bluuebunny/crossref_metadata_2025 huggingface dataset:
The antigen 85 complex: a major secretion product of Mycobacterium tuberculosis
Authors: Wiker H G , Harboe M
Published: December 2020

The large number of different proteins synthesized by the mycobacterial cell are currently classified and studied in terms of groups of proteins with certain common properties such as physical and chemical characteristics, function, and localization in the mycobacterial cell. Proteins that are actively secreted during culture on synthetic media represent a particular group of great current interest. At least eight proteins secreted by Mycobacterium tuberculosis have been isolated and characterized to various extents. The genes coding for five proteins secreted from M. tuberculosis and/or Mycobacterium bovis BCG have been cloned and sequenced. All of them contain typical signal sequences. The proteins of the antigen 85 complex, which form the main subject of this review, are often the most common proteins in M. tuberculosis culture fluid. The constituents denoted 85A, 85B, and 85C are encoded by three genes located at different sites in the mycobacterial genome and show extensive cross-reactivity as well as homology at amino acid and gene levels. The proteins differ slightly in molecular mass in the 30- to 31-kDa region, and all of them are fibronectin-binding proteins, but the significance of the latter observation and the role of these proteins in mycobacterial physiology and interaction with the infected host remain to be elucidated. The antigen 85 complex proteins are strongly immunogenic in natural and experimental mycobacterial infections in terms of both induction of antibody synthesis and T-cell-mediated reactions. The well-recognized difference in the efficacy of live and dead mycobacterial vaccines should be considered in relation to the group of secreted antigens. After inoculation, live bacteria in vaccines such as BCG multiply in the host, probably releasing several constituents belonging to the class of secreted proteins and hence resulting in more efficient stimulation of the immune system. Secreted mycobacterial antigens are expected to be of particular significance in induction of various immune responses that are responsible for development of protective immunity in some individuals and for clinical symptoms and complications of the ensuing disease in others.
Bacillus subtilis sporulation: regulation of gene expression and control of morphogenesis
Authors: Errington J
Published: December 2020

Bacillus subtilis sporulation is an adaptive response to nutritional stress and involves the differential development of two cells. In the last 10 years or so, virtually all of the regulatory genes controlling sporulation, and many genes directing the structural and morphological changes that accompany sporulation, have been cloned and characterized. This review describes our current knowledge of the program of gene expression during sporulation and summarizes what is known about the functions of the genes that determine the specialized biochemical and morphological properties of sporulating cells. Most steps in the genetic program are controlled by transcription factors that have been characterized in vitro. Two sporulation-specific sigma factors, sigma E and sigma F, appear to segregate at septation, effectively determining the differential development of the mother cell and prespore. Later, each sigma is replaced by a second cell-specific sigma factor, sigma K in the mother cell and sigma G in the prespore. The synthesis of each sigma factor is tightly regulated at both the transcriptional and posttranslational levels. Usually this regulation involves an intercellular interaction that coordinates the developmental programmes of the two cells. At least two other transcription factors fine tune the timing and levels of expression of genes in the sigma E and sigma K regulons. The controlled synthesis of the sigma factors and other transcription factors leads to a spatially and temporally ordered program of gene expression. The gene products made during each successive stage of sporulation help to bring about a sequence of gross morphological changes and biochemical adaptations. The formation of the asymmetric spore septum, engulfment of the prespore by the mother cell, and formation of the spore core, cortex, and coat are described. The importance of these structures in the development of the resistance, dormancy, and germination properties of the spore is assessed.
Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria
Authors: Tam R , Saier M H
Published: December 2020

Extracellular solute-binding proteins of bacteria serve as chemoreceptors, recognition constituents of transport systems, and initiators of signal transduction pathways. Over 50 sequenced periplasmic solute-binding proteins of gram-negative bacteria and homologous extracytoplasmic lipoproteins of gram-positive bacteria have been analyzed for sequence similarities, and their degrees of relatedness have been determined. Some of these proteins are homologous to cytoplasmic transcriptional regulatory proteins of bacteria; however, with the sole exception of the vitamin B12-binding protein of Escherichia coli, which is homologous to human glutathione peroxidase, they are not demonstrably homologous to any of the several thousand sequenced eukaryotic proteins. Most of these proteins fall into eight distinct clusters as follows. Cluster 1 solute-binding proteins are specific for malto-oligosaccharides, multiple oligosaccharides, glycerol 3-phosphate, and iron. Cluster 2 proteins are specific for galactose, ribose, arabinose, and multiple monosaccharides, and they are homologous to a number of transcriptional regulatory proteins including the lactose, galactose, and fructose repressors of E. coli. Cluster 3 proteins are specific for histidine, lysine-arginine-ornithine, glutamine, octopine, nopaline, and basic amino acids. Cluster 4 proteins are specific for leucine and leucine-isoleucine-valine, and they are homologous to the aliphatic amidase transcriptional repressor, AmiC, of Pseudomonas aeruginosa. Cluster 5 proteins are specific for dipeptides and oligopeptides as well as nickel. Cluster 6 proteins are specific for sulfate, thiosulfate, and possibly phosphate. Cluster 7 proteins are specific for dicarboxylates and tricarboxylates, but these two proteins exhibit insufficient sequence similarity to establish homology. Finally, cluster 8 proteins are specific for iron complexes and possibly vitamin B12. Members of each cluster of binding proteins exhibit greater sequence conservation in their N-terminal domains than in their C-terminal domains. Signature sequences for these eight protein families are presented. The results reveal that binding proteins specific for the same solute from different bacteria are generally more closely related to each other than are binding proteins specific for different solutes from the same organism, although exceptions exist. They also suggest that a requirement for high-affinity solute binding imposes severe structural constraints on a protein. The occurrence of two distinct classes of bacterial cytoplasmic repressor proteins which are homologous to two different clusters of periplasmic binding proteins suggests that the gene-splicing events which allowed functional conversion of these proteins with retention of domain structure have occurred repeatedly during evolutionary history.(ABSTRACT TRUNCATED AT 400 WORDS)
Biology, ecology, and biotechnological applications of anaerobic bacteria adapted to environmental stresses in temperature, pH, salinity, or substrates
Authors: Lowe S E , Jain M K , Zeikus J G
Published: December 2020

Anaerobic bacteria include diverse species that can grow at environmental extremes of temperature, pH, salinity, substrate toxicity, or available free energy. The first evolved archaebacterial and eubacterial species appear to have been anaerobes adapted to high temperatures. Thermoanaerobes and their stable enzymes have served as model systems for basic and applied studies of microbial cellulose and starch degradation, methanogenesis, ethanologenesis, acetogenesis, autotrophic CO2 fixation, saccharidases, hydrogenases, and alcohol dehydrogenases. Anaerobes, unlike aerobes, appear to have evolved more energy-conserving mechanisms for physiological adaptation to environmental stresses such as novel enzyme activities and stabilities and novel membrane lipid compositions and functions. Anaerobic syntrophs do not have similar aerobic bacterial counterparts. The metabolic end products of syntrophs are potent thermodynamic inhibitors of energy conservation mechanisms, and they require coordinated consumption by a second partner organism for species growth. Anaerobes adapted to environmental stresses and their enzymes have biotechnological applications in organic waste treatment systems and chemical and fuel production systems based on biomass-derived substrates or syngas. These kinds of anaerobes have only recently been examined by biologists, and considerably more study is required before they are fully appreciated by science and technology.
Molecular biology of the lignin-degrading basidiomycete Phanerochaete chrysosporium
Authors: Gold M H , Alic M
Published: December 2020

The white rot basidiomycete Phanerochaete chrysosporium completely degrades lignin and a variety of aromatic pollutants during the secondary metabolic phase of growth. Two families of secreted heme enzymes, lignin peroxidase (LiP) and manganese peroxidase (MnP), are major components of the extracellular lignin degradative system of this organism. MnP and LiP both are encoded by families of genes, and the lip genes appear to be clustered. The lip genes contain eight or nine short introns; the mnp genes contain six or seven short introns. The sequences surrounding active-site residues are conserved among LiP, MnP, cytochrome c peroxidase, and plant peroxidases. The eight LiP cysteine residues align with 8 of the 10 cysteines in MnP. LiPs are synthesized as preproenzymes with a 21-amino-acid signal sequence followed by a 6- or 7-amino-acid propeptide. MnPs have a 21- or 24-amino-acid signal sequence but apparently lack a propeptide. Both LiP and MnP are regulated at the mRNA level by nitrogen, and the various isozymes may be differentially regulated by carbon and nitrogen. MnP also is regulated at the level of gene transcription by Mn(II), the substrate for the enzyme, and by heat shock. The promoter regions of mnp genes contain multiple heat shock elements as well as sequences that are identical to the consensus metal regulatory elements found in mammalian metallothionein genes. DNA transformation systems have been developed for P. chrysosporium and are being used for studies on gene regulation and for gene replacement experiments.
Expression of virus-encoded proteinases: functional and structural similarities with cellular enzymes
Authors: Dougherty W G , Semler B L
Published: December 2020

Many viruses express their genome, or part of their genome, initially as a polyprotein precursor that undergoes proteolytic processing. Molecular genetic analyses of viral gene expression have revealed that many of these processing events are mediated by virus-encoded proteinases. Biochemical activity studies and structural analyses of these viral enzymes reveal that they have remarkable similarities to cellular proteinases. However, the viral proteinases have evolved unique features that permit them to function in a cellular environment. In this article, the current status of plant and animal virus proteinases is described along with their role in the viral replication cycle. The reactions catalyzed by viral proteinases are not simple enzyme-substrate interactions; rather, the processing steps are highly regulated, are coordinated with other viral processes, and frequently involve the participation of other factors.
Bacterial extracellular zinc-containing metalloproteases
Authors: Häse C C , Finkelstein R A
Published: December 2020

Extracellular zinc-containing metalloproteases are widely distributed in the bacterial world. The most extensively studied are those which are associated with pathogenic bacteria or bacteria which have industrial significance. They are found practically wherever they are sought in both gram-negative and gram-positive microorganisms, be they aerobic or anaerobic. This ubiquity in itself implies that these enzymes serve important functions for the organisms which produce them. Because of the importance of zinc to enzymatic activity, it is not surprising that there is a pervasive amino acid sequence homology in the primary structure of this family of enzymes regardless of their source. The evidence suggests that both convergent and divergent evolutionary forces are at work. Within the large family of bacterial zinc-containing metalloendopeptidases, smaller family units are observed, such as thermolysin-like, elastase-like, and Serratia protease-like metalloproteases from various bacterial species. While this review was in the process of construction, a new function for zinc-containing metalloproteases was discovered: the neurotoxins of Clostridium tetani and Clostridium botulinum type B have been shown to be zinc metalloproteases with specificity for synaptobrevin, an integral membrane protein of small synaptic vesicles which is involved in neurotransmission. Additional understanding of the mode of action of proteases which contribute to pathogenicity could lead to the development of inhibitors, such as chelators, surrogate substrates, or antibodies, which could prevent or interrupt the disease process. Further studies of this broad family of metalloproteases will provide important additional insights into the pathogenesis and structure-function relationships of enzymes and will lead to the development of products, including "designer proteins," which might be industrially and/or therapeutically useful.
ABC transporters: bacterial exporters
Authors: Fath M J , Kolter R
Published: December 2020

The ABC transporters (also called traffic ATPases) make up a large superfamily of proteins which share a common function and a common ATP-binding domain. ABC transporters are classified into three major groups: bacterial importers (the periplasmic permeases), eukaryotic transporters, and bacterial exporters. We present a comprehensive review of the bacterial ABC exporter group, which currently includes over 40 systems. The bacterial ABC exporter systems are functionally subdivided on the basis of the type of substrate that each translocates. We describe three main groups: protein exporters, peptide exporters, and systems that transport nonprotein substrates. Prototype exporters from each group are described in detail to illustrate our current understanding of this protein family. The prototype systems include the alpha-hemolysin, colicin V, and capsular polysaccharide exporters from Escherichia coli, the protease exporter from Erwinia chrysanthemi, and the glucan exporters from Agrobacterium tumefaciens and Rhizobium meliloti. Phylogenetic analysis of the ATP-binding domains from 29 bacterial ABC exporters indicates that the bacterial ABC exporters can be divided into two primary branches. One branch contains the transport systems where the ATP-binding domain and the membrane-spanning domain are present on the same polypeptide, and the other branch contains the systems where these domains are found on separate polypeptides. Differences in substrate specificity do not correlate with evolutionary relatedness. A complete survey of the known and putative bacterial ABC exporters is included at the end of the review.
Control of meiotic gene expression in Saccharomyces cerevisiae
Authors: Mitchell A P
Published: December 2020

Sporulation of the yeast Saccharomyces cerevisiae is restricted to one type of cell, the a/alpha cell, and is initiated after starvation for nitrogen in the absence of a fermentable carbon source. More than 25 characterized genes are expressed only during sporulation and are referred to as meiotic genes or sporulation-specific genes. These genes are in the early, middle, and late expression classes. Most early genes have a 5' regulatory site, URS1, and one of two additional sequences, UASH or a T4C site. URS1 is required both to repress meiotic genes during vegetative growth and to activate these genes during meiosis. UASH and the T4C site also contribute to meiotic expression. A different type of site, the NRE, is found in at least two late genes. The NRE behaves as a repression site in vegetative cells and is neutral in meiotic cells. Many regulatory genes that either repress or activate meiotic genes have been identified. One group of regulators affects the expression of IME1, which specifies a positive regulator of meiotic genes and is expressed at the highest levels in meiotic cells. A second group of regulators acts in parallel with or downstream of IME1 to influence meiotic gene expression. This group includes UME6, which is required both for repression through the URS1 site in vegetative cells and for IME1-dependent activation of an upstream region containing URS1 and T4C sites. IME1 may activate meiotic genes by modifying a UME6-dependent repression complex at a URS1 site. Several additional mechanisms restrict functional expression of some genes to meiotic cells. Translation of IME1 has been proposed to occur only in meiotic cells; several meiotic transcripts are more stable in acetate medium than in glucose medium; and splicing of MER2 RNA depends on a meiosis-specific gene, MER1.
Analysis of the sequence and gene products of the transfer region of the F sex factor
Authors: Frost L S , Ippen-Ihler K , Skurray R A
Published: December 2020

Bacterial conjugation results in the transfer of DNA of either plasmid or chromosomal origin between microorganisms. Transfer begins at a defined point in the DNA sequence, usually called the origin of transfer (oriT). The capacity of conjugative DNA transfer is a property of self-transmissible plasmids and conjugative transposons, which will mobilize other plasmids and DNA sequences that include a compatible oriT locus. This review will concentrate on the genes required for bacterial conjugation that are encoded within the transfer region (or regions) of conjugative plasmids. One of the best-defined conjugation systems is that of the F plasmid, which has been the paradigm for conjugation systems since it was discovered nearly 50 years ago. The F transfer region (over 33 kb) contains about 40 genes, arranged contiguously. These are involved in the synthesis of pili, extracellular filaments which establish contact between donor and recipient cells; mating-pair stabilization; prevention of mating between similar donor cells in a process termed surface exclusions; DNA nicking and transfer during conjugation; and the regulation of expression of these functions. This review is a compendium of the products and other features found in the F transfer region as well as a discussion of their role in conjugation. While the genetics of F transfer have been described extensively, the mechanism of conjugation has proved elusive, in large part because of the low levels of expression of the pilus and the numerous envelope components essential for F plasmid transfer. The advent of molecular genetic techniques has, however, resulted in considerable recent progress. This summary of the known properties of the F transfer region is provided in the hope that it will form a useful basis for future comparison with other conjugation systems.
The bacterial nucleoid revisited
Authors: Robinow C , Kellenberger E
Published: December 2020

This review compares the results of different methods of investigating the morphology of nucleoids of bacteria grown under conditions favoring short generation times. We consider the evidence from fixed and stained specimens, from phase-contrast and fluorescence microscopy of growing bacteria, and from electron microscopy of whole as well as thinly sectioned ones. It is concluded that the nucleoid of growing cells is in a dynamic state: part of the chromatin is "pulled out" of the bulk of the nucleoid in order to be transcribed. This activity is performed by excrescences which extend far into the cytoplasm so as to reach the maximum of available ribosomes. Different means of fixation provide markedly different views of the texture of the DNA-containing plasm of the bulk of the nucleoid. Conventional chemical fixatives stabilize the cytoplasm of bacteria but not their protein-low chromatin. Uranyl acetate does cross-link the latter well but only if the cytoplasm has first been fixed conventionally. In the interval between the two fixations, the DNA arranges itself in liquid-crystalline form, supposedly because of loss of supercoiling. In stark contrast, cryofixation preserves bacterial chromatin in a finely granular form, believed to reflect its native strongly negatively supercoiled state. In dinoflagellates the DNA of their permanently visible chromosomes (also low in histone-like protein) is natively present as a liquid crystal. The arrangement of chromatin in Epulocystis fishelsoni, one of the largest known prokaryotes, is briefly described.
Biochemistry of homologous recombination in Escherichia coli
Authors: Kowalczykowski S C , Dixon D A , Eggleston A K , Lauder S D , Rehrauer W M
Published: December 2020

Homologous recombination is a fundamental biological process. Biochemical understanding of this process is most advanced for Escherichia coli. At least 25 gene products are involved in promoting genetic exchange. At present, this includes the RecA, RecBCD (exonuclease V), RecE (exonuclease VIII), RecF, RecG, RecJ, RecN, RecOR, RecQ, RecT, RuvAB, RuvC, SbcCD, and SSB proteins, as well as DNA polymerase I, DNA gyrase, DNA topoisomerase I, DNA ligase, and DNA helicases. The activities displayed by these enzymes include homologous DNA pairing and strand exchange, helicase, branch migration, Holliday junction binding and cleavage, nuclease, ATPase, topoisomerase, DNA binding, ATP binding, polymerase, and ligase, and, collectively, they define biochemical events that are essential for efficient recombination. In addition to these needed proteins, a cis-acting recombination hot spot known as Chi (chi: 5'-GCTGGTGG-3') plays a crucial regulatory function. The biochemical steps that comprise homologous recombination can be formally divided into four parts: (i) processing of DNA molecules into suitable recombination substrates, (ii) homologous pairing of the DNA partners and the exchange of DNA strands, (iii) extension of the nascent DNA heteroduplex; and (iv) resolution of the resulting crossover structure. This review focuses on the biochemical mechanisms underlying these steps, with particular emphases on the activities of the proteins involved and on the integration of these activities into likely biochemical pathways for recombination.
The leucine-responsive regulatory protein, a global regulator of metabolism in Escherichia coli
Authors: Calvo J M , Matthews R G
Published: December 2020

The leucine-responsive regulatory protein (Lrp) regulates the expression of more than 40 genes and proteins in Escherichia coli. Among the operons that are positively regulated by Lrp are operons involved in amino acid biosynthesis (ilvIH, serA)), in the biosynthesis of pili (pap, fan, fim), and in the assimilation of ammonia (glnA, gltBD). Negatively regulated operons include operons involved in amino acid catabolism (sdaA, tdh) and peptide transport (opp) and the operon coding for Lrp itself (lrp). Detailed studies of a few members of the regulon have shown that Lrp can act directly to activate or repress transcription of target operons. A substantial fraction of operons regulated by Lrp are also regulated by leucine, and the effect of leucine on expression of these operons requires a functional Lrp protein. The patterns of regulation are surprising and interesting: in some cases activation or repression mediated by Lrp is antagonized by leucine, in other cases Lrp-mediated activation or repression is potentiated by leucine, and in still other cases leucine has no effect on Lrp-mediated regulation. Current research is just beginning to elucidate the detailed mechanisms by which Lrp can mediate such a broad spectrum of regulatory effects. Our view of the role of Lrp in metabolism may change as more members of the regulon are identified and their regulation characterized, but at this point Lrp seems to be important in regulating nitrogen metabolism and one-carbon metabolism, permitting adaptations to feast and to famine.
Desiccation tolerance of prokaryotes
Authors: Potts M
Published: December 2020

The removal of cell-bound water through air drying and the addition of water to air-dried cells are forces that have played a pivotal role in the evolution of the prokaryotes. In bacterial cells that have been subjected to air drying, the evaporation of free cytoplasmic water (Vf) can be instantaneous, and an equilibrium between cell-bound water (Vb) and the environmental water (vapor) potential (psi wv) may be achieved rapidly. In the air-dried state some bacteria survive only for seconds whereas others can tolerate desiccation for thousands, perhaps millions, of years. The desiccated (anhydrobiotic) cell is characterized by its singular lack of water--with contents as low as 0.02 g of H2O g (dry weight)-1. At these levels the monolayer coverage by water of macromolecules, including DNA and proteins, is disturbed. As a consequence the mechanisms that confer desiccation tolerance upon air-dried bacteria are markedly different from those, such as the mechanism of preferential exclusion of compatible solutes, that preserve the integrity of salt-, osmotically, and freeze-thaw-stressed cells. Desiccation tolerance reflects a complex array of interactions at the structural, physiological, and molecular levels. Many of the mechanisms remain cryptic, but it is clear that they involve interactions, such as those between proteins and co-solvents, that derive from the unique properties of the water molecule. A water replacement hypothesis accounts for how the nonreducing disaccharides trehalose and sucrose preserve the integrity of membranes and proteins. Nevertheless, we have virtually no insight into the state of the cytoplasm of an air-dried cell. There is no evidence for any obvious adaptations of proteins that can counter the effects of air drying or for the occurrence of any proteins that provide a direct and a tangible contribution to cell stability. Among the prokaryotes that can exist as anhydrobiotic cells, the cyanobacteria have a marked capacity to do so. One form, Nostoc commune, encompasses a number of the features that appear to be critical to the withstanding of a long-term water deficit, including the elaboration of a conspicuous extracellular glycan, synthesis of abundant UV-absorbing pigments, and maintenance of protein stability and structural integrity. There are indications of a growing technology for air-dried cells and enzymes. Paradoxically, desiccation tolerance of bacteria has virtually been ignored for the past quarter century. The present review considers what is known, and what is not known, about desiccation, a phenomenon that impinges upon every facet of the distributions and activities of prokaryotic cells.
The Rhizobium-plant symbiosis
Authors: van Rhijn P , Vanderleyden J
Published: December 2020

Rhizobium, Bradyrhizobium, and Azorhizobium species are able to elicit the formation of unique structures, called nodules, on the roots or stems of the leguminous host. In these nodules, the rhizobia convert atmospheric N2 into ammonia for the plant. To establish this symbiosis, signals are produced early in the interaction between plant and rhizobia and they elicit discrete responses by the two symbiotic partners. First, transcription of the bacterial nodulation (nod) genes is under control of the NodD regulatory protein, which is activated by specific plant signals, flavonoids, present in the root exudates. In return, the nod-encoded enzymes are involved in the synthesis and excretion of specific lipooligosaccharides, which are able to trigger on the host plant the organogenic program leading to the formation of nodules. An overview of the organization, regulation, and function of the nod genes and their participation in the determination of the host specificity is presented.
Regulation of cellular differentiation in Caulobacter crescentus
Authors: Gober J W , Marques M V
Published: December 2020

In Caulobacter crescentus, asymmetry is generated in the predivisional cell, resulting in the formation of two distinct cell types upon cell division: a motile swarmer cell and a sessile stalked cell. These progeny cell types differ in their relative programs of gene expression and DNA replication. In progeny swarmer cells, DNA replication is silenced for a defined period, but stalked cells reinitiate chromosomal DNA replication immediately following cell division. The establishment of these differential programs of DNA replication may be due to the polar localization of DNA replication proteins, differences in chromosome higher-order structure, or pole-specific transcription. The best-understood aspect of Caulobacter development is biogenesis of the polar flagellum. The genes encoding the flagellum are expressed under cell cycle control predominantly in the predivisional cell type. Transcription of flagellar genes is regulated by a trans-acting hierarchy that responds to both flagellar assembly and cell cycle cues. As the flagellar genes are expressed, their products are targeted to the swarmer pole of the predivisional cell, where assembly occurs. Specific protein targeting and compartmentalized transcription are two mechanisms that contribute to the positioning of flagellar gene products at the swarmer pole of the predivisional cell.
The human immunodeficiency virus type 1 (HIV-1) CD4 receptor and its central role in promotion of HIV-1 infection
Authors: Bour S , Geleziunas R , Wainberg M A
Published: December 2020

Interactions between the viral envelope glycoprotein gp120 and the cell surface receptor CD4 are responsible for the entry of human immunodeficiency virus type 1 (HIV-1) into host cells in the vast majority of cases. HIV-1 replication is commonly followed by the disappearance or receptor downmodulation of cell surface CD4. This potentially renders cells nonsusceptible to subsequent infection by HIV-1, as well as by other viruses that use CD4 as a portal of entry. Disappearance of CD4 from the cell surface is mediated by several different viral proteins that act at various stages through the course of the viral life cycle, and it occurs in T-cell lines, peripheral blood CD4+ lymphocytes, and monocytes of both primary and cell line origin. At the cell surface, gp120 itself and in the form of antigen-antibody complexes can trigger cellular pathways leading to CD4 internalization. Intracellularly, the mechanisms leading to CD4 downmodulation by HIV-1 are multiple and complex; these include degradation of CD4 by Vpu, formation of intracellular complexes between CD4 and the envelope precursor gp160, and internalization by the Nef protein. Each of the above doubtless contributes to the ultimate depletion of cell surface CD4, although the relative contribution of each mechanism and the manner in which they interact remain to be definitively established.
Immune regulation in Epstein-Barr virus-associated diseases
Authors: Khanna R , Burrows S R , Moss D J
Published: December 2020

Epstein-Barr virus (EBV) is a member of the human herpesvirus family and, like many other herpesviruses, maintains a lifelong latent association with B lymphocytes and a permissive association with stratified epithelium in the oropharynx. Clinical manifestations of primary EBV infection range from acute infectious mononucleosis to an asymptomatic persistent infection. EBV is also associated with a number of malignancies in humans. This review discusses features of the biology of the virus, both in cell culture systems and in the natural host, before turning to the role of the immune system in controlling EBV infection in healthy individuals and in individuals with EBV-associated diseases. Cytotoxic T cells that recognize virally determined epitopes on infected cells make up the major effector arm and control the persistent infection. In contrast, the options for immune control of EBV-associated malignancies are more restricted. Not only is antigen expression restricted to a single nuclear antigen, EBNA1, but also these tumor cells are unable to process EBV latent antigens, presumably because of a transcriptional defect in antigen-processing genes (such as TAP1 and TAP2). The likelihood of producing a vaccine capable of controlling the acute viral infection and EBV-associated malignancies is also discussed.
Stress-induced transcriptional activation
Authors: Mager W H , De Kruijff A J
Published: December 2020

Living cells, both prokaryotic and eukaryotic, employ specific sensory and signalling systems to obtain and transmit information from their environment in order to adjust cellular metabolism, growth, and development to environmental alterations. Among external factors that trigger such molecular communications are nutrients, ions, drugs and other compounds, and physical parameters such as temperature and pressure. One could consider stress imposed on cells as any disturbance of the normal growth condition and even as any deviation from optimal growth circumstances. It may be worthwhile to distinguish specific and general stress circumstances. Reasoning from this angle, the extensively studied response to heat stress on the one hand is a specific response of cells challenged with supra-optimal temperatures. This response makes use of the sophisticated chaperoning mechanisms playing a role during normal protein folding and turnover. The response is aimed primarily at protection and repair of cellular components and partly at acquisition of heat tolerance. In addition, heat stress conditions induce a general response, in common with other metabolically adverse circumstances leading to physiological perturbations, such as oxidative stress or osmostress. Furthermore, it is obvious that limitation of essential nutrients, such as glucose or amino acids for yeasts, leads to such a metabolic response. The purpose of the general response may be to promote rapid recovery from the stressful condition and resumption of normal growth. This review focuses on the changes in gene expression that occur when cells are challenged by stress, with major emphasis on the transcription factors involved, their cognate promoter elements, and the modulation of their activity upon stress signal transduction. With respect to heat shock-induced changes, a wealth of information on both prokaryotic and eukaryotic organisms, including yeasts, is available. As far as the concept of the general (metabolic) stress response is concerned, major attention will be paid to Saccharomyces cerevisiae.
Branhamella catarrhalis: epidemiology, surface antigenic structure, and immune response
Authors: Murphy T F
Published: December 2020

Over the past decade, Branhamella catarrhalis has emerged as an important human pathogen. The bacterium is a common cause of otitis media in children and of lower respiratory tract infections in adults with chronic obstructive pulmonary disease. B. catarrhalis is exclusively a human pathogen. It colonizes the respiratory tract of a small proportion of adults and a larger proportion of children. Studies involving restriction enzyme analysis of genomic DNA show that colonization is a dynamic process, with the human host eliminating and acquiring new strains frequently. The surface of B. catarrhalis contains outer membrane proteins, lipooligosaccharide, and pili. The genes which encode several outer membrane proteins have been cloned, and some of these proteins are being studied as potential vaccine antigens. Analysis of the immune response has been limited by the lack of an adequate animal model of B. catarrhalis infection. New information regarding outer membrane structure should guide studies of the human immune response to B. catarrhalis. Immunoassays which specifically detect antibodies to determinants exposed on the bacterial surface will elucidate the most relevant immune response. The recognition of B. catarrhalis as an important human pathogen has stimulated research on the epidemiology and surface structures of the bacterium. Future studies to understand the mechanisms of infection and to elucidate the human immune response to infection hold promise of developing new methods to treat and prevent infections caused by B. catarrhalis.
Artemisinin and the antimalarial endoperoxides: from herbal remedy to targeted chemotherapy
Authors: Meshnick S R , Taylor T E , Kamchonwongpaisan S
Published: December 2020

Artemisinin and its derivatives are endoperoxide-containing compounds which represent a promising new class of antimalarial drugs. In the presence of intraparasitic iron, these drugs are converted into free radicals and other electrophilic intermediates which then alkylate specific malaria target proteins. Combinations of available derivatives and other antimalarial agents show promise both as first-line agents and in the treatment of severe disease.
Strategies for achieving high-level expression of genes in Escherichia coli
Authors: Makrides S C
Published: December 2020

Progress in our understanding of several biological processes promises to broaden the usefulness of Escherichia coli as a tool for gene expression. There is an expanding choice of tightly regulated prokaryotic promoters suitable for achieving high-level gene expression. New host strains facilitate the formation of disulfide bonds in the reducing environment of the cytoplasm and offer higher protein yields by minimizing proteolytic degradation. Insights into the process of protein translocation across the bacterial membranes may eventually make it possible to achieve robust secretion of specific proteins into the culture medium. Studies involving molecular chaperones have shown that in specific cases, chaperones can be very effective for improved protein folding, solubility, and membrane transport. Negative results derived from such studies are also instructive in formulating different strategies. The remarkable increase in the availability of fusion partners offers a wide range of tools for improved protein folding, solubility, protection from proteases, yield, and secretion into the culture medium, as well as for detection and purification of recombinant proteins. Codon usage is known to present a potential impediment to high-level gene expression in E. coli. Although we still do not understand all the rules governing this phenomenon, it is apparent that "rare" codons, depending on their frequency and context, can have an adverse effect on protein levels. Usually, this problem can be alleviated by modification of the relevant codons or by coexpression of the cognate tRNA genes. Finally, the elucidation of specific determinants of protein degradation, a plethora of protease-deficient host strains, and methods to stabilize proteins afford new strategies to minimize proteolytic susceptibility of recombinant proteins in E. coli.
Family caregiver emotional distress in advanced cancer: the DME-C scale psychometric properties
Authors: Limonero Joaquín T , Maté-Méndez Jorge , Gómez-Romero María José , Mateo-Ortega Dolors , González-Barboteo Jesús , Bernaus Montserrat , López-Postigo Montserrat , Sirgo Agustina , Viel Silvia , Sánchez-Julve Cruz , Bayés Ramon , Gómez-Batiste Xavier , Tomás-Sábado Joaquín
Published: December 2020

Background

Family caregivers of patients with advanced illness at end of life often report high levels of emotional distress. To address this emotional distress is necessary to have adequate and reliable screening tools.

Aim

This study analyses the psychometric properties and clinical utility of the Family Caregiver Emotional Detection Scale for caregivers of patients with end-stage cancer (DME-C, Spanish acronym) who are receiving palliative care (PC).

Design

Multicentre, cross-sectional study.

Settings/participants

Family caregivers of patients with advanced cancer at end of life receiving palliative treatment were interviewed to explore their emotional distress through the DME-C scale and other instruments measuring anxiety and depression (Hospital Anxiety and Depression Scale (HADS)), distress thermometer (DT) and overload (B), as well as a clinical psychological assessment (CPA).

Results

138 family caregivers, 85 (61.6%) female and 53 (38.4%) male, with an average age of 59.69±13.3 participated in the study. The reliability of the scale, as measured by Cronbach’s alpha, was 0.76, and its stability over time was 0.734. Positive, significant correlations were found between the DME-C and the scores for anxiety and depression registered on the HADS scale, as well as with the total result of this latter scale and the results for B, the DT and the CPA. A statistical analysis of the receiver-operating characteristic curves showed that the scale has a sensitivity and specificity of 75%, and that the cut-off point for the detection of emotional distress was a score ≥11. Fifty-four per cent of the caregivers displayed emotional distress according to this scale.

Conclusions

The DME-C displays good psychometric properties. It is simple, short, reliable and easy to administer. We believe that the instrument is useful for the detection of emotional distress in the family caregivers of hospitalised patients suffering from end-stage illnesses and receiving PC.
Compassionate leadership during COVID-19: an ABC approach to the introduction of new medical graduates as Foundation interim Year 1s (FiY1s)
Authors: Dougan Claire , Philips Sally-Anne , Hughes Denise , Gardiner Keith
Published: December 2020

Background

Increasingly challenging workplaces detrimentally affect doctors’ well-being and patient care. The General Medical Council’s ‘ABC’ compassionate leadership model aims to improve doctor well-being. When COVID-19 emerged, a 4 Nation agreement facilitated early graduation and provisional registration of final year medical students and deployment of new graduates into Foundation interim Year 1 (FiY1) positions. We report how the Northern Ireland Medical and Dental Training Agency (NIMDTA) applied compassionate leadership to the induction of FiY1s.

Methods

Employing ‘What matters to you’, we identified FiY1s’ educational objectives and reviewed information dissemination options within distancing restrictions.

A dedicated FiY1 webpage summarised requirements and resources. A regional digital induction with a well-being emphasis facilitated flexible completion. Welcome packs promoted belonging while a ‘buddy system’ delivered support. Collaboration with other stakeholders created staggered follow-up video conferences providing practical and psychological support, removing communication barriers.

Findings

Feedback showed high FiY1 satisfaction with the global introduction to practice (83%) and 82% felt valued by NIMDTA and by Trusts after process completion.

Conclusion

Applying compassionate leadership to induction creates positive effects on doctors’ feeling of value and aligns with organisational strategic aims to support, develop and retain doctors in training programmes. We envision this model being applied to future postgraduate induction programmes.
Distilling the core meaning of medical engagement to three junior doctor staff groups in a Welsh Health Board
Authors: Cromarty Thomas , Rayment Rachel , Mazelan Patti , Barwell Fred , Spurgeon Peter , Shortland Graham
Published: December 2020

Background

Health systems demonstrate that levels of staff engagement correlate with a variety of performance indicators, including mortality, morbidity, staff sickness. The purpose of this paper is to help healthcare managers and clinical leaders gain greater clarity in understanding the core concepts which drive medical engagement for junior doctor staff groups.

Methods

A total of 245 members of medical staff completed the Medical Engagement Survey (MES) with a local focus in a participating Welsh University Health Board in April 2018. In this paper a‘mixed-methods’research approach is described. Both quantitative and qualitative data have been collected and analysed as part of the MES and these are interpreted and integrated with the aim of highlighting insightful links between the various methodological perspectives (as described by Shorten and Smith).

Results

The findings reported are the results of the first purposive sample from an application of the MES targeted specifically at junior doctors.

Though improvements in medical engagement often require a cultural change over the longer term, trainees have highlighted to the organisation valuable opportunities for quick wins. These capture the essence of what medical engagement really means to Junior Doctor Staff groups.

Being kept informed in a flexible and timely manner about any changes in systems, job roles and rotas.

Having more time outside ward duties to develop and progress effectively through training.

Being undervalued by senior management and poor communication with medical staffing.

Conclusion

The systematic surfacing of these core issues may potentially help keep sight of fundamental staff priorities when attempting to enhance levels of medical engagement. Although these views are from one Health Board, they mirror findings elsewhere. Disengaged junior doctors may be part of continuing the wider problem of lack of engagement in senior staff as they themselves become more senior and influential.
Quantitative Stability and Empirical Approximation of Risk-Averse Models Induced by Two-Stage Stochastic Programs with Full Random Recourse
Authors: Chen Zhiping , Hu He , Jiang Jie
Published: December 2020

In this paper, we consider the quantitative stability analysis and empirical approximation of risk-averse models induced by two-stage stochastic programs with full random recourse. We first establish the quantitative stability under the mean-coherent risk measure framework and the expected utility framework, respectively, under suitable probability metrics. Based on the obtained quantitative stability results, we then investigate the empirical approximation to these models, and estimate the rates of convergence for the optimal value and optimal solution set with the aid of Ky Fan distance.
Optimization of LNN Reversible Circuits Using an Analytic Sifting Method
Authors: Lukac Martin , Kerntopf Pawel , Kameyama Michitaka
Published: December 2020

In this paper, we propose an analytic approach to the variable sifting based on weighting of qubits and gates. The proposed scheme allows us to optimally sift gates (multi-control single-target reversible gates) within a linear number of steps of computation and provides, in general, that a smaller number of SWAP gates are required to transform a reversible circuit into an Linear Nearest Neighbor (LNN) model than other competing approaches. The method is analyzed for two different models of implementations; it is verified on the experimental data and results are compared with the state-of-the-art algorithms for the design of LNN circuits.
Efficient Reversible Data Hiding Using Dynamic Variance Mean Sorting and Fitting Weight Rhombus Predictor
Authors: Panyindee Chaiyaporn
Published: December 2020

Reversible data hiding (RDH) together with sorting is one of the key goals for reducing image distortion. This paper presents an improvement in sorting based on the double-layered RDH algorithm by modifying the dynamic variance mean (DVM) sorting models and applying an effective predictor. Seven models are investigated to achieve suitable sorting with the best prediction error (PE) for each capacity and image. The fitting weight rhombus (FWR) predictor and two-pass testing (TPT) strategy are significantly utilized to achieve small PEs and reduce distortion. The performance of the proposed RDH algorithm is compared with other similar methods using eight different images. Experiment results demonstrate that the sorting performance of the proposed method is superior to those of the previous methods.