have a surprisingly broad host range, and they probably contribute as much as plasmids to the spread of antibiotic resistance genes in some genera of disease-causing bacteria. Resistance genes need not be carried on the conjugative transposon to be transferred. Many conjugative transposons can mobilize coresident plasmids, and the Bacteroides conjugative transposons can even excise and mobilize unlinked integrated elements. The Bacteroides conjugative transposons are also unusual in that their transfer activities are regulated by tetracycline via a complex regulatory network.
Envelope glycoproteins of human immunodeficiency virus type 1: profound influences on immune functions
Authors: Chirmule N , Pahwa S
Published: December 2020

Infection by human immunodeficiency virus type 1 (HIV-1) leads to progressive destruction of the CD4+ T-cell subset, resulting in immune deficiency and AIDS. The specific binding of the viral external envelope glycoprotein of HIV-1, gp120, to the CD4 molecules initiates viral entry. In the past few years, several studies have indicated that the interaction of HIV-1 envelope glycoprotein with cells and molecules of the immune system leads to pleiotropic biological effects on immune functions, which include effects on differentiation of CD34+ lymphoid progenitor cells and thymocytes, aberrant activation and cytokine secretion patterns of mature T cells, induction of apoptosis, B-cell hyperactivity, inhibition of T-cell dependent B-cell differentiation, modulation of macrophage functions, interactions with components of complement, and effects on neuronal cells. The amino acid sequence homologies of the envelope glycoproteins with several cellular proteins have suggested that molecular mimicry may play a role in the pathogenesis of the disease. This review summarizes work done by several investigators demonstrating the profound biological effects of envelope glycoproteins of HIV-1 on immune system cells. Extensive studies have also been done on interactions of the viral envelope proteins with components of the immune system which may be important for eliciting a "protective immune response." Understanding the influences of HIV-1 envelope glycoproteins on the immune system may provide valuable insights into HIV-1 disease pathogenesis and carries implications for the trials of HIV-1 envelope protein vaccines and immunotherapeutics.
Polyphasic taxonomy, a consensus approach to bacterial systematics
Authors: Vandamme P , Pot B , Gillis M , de Vos P , Kersters K , Swings J
Published: December 2020

Over the last 25 years, a much broader range of taxonomic studies of bacteria has gradually replaced the former reliance upon morphological, physiological, and biochemical characterization. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them in a consensus type of classification, framed in a general phylogeny derived from 16S rRNA sequence analysis. In some cases, the consensus classification is a compromise containing a minimum of contradictions. It is thought that the more parameters that will become available in the future, the more polyphasic classification will gain stability. In this review, the practice of polyphasic taxonomy is discussed for four groups of bacteria chosen for their relevance, complexity, or both: the genera Xanthomonas and Campylobacter, the lactic acid bacteria, and the family Comamonadaceae. An evaluation of our present insights, the conclusions derived from it, and the perspectives of polyphasic taxonomy are discussed, emphasizing the keystone role of the species. Taxonomists did not succeed in standardizing species delimitation by using percent DNA hybridization values. Together with the absence of another "gold standard" for species definition, this has an enormous repercussion on bacterial taxonomy. This problem is faced in polyphasic taxonomy, which does not depend on a theory, a hypothesis, or a set of rules, presenting a pragmatic approach to a consensus type of taxonomy, integrating all available data maximally. In the future, polyphasic taxonomy will have to cope with (i) enormous amounts of data, (ii) large numbers of strains, and (iii) data fusion (data aggregation), which will demand efficient and centralized data storage. In the future, taxonomic studies will require collaborative efforts by specialized laboratories even more than now is the case. Whether these future developments will guarantee a more stable consensus classification remains an open question.
Low assets and financial stressors associated with higher depression during COVID-19 in a nationally representative sample of US adults
Authors: Ettman Catherine K , Abdalla Salma M , Cohen Gregory H , Sampson Laura , Vivier Patrick M , Galea Sandro
Published: December 2020

Background

COVID-19 and related containment policies have caused or heightened financial stressors for many in the USA. We assessed the relation between assets, financial stressors and probable depression during the COVID-19 pandemic.

Methods

Between 31 March 2020 and 13 April 2020, we surveyed a probability-based, nationally representative sample of US adults ages 18 and older using the COVID-19 and Life stressors Impact on Mental Health and Well-being survey (n=1441). We calculated the prevalence of probable depression using the Patient Health Questionnaire-9 (cut-off ≥10) and exposure to financial stressors by financial, physical and social assets categories (household income, household savings, home ownership, educational attainment and marital status). We estimated adjusted ORs and predicted probabilities of probable depression across assets categories and COVID-19 financial stressor exposure groups.

Results

We found that (1) 40% of US adults experienced COVID-19-related financial stressors during this time period; (2) low assets (OR: 3.0, 95% CI 2.1 to 4.2) and COVID-19 financial stressor exposure (OR: 2.8, 95% CI 2.1 to 3.9) were each associated with higher odds of probable depression; and (3) among persons with low assets and high COVID-19 financial stressors, 42.7% had probable depression; and among persons with high assets and low COVID-19 financial stressors, 11.1% had probable depression. Persons with high assets and high COVID-19 financial stressors had a similar prevalence of probable depression (33.5%) as persons with low assets and low COVID-19 financial stressors (33.5%). The more assets a person had, the lower the level of probable depression.

Conclusion

Populations with low assets are bearing a greater burden of mental illness during the COVID-19 pandemic.
Leading the spread and adoption of innovation at scale: an Academic Health Science Network’s perspective
Authors: Walker Andrew , Dale Catherine , Curran Natasha , Boaz Annette , Hurley Michael V
Published: December 2020

Background

There is virtually no limit to the number of innovations being developed, tested and piloted at any one time to improve the quality and safety of care. The perennial problem is spreading innovations that are proven to be effective on a smaller scale or under controlled conditions. Much of the literature on spread refers to the important role played by external agencies in supporting the spread of innovations.

Academic Health Science Networks and the spread of innovation

External agencies can provide additional capacity and capabilities to adopter organisations, such as technical expertise, resources and tools to assist with operational issues. In England, the National Health Service (NHS) established 15 Academic Health Science Networks (AHSNs) to help accelerate the spread and adoption of innovation in healthcare. However, formal clinical-academic networks (such as AHSNs) themselves will not deliver positive, tangible outcomes on the ground (ie, evidence-based innovations embedded at scale across a system). This begs the question of how do AHSNs practically go about achieving this change successfully? We provide an AHSN’s perspective on how we conceptualise and undertake our work in leading implementation of innovation at scale.

An AHSN"s perspective

Our approach is a collaborative process of widening understanding of the innovation and its implementation. At its core, the implementation and spread of innovation into practice is a collective social process. Healthcare comprises complex adaptive systems, where contexts need to be negotiated for implementation to be successful. As AHSNs, we aim to lead this negotiation through facilitating knowledge exchange and production across the system to mobilise the resources and collective action necessary for achieving spread.
Recognising our ‘invisible infants’: there is no internationally agreed definition of live birth—is this ethically acceptable?
Authors: Peterson Jennifer
Published: December 2020

Globally, there is a lack of adherence to the WHO definition of live birth. This is leading to untenable ethical inconsistencies due to significant variation in which infants are being acknowledged and registered as alive. If an infant is not registered as alive, there can be no acknowledgement of their rights as a child, and there are subsequent implications for worldwide child health resources and funding. Being alive should not be a quality that is geographically determined. This paper explores the differing definitions that are used regarding live birth and the ethical and practical implications for infants, their families and child health worldwide.
On the need for an ecologically dimensioned medical humanities
Authors: Coope Jonathan
Published: December 2020

Increasing calls from medical professionals and scholars suggest an urgent need for better and more widespread understandings of the ecological dimensions of health. Such calls have included: two recentLancetspecial commissions on impacts of climate change on health; and recognition by senior figures from the WHO and United Nations of relationships between human impacts on the natural world and disease pandemics, with some suggesting prevention of future pandemics may require a radical reassessment of modernity’s relationship with the natural world.

Among the medical humanities as a whole, however, calls for better and more widespread understandings of the ecological dimensions of health have not always been as prominent, or urgently expressed, as they might be.

This paper, which presumes there is an urgent need for better and more widespread understandings of the ecological dimensions of human health, draws on ecological public health and other models to propose an ecological re-visioning of our conceptions of health and medical humanities; and in ways that challenge some contemporary assumptions about health, well-being and the ‘good society’. Indeed, once we begin to heed what ecocritic Tim Morton terms ‘the ecological thought’, we may discover few areas of healthcare and the humanities remain untouched by its implications.

With growing recognition that the fate of global human health and the fate of the biosphere are inextricably entwined, the project of a more ecologically dimensioned medical humanities appears both timely and urgent. Such a project may represent a significant opportunity for the medical humanities, and a significant responsibility.
Multiple, objectively measured sleep dimensions including hypoxic burden and chronic kidney disease: findings from the Multi-Ethnic Study of Atherosclerosis
Authors: Jackson Chandra L , Umesi Chizoba , Gaston Symielle A , Azarbarzin Ali , Lunyera Joseph , McGrath John A , Jackson II W Braxton , Diamantidis Clarissa J , Boulware Ebony , Lutsey Pamela L , Redline Susan
Published: December 2020

Background

Poor sleep may contribute to chronic kidney disease (CKD) through several pathways, including hypoxia-induced systemic and intraglomerular pressure, inflammation, oxidative stress and endothelial dysfunction. However, few studies have investigated the association between multiple objectively measured sleep dimensions and CKD.

Methods

We investigated the cross-sectional association between sleep dimensions and CKD among 1895 Multi-Ethnic Study of Atherosclerosis Sleep Ancillary Study participants who completed in-home polysomnography, wrist actigraphy and a sleep questionnaire. Using Poisson regression models with robust variance, we estimated separate prevalence ratios (PR) and 95% CIs for moderate-to-severe CKD (glomerular filtration rate <60 mL/min/1.73 m
2
or albuminuria >30 mg/g) among participants according to multiple sleep dimensions, including very short (≤5 hours) sleep, Apnoea−Hypopnoea Index and sleep apnoea-specific hypoxic burden (SASHB) (total area under the respiratory event-related desaturation curve divided by total sleep duration, %min/hour)). Regression models were adjusted for sociodemographic characteristics, health behaviours and clinical characteristics.

Results

Of the 1895 participants, mean age was 68.2±9.1 years, 54% were women, 37% were white, 28% black, 24% Hispanic/Latino and 11% Asian. Several sleep metrics were associated with higher adjusted PR of moderate-to-severe CKD: very short versus recommended sleep duration (PR=1.40, 95% CI 1.06 to 1.83); SASHB (Box-Cox transformed SASHB: PR=1.06, 95% CI 1.02 to 1.12); and for participants in the highest quintile of SASHB plus sleep apnoea: PR=1.28, 95% CI 1.01 to 1.63.

Conclusions

Sleep apnoea associated hypoxia and very short sleep, likely representing independent biological mechanisms, were associated with a higher moderate-to-severe CKD prevalence, which highlights the potential role for novel interventions.
Fingerprinting the contribution of colored scalars to the $$H^+ W^- Z(\gamma )$$ vertex
Authors: Chakrabarty Nabarun , Chakraborty Indrani , Ghosh Dilip Kumar
Published: December 2020

Color-octet scalars arise in various Grand Unification scenarios and also in other models of new physics. They are also postulated for minimal flavour violation. Purely phenomenological imprints of such scalars are therefore worth looking at. Motivated by this, we perform a complete one-loop calculation of the $$H^+ \rightarrow W^+ Z (\gamma )$$

H
+

→

W
+

Z

(
γ
)

decay in a two Higgs doublet model augmented by a color-octet $$SU(2)_L$$

S
U

(
2
)

L

scalar doublet. The computation is conveniently segregated into colorless and colored components. The color-octet part of the amplitude, being scaled by the color-factor, provides an overall enhancement to the form factors. Crucial constraints from perturbative unitarity, positivity of the scalar potential, oblique parameters, Higgs signal strengths and direct search of a charged Higgs and color-octet scalars are folded-in into the analysis. Sensitivity of the loop-induced $$H^+ \rightarrow W^+ Z (\gamma )$$

H
+

→

W
+

Z

(
γ
)

vertex to other model parameters is elucidated. Finally, the prospect of observing a loop-induced $$H^+ \rightarrow W^+ Z (\gamma )$$

H
+

→

W
+

Z

(
γ
)

interaction at the future hadronic collisions is also discussed.
ATLAS results on quarkonia and heavy flavor production
Authors: Lyubushkina Tatiana
Published: December 2020

The associated production a vector boson with [Formula: see text] is a key observable for understanding of the quarkonium production mechanisms, including the separation of single and double parton scattering components. Measurements from the ATLAS detector at LHC on quarkonium production, including associated production of a [Formula: see text] and [Formula: see text] are presented. A study of the hidden-charm states [Formula: see text] is also provided.
Stock Turnover Prediction Using Search Engine Data
Authors: Wang Zhijin , Huang Yaohui , Cai Bing , Ma Rui , Wang Zongyue
Published: December 2020

The stock turnover values are sensitive to external factors, and remain great challenges in its prediction. The consideration is that search engine data can reflect market environment, policies and attentions on stocks. Therefore, a dual sides autoregression (DSAR) method is proposed to benefit from both observed turnover values and exogenous data. The proposed DSAR consists of linear representation stage and combination stage. In linear representation stage, the short-term patterns of turnover values and query data are represented, respectively. In combination stage, the outputs from previous stages are combined. Intensive experiments on two groups of data collections show the effectiveness of our proposed method.
Improved Signed Binary Multiplier Through New Partial Product Generation Scheme
Authors: Thabah Sheba Diamond , Saha Prabir
Published: December 2020

In this paper, a novel partial product generation (PPG) scheme has been proposed based on the shift and the add logic of multiplier bits to introduce a radix-4 and radix-16 signed binary multiplications (SBMs). The proposed PPG methodology encodes two bits for radix-4 and four bits for radix-16 at a time, whereas the traditional modified Booth encoding (MBE) for radix-4 and radix-16 encodes three bits and five bits, respectively, at a time, which offers the reduction of the encoder combinations. In the proposed design, the multiplication sign extension is pre-decided from the most significant bit (MSB) of the multiplier and the multiplicand, thereby subtraction operation for multiplication is removed from traditional MBE. The simulation results of the proposed SBMs architecture offer a significant improvement in power, delay and power-delay-product (PDP). The PDP was reduced by [Formula: see text]%, [Formula: see text]% and [Formula: see text]%, respectively, with proposed radix-4 SBM and by [Formula: see text]%, [Formula: see text]% and [Formula: see text]%, respectively, with proposed radix-16 SBM for [Formula: see text]-, and [Formula: see text]-bit multiplication, respectively, when compared with the existing state-of-the-art designs.
Analytical and Numerical Study on Dual-Mode Patch Resonator Filters with Real or Imaginary Transmission Zeros
Authors: Xia Lei , Li Jia-Lin , Twumasi Baidenger Agyekum , Gao Shan-Shan
Published: December 2020

Dual-mode patch resonator-based microstrip filters with finite real or imaginary transmission zeros are discussed by combining the analytical studies with numerical investigations. The analytical study presents the coupling scheme of a dual-mode patch resonator, while the numerical simulation discusses the coupling nature between the source (input) and load (output), which constitutes the presented half-analytical model. Furthermore, the difference of in-band losses between the two different responses can also be qualified based on this model. The contribution and novelty of this work is the coupling nature between the source and load which is explained for the first time, and based on this, the half-analytical model can further estimate the transmission zeros of the microstrip patch resonator filter. For demonstration purposes, two prototype filters that exhibit transmission zeros at the real and imaginary frequencies, respectively, are developed and confirmed experimentally. The measurements agree closely with the predications.
Photon spectrum of asymmetric dark stars
Authors: Maselli Andrea , Kouvaris Chris , Kokkotas Kostas D.
Published: December 2020

Asymmetric Dark Stars, i.e. compact objects formed from the collapse of asymmetric dark matter could potentially produce a detectable photon flux if dark matter particles self-interact via dark photons that kinetically mix with ordinary photons. The morphology of the emitted spectrum is significantly different and therefore distinguishable from a typical black-body one. Given the above and the fact that asymmetric dark stars can have masses outside the range of neutron stars, the detection of such a spectrum can be considered as a smoking gun signature for the existence of these exotic stars.