bluuebunny/crossref_metadata_2025 huggingface dataset:
Redefining the global populations of Pseudomonas syringae pv. actinidiae based on pathogenic, molecular and phenotypic characteristics
Authors: Ferrante P. , Scortichini M.
Published: May 2014

Knowing the population structure of a pathogen is fundamental for developing reliable phytosanitary legislation, detection techniques, and control strategies based on the actual aggressiveness and distribution of the pathogen. Currently, four populations of Pseudomonas syringae pv. actinidiae (Psa) have been described: Psa 1, Psa 2, Psa 3 and Psa 4. However, diagnostic assays specific for Psa populations do not detect Psa 4, the less virulent (LV) strains isolated in New Zealand. Similarly, multilocus sequence typing (MLST) of housekeeping genes, or broad Psa strain genome comparisons, revealed that Psa 4‐LV strains clustered separately from other Psa populations. In order to examine whether the placement of Psa 4 in the pathovar actinidiae was appropriate, various tests were carried out. It was shown that the Psa 4‐LV strains induced leaf and shoot wilting in Prunus cerasus, extensive necrotic lesions in Capsicum annuum fruits, and no significant symptoms in Actinidia deliciosa. Moreover, repetitive‐sequence PCR fingerprinting, type III secretion system effector protein genes detection and colony morphology clearly indicated the distinctiveness of Psa 4‐LV strains from the other three Psa populations. Rep‐PCR molecular typing revealed a high similarity of the Psa 4‐LV strains with members of Pseudomonas avellanae species. The Psa 4‐LV strains, most probably, belong to a new, still unnamed pathovar. It was concluded that the Psa 4‐LV strains isolated in New Zealand do not belong to the pathovar actinidiae, and, consequently, three Psa populations pathogenic to Actinidia spp. should currently include Psa 1, Psa 2 and Psa 3.
Changes in antioxidants are critical in determining cell responses to short‐ and long‐term heat stress
Authors: Sgobba Alessandra , Paradiso Annalisa , Dipierro Silvio , De Gara Laura , de Pinto Maria Concetta
Published: May 2014

Heat stress can have deleterious effects on plant growth by impairing several physiological processes. Plants have several defense mechanisms that enable them to cope with high temperatures. The synthesis and accumulation of heat shock proteins (HSPs), as well as the maintenance of an opportune redox balance play key roles in conferring thermotolerance to plants. In this study changes in redox parameters, the activity and/or expression of reactive oxygen species (ROS) scavenging enzymes and the expression of two HSPs were studied in tobacco Bright Yellow‐2 (TBY‐2) cells subjected to moderate short‐term heat stress (SHS) and long‐term heat stress (LHS). The results indicate that TBY‐2 cells subjected to SHS suddenly and transiently enhance antioxidant systems, thus maintaining redox homeostasis and avoiding oxidative damage. The simultaneous increase in HSPs overcomes the SHS and maintains the metabolic functionality of cells. In contrast the exposure of cells to LHS significantly reduces cell growth and increases cell death. In the first phase of LHS, cells enhance antioxidant systems to prevent the formation of an oxidizing environment. Under prolonged heat stress, the antioxidant systems, and particularly the enzymatic ones, are inactivated. As a consequence, an increase in H2O2, lipid peroxidation and protein oxidation occurs. This establishment of oxidative stress could be responsible for the increased cell death. The rescue of cell growth and cell viability, observed when TBY‐2 cells were pretreated with galactone‐γ‐lactone, the last precursor of ascorbate, and glutathione before exposure to LHS, highlights the crucial role of antioxidants in the acquisition of basal thermotolerance.
Religion and Capital Punishment in the United States
Authors: Santoro Anthony
Published: May 2014

Religion and the death penalty have long been linked in the United States, from colonial establishments that used biblical law as one basis for criminal statutes to the contemporary use of religion to support or oppose executions. This article begins by analyzing the literature on these links at the most abstract before using religiously motivated opposition to capital punishment to survey the history and historiography on the subject. It then looks at how religious institutions engage the issue before bringing the discussion into the courtroom to look at how religion impacts the legal process and how this has been studied. The article concludes by suggesting some avenues for future research.
On the Importance of Attribution Theory in Political Psychology
Authors: Sahar Gail
Published: May 2014

Attribution theory, which was initially applied to the study of academic achievement, has generated a large amount of research in psychology. Judgments of causal responsibility, an important facet of attributions, have since been studied in a variety of other contexts, revealing that they pervade our understanding of the social world. The present paper considers the many ways in which causal judgments, particularly attributions of responsibility, influence political life. Examining scholarship primarily from the fields of psychology, political science, and sociology, I discuss how perceptions of responsibility are linked to ideology and how they influence policy attitudes (welfare, affirmative action, abortion, gay rights) and perceptions of international conflict (beliefs about terrorism and war). An argument is made for increased communication among fields and a more systematic application of attributional models to the study of political judgments.
No association between CCL2 gene polymorphisms and risk of inflammatory demyelinating diseases in a Korean population
Authors: Namgoong S. , Bae J. S. , Cheong H. S. , Kim J.‐H. , Kim J. Y. , Kim L. H. , Kim H. J. , Shin H. D.
Published: May 2014

Inflammatory demyelinating disease (IDD), which includes multiple sclerosis (MS) and neuromyelitis optica (NMO), affects the central nervous system. Chemokine ligand 2 (CCL2/MCP‐1) is considered an important contributor to the development or progression of IDD. However, genetic association studies of Asian populations are lacking. In this study, we investigated a possible association between CCL2 polymorphisms (rs1024611, rs28730833, and rs2857657) and a Korean population (178 IDD patients and 237 healthy controls) using multiple logistic regression models. However, we did not find any association, which was consistent with other studies in Caucasian populations. In conclusion, our results suggest that CCL2 variants may not contribute to the pathogenesis of IDD.
Impact of repeat testing of living kidney donors within 14 days of the transplant procedure: a multicenter retrospective survey
Authors: Echenique I.A. , Cohen D. , Rudow D.L. , Ison M.G.
Published: May 2014

Background

A transmission of human immunodeficiency virus (HIV) from a live kidney donor prompted recommendations by the New York State Department of Health and the US Centers for Disease Control and Prevention that all live donors undergo additional screening for HIV, hepatitis B virus (HBV), and hepatitis C virus (HCV) within 7–14 days of the donation procedure. There are concerns that re‐screening will result in delays and cancelled transplants.

Methods

We surveyed live‐donor transplant centers in New York State to assess their screening protocols and outcomes. Nine live‐donor programs (kidney and liver centers) responded.

Results

All but 1 program has a formal repeat screening policy. Overall, no cancellations occurred, but 2 centers experienced transplantation delays, generally as the result of technician and laboratory procedural mistakes necessitating repeat phlebotomy. Testing is typically coordinated with pre‐surgical visits, additional laboratory tests, and physical examinations. In the initial evaluation, serology was most frequently used (all 9 centers), with few centers utilizing nucleic acid testing (NAT) (HIV NAT, 1; HBV NAT, 2; HCV NAT, 2). Repeat testing modalities varied: HIV antibody (5, 55%), HIV NAT (8, 88%), hepatitis B surface antigen (5, 55%), hepatitis B surface antibody (2, 22%), hepatitis B core antibody (3, 33%), HBV NAT (3, 33%), HCV antibody (3, 33%), and HCV NAT (5, 55%).

Conclusion

Most respondents have policies to re‐test living donors within 14 days of the transplant procedures. Rarely, centers encountered repeat testing‐associated delays, but no cancellations occurred.
Teachers' attitudes towards Korean English in South Korea
Authors: AHN HYEJEONG
Published: May 2014

This study explores the attitudes of English teachers, both Korean and non‐Korean, towards ‘Korean English’ (KoE) in South Korea. Data about these attitudes were collected via 204 questionnaires and 25 post‐survey individual interviews, from two major regions, Busan Gyeongnam and Seoul Gyeonggi, and were analysed both qualitatively and quantitatively. The results indicate that the majority of participants displayed a positive attitude towards KoE, especially regarding to the ‘cognitive’ component of attitude, while they showed ‘confused’ and ‘conflicting’ attitudes in the behavioural element. The unique features of KoE, its intelligibility, demographic and widespread use of KoE were perceived by participants as the most influential factors shaping their cognitive attitudes towards the language. Language variation and an acceptance of a pluralistic model of English language norms played a critical role in developing positive attitudes towards KoE in both the cognitive and behavioural components of participants’ attitudes.
World Englishes in international proficiency tests
Authors: HAMID M. OBAIDUL
Published: May 2014

The demographic dominance of ‘non‐native’ speakers of English and the growing recognition of world Englishes (WE) call for critical examinations of varieties of English underpinning international proficiency tests. Expectedly, there has been an ongoing debate between those who argue for British and American norms and those who argue for all English norms including WE in international tests. While this welcome debate may develop awareness of WE issues among stakeholders, there has been little research on test‐takers and their perspectives on the relevance of WE to high‐stakes tests. This paper reports on data from an International English Language Testing System (IELTS) study to explore two questions: (1) How do IELTS test‐takers perceive the relevance of WE to the test and why? (2) What are the implications of their perceptions for WE research? Analyses of quantitative and qualitative data show test‐takers’ mixed views and attitudes: While the majority of them supported WE in an abstract, ideological sense, they were against the inclusion of WE in the test for reasons related to maintaining standards, fairness, equality and test‐taker interests. A critical discussion of the findings is undertaken to draw out implications for WE and WE researchers in the context of the dominance of English tests and their hegemonic discourses.
ASME Section III Treatment of Stress Distribution in Cylindrical Vessels With Symmetric Thin-Walled Discontinuity
Authors: Ezekoye L. Ike , Riegel Gerald A. , Ristau David , Way Richard
Published: May 2014

In equipment design, the designer often attempts to minimize cost and maximize performance while meeting the design specification requirements. In the Power Industry, for example, a significant portion of the design requirements are user defined and the rest are dictated by Codes and Standards. In most applications such as tanks, valves, and pumps, the designers are familiar with the technical issues and are able to meet them. In some cases, however, balancing the two requirements (i.e., the user defined requirements and the ASME Codes and Standards) is complex. An example of this challenge can be found in the design and analysis of a pressurized cylindrical vessel that allows the user to impose a “weak-link” section that under certain operating scenarios can cause the vessel to rupture or fail. In such a case, the designers have to address the discontinuity that is imposed on the structure while still meeting the ASME required stress criteria for structural integrity. The term “weak-link” is used herein to identify the subcomponent or subsystem which is most likely to fail under a postulated operating condition. The loading condition can be either internal or external. In internal loading, the loading is generally an overpressure excursion. In the external case, the load can be seismically induced or an applied actuator load for operation. This paper presents a case study of internally induced loading condition in an ASME Section III cylindrical pressurized vessel where the cylinder is required to fail or rupture only when it is impacted by an actuating load. In this case, the ASME Section III requirements for pressure integrity are combined with the failure mechanism of a symmetrical discontinuity in the design and analysis to ensure that the operational intent of the valve is met. The challenge for this design is two fold; (a) ensure that the device maintains structural integrity without any leakage during normal operation, and (b) guarantee vessel rupture and relieve pressure predictably. This paper presents the ASME treatment of such a design using finite element analysis (FEA).
Ag:TiN nanocomposite thin films for bioelectrodes: The effect of annealing treatments on the electrical and mechanical behavior
Authors: Pedrosa Paulo , Machado Diogo , Evaristo Manuel , Cavaleiro Albano , Fonseca Carlos , Vaz Filipe
Published: May 2014

Magnetron sputtered Ag:TiN thin films, with Ag contents ranging from 0 to ∼50 at. %, were subjected to a set of annealing treatments at four different temperatures (from 200 to 500 °C), aiming at studying the effect of Ag addition on their morphological and structural features, as well as on their electrical and mechanical properties. The increase of the annealing temperature revealed that significant morphological modifications were induced, mainly in the samples with higher Ag contents (represented by the sample with an Ag content of 36.3 at. %), which revealed extensive Ag segregation to the surface. The increase of the annealing temperature up to 500 °C, besides confirming the presence of metallic Ag in the coatings, also resulted in some major structural changes, promoting an increase in the coating's crystallinity and an extensive Ag grain growth phenomenon. Nevertheless, the resistivity values of all annealed samples were found to be only slightly higher when comparing to the as-deposited ones, which indicated that beyond the significant changes in the samples morphology (e.g., Ag segregation), there seemed to be some important coating resistance in terms of the electrical response. Furthermore, the annealed samples also exhibited lower reduced modulus up to 400 °C when compared with the unannealed ones, consistent with some increase of the samples' elasticity.
Activation energies for the growth of diamond films and the renucleation of diamond grains during film growth
Authors: Barbosa Divani Carvalho , Baldan Mauricio Ribeiro , Trava-Airoldi Vladimir Jesus , Corat Evaldo Jose
Published: May 2014

The effect of substrate temperature upon the growth rate and the properties of diamond thin films grown with different grains sizes is explored. An argon-free and argon-rich gas mixture of methane and hydrogen is used in a hot filament chemical vapor deposition reactor. Characterization of the films is accomplished by scanning electron microscopy, Raman spectroscopy and high-resolution x-ray diffraction. Arrhenius plots of the mass gain, thickness growth, and renucleation rate as a function of the substrate temperature are used to obtain the values of the activation energies. An extensive comparison of the activation energy values obtained in this study with those found in the literature suggests that there are distinct common trends for microcrystalline and ballaslike diamond growth. Besides the activation energy values, the morphology, crystallite size, sp2 quantification, mass gain, thickness growth, and renucleation rate present similar tendencies with the substrate temperature, despite a large variation in the gas mixture composition. Included is a discussion of the possible reasons for these observations.
Initial results for epitaxial growth of InN on gallium oxide and improved Migration-Enhanced Afterglow Epitaxy growth on gallium nitride
Authors: Gergova Rositsa , Butcher Kenneth Scott Alexander , Binsted Peter W. , Gogova Daniela
Published: May 2014

In this paper, the authors report on epitaxial thin InN layers grown on commercially available undoped GaN buffer layers and on Ga2O3 interlayers produced by Migration-Enhanced Afterglow Epitaxy (MEAglow). The InN layers reported here, also grown by the MEAglow technique, are 100–200 nm thick and have a measured absorption edge between 1.3 and 1.95 eV. Advancements in the growth process have now allowed the authors to improve the InN layers so that the growth has excellent two-dimensional morphology. Scanning electron microscope images show that terracing is strongly evident for samples grown on GaN templates. Atomic force microscopy shows a maximum height of the steps of about 2 nm. For the samples grown on Ga2O3, crystal quality is superior to InN grown on AlN buffers with similar thicknesses. X-ray diffraction ω-2θ measurements indicate a full width of half maximum (FWHM) of 342–389 arcseconds for these extremely thin layers; a good part of this x-ray diffraction FWHM is likely due to residual strain between the InN and GaN or between the InN and oxide.
Genomic Signatures of Specialized Metabolism in Plants
Authors: Chae Lee , Kim Taehyong , Nilo-Poyanco Ricardo , Rhee Seung Y.
Published: May 2014

Specialized Evolution

Many plants make chemical compounds that are potentially of use to humans, but their evolutionary histories are unknown.

Chae
et al.

(p.
510
) examined how algae and land plants have been able to evolve secondary metabolism biochemistry—those compounds produced in response to their environment—in the face of purifying evolutionary pressure to maintain primary and necessary metabolic pathways. Genomic data was used to separate the primary from the secondary metabolism pathway genes and to construct the evolutionary trajectories of secondary metabolism. Secondary metabolic pathways tend to be controlled by clustered, co-regulated sets of newly duplicated and maintained genes.
Chemical Inhibition of NAT10 Corrects Defects of Laminopathic Cells
Authors: Larrieu Delphine , Britton Sébastien , Demir Mukerrem , Rodriguez Raphaël , Jackson Stephen P.
Published: May 2014

Remodelin Nuclear Defects

Deregulation of A-type lamin proteins leads to disorganization of chromatin structure and misshapen nuclei, which are believed to underlie the pathologies of various human diseases, including the premature aging disorder Hutchinson Gilford progeria syndrome (HGPS) and various cancers.

Larrieu
et al.

(p.
527
) developed a small molecule, Remodelin, that not only improved nuclear shape defects of human lamin A/C–depleted cells, HGPS cells, and aged normal cells, but also decreased the levels of a DNA damage marker and improved global cellular fitness.
Seroepidemiology of Astrovirus MLB1
Authors: Holtz Lori R. , Bauer Irma K. , Jiang Hongbing , Belshe Robert , Freiden Pamela , Schultz-Cherry Stacey L. , Wang David
Published: May 2014

To determine the seroprevalence of astrovirus MLB1 (MLB1), an indirect enzyme-linked immunosorbent assay (ELISA) was established. MLB1 seropositivity was high in children <6 months old, decreased to a nadir at 12 to 23 months old, and increased to 100% by adulthood. MLB1 infection is common, and primary exposure occurs in childhood.
Escherichia coli
and the Emergence of Molecular Biology
Authors: Ullmann Agnes
Published: May 2014

The creation of the "Phage group" by M. Delbrück, S. E. Luria, and A. D. Hershey in 1940 at Cold Spring Harbor played a crucial role in the development of molecular biology. In the 1940s, working with
Escherichia coli
and its viruses, Luria and Delbrück discovered the spontaneous nature of bacterial mutations and Hershey described recombination in bacteriophages and demonstrated with M. Chase that the genetic material that infects bacteria is DNA. At the same time, S. Benzer defined the structure of a functional genetic unit and J. Lederberg and E. Tatum discovered sexual recombination between bacteria. Some years later, Lederberg's group discovered extrachromosomal particles, the plasmids, and a novel way of genetic transfer through bacteriophages, called transduction. In 1949, at the Pasteur Institute in Paris, A. Lwoff uncovered the mechanism of lysogeny. Shortly afterwards, F. Jacob and E. Wollman unraveled the mechanism of the sexual process in
E. coli
and established the circularity of the bacterial chromosome. In the 1960s, J. Monod and F. Jacob, by genetic analysis of the
E. coli
lactose system, proposed the operon model for gene regulation and introduced the concept of messenger RNA. The elucidation of the double helix structure of DNA in 1953 by F. Crick and J. Watson had major consequences: the establishment of the copying mechanism (Meselson and Stahl), the discovery of the nature of the genetic code (S. Brenner) leading to its deciphering.
E. coli
and its phages were instrumental in the development of recombinant DNA technology based on the discovery of the restriction-modification system by W. Arber.
Escherichia coli
and
Salmonella
2000: the View From Here
Authors: Schaechter Moselio ,   The View From Here Group
Published: May 2014

In 1995, an editorial in
Science
(
267:
1575) commented that predictions made some 25 years previously regarding “Biology and the Future of Man” were largely fulfilled but that “the most revolutionary and unexpected findings were not predicted.” We would be glad to do as well! As we stated at the beginning, our work as editors of the
Escherichia coli
and
Salmonella
book did not endow us with special powers of prophecy but it does permit us to express our excitement for the future. In our opinion,
E. coli
and
S. enterica
will continue to play a central role in biological research. This is not because they are intrinsically more interesting than any other bacteria, as we believe that all bacteria are equally interesting. However, knowledge builds on knowledge, and it is here that these two species continue to have a large edge not only over other microorganisms but also, for some time to come, over all other forms of life. It is interesting in this connection that biotechnology, having made detours through other microorganisms, always seems to return to
E. coli
.
Reconstruction and Use of Microbial Metabolic Networks: the Core
Escherichia coli
Metabolic Model as an Educational Guide
Authors: Orth Jeffrey D. , Fleming R. M. T. , Palsson Bernhard Ø.
Published: May 2014

Biochemical network reconstructions have become popular tools in systems biology. Metabolicnetwork reconstructions are biochemically, genetically, and genomically (BiGG) structured databases of biochemical reactions and metabolites. They contain information such as exact reaction stoichiometry, reaction reversibility, and the relationships between genes, proteins, and reactions. Network reconstructions have been used extensively to study the phenotypic behavior of wild-type and mutant stains under a variety of conditions, linking genotypes with phenotypes. Such phenotypic simulations have allowed for the prediction of growth after genetic manipulations, prediction of growth phenotypes after adaptive evolution, and prediction of essential genes. Additionally, because network reconstructions are organism specific, they can be used to understand differences between organisms of species in a functional context.There are different types of reconstructions representing various types of biological networks (metabolic, regulatory, transcription/translation). This chapter serves as an introduction to metabolic and regulatory network reconstructions and models and gives a complete description of the core
Escherichia coli
metabolic model. This model can be analyzed in any computational format (such as MATLAB or Mathematica) based on the information given in this chapter. The core
E. coli
model is a small-scale model that can be used for educational purposes. It is meant to be used by senior undergraduate and first-year graduate students learning about constraint-based modeling and systems biology. This model has enough reactions and pathways to enable interesting and insightful calculations, but it is also simple enough that the results of such calculations can be understoodeasily.
The Cytology of Bacterial Conjugation
Authors: Gilmour Matthew W. , Lawley Trevor D. , Taylor Diane E.
Published: May 2014

This review focuses on the membrane-associated structures present at cell-cell contact sites during bacterial conjugation. These transfer proteins/structures have roles in the formation and stabilization of mating contacts and ultimately the passage of substrate across the cell envelope between two bacterial cells. The review presents evidence for the dynamic interaction between donor and recipient cells, including the assembly of a transmembrane protein complex, and concludes with a refined model for the mechanism of bacterial conjugation. Bacterial conjugation, in addition to being a mechanism for genome evolution, can be considered as a mechanism for macromolecular secretion. In particular, plasmid-conjugative transfer is classified as a type IV secretion (T4S) system and represents the only known bacterial system for secretion of DNA. In all known conjugative transfer systems, a multitude of proteins are required for both plasmid transfer and pilus production. The plasmids discussed in the review include the F factor; the P group of plasmids, including RP4 and R751 (rigid); and the H plasmid group, including R27 (also thick flexible). With the LacI-GFP/
lacO
system, the F, P, and H plasmids were observed to reside at well-defined positions located at the mid and quarter-cell positions of
Escherichia coli
throughout the vegetative cycle. In this review, recent observations based on bacterial cell biology techniques, including visualization of plasmid DNA and proteins at the subcellular level, have been combined with electron and light microscopy studies of mating cells to create an integrated overview of gram-negative bacterial conjugation, a concept referred to as the conjugative cycle.
Assembly of the 30S Ribosomal Subunit
Authors: Culver Gloria M. , Kirthi Narayanaswamy
Published: May 2014

Protein synthesis involves nearly a third of the total molecules in a typical bacterial cell. Within the cell, protein synthesis is performed by the ribosomes, and research over several decades has investigated ribosomal formation, structure, and function. This review provides an overview of the current understanding of the assembly of the
Escherichia coli
30S ribosomal subunit. The
E. coli
30S subunit contains one rRNA molecule (16S) and 21 ribosomal proteins (r-proteins; S1 to S21). The formation of functional subunits can occur as a self-assembly process in vitro; i.e., all the information required for the formation of active ribosomes resides in the primary sequences of the r-proteins and rRNAs. In vitro reconstitution of functional 30S subunits is carried out by using a mixture of TP30, individually purified natural or recombinant r-proteins, and natural 16S rRNA. Chemical probing and primer extension analysis have been used extensively to monitor changes in the reactivities of nucleotides in 16S rRNA during the in vitro reconstitution of 30S subunits. The potential roles for r-proteins in 30S subunit assembly were determined by omitting single proteins in reconstitution experiments. The RNPs resulting from single protein omissions were examined in terms of their composition and function to determine the roles of the absent proteins. Recent developments in understanding the structure of the 30S subunit have led to speculation about roles for some of the r-proteins in assembly. The crystal structures of the 30S subunit (
1
,
2
) and the 70S ribosome (
3
) reveal details of the r-protein and rRNA interactions.
Antibiotic Resistance Mechanisms, with an Emphasis on Those Related to the Ribosome
Authors: Long Katherine S. , Vester Birte
Published: May 2014

Antibiotic resistance is a fundamental aspect of microbiology, but it is also a phenomenon of vital importance in the treatment of diseases caused by pathogenic microorganisms. A resistance mechanism can involve an inherent trait or the acquisition of a new characteristic through either mutation or horizontal gene transfer. The natural susceptibilities of bacteria to a certain drug vary significantly from one species of bacteria to another and even from one strain to another. Once inside the cell, most antibiotics affect all bacteria similarly. The ribosome is a major site of antibiotic action and is targeted by a large and chemically diverse group of antibiotics. A number of these antibiotics have important applications in human and veterinary medicine in the treatment of bacterial infections. The antibiotic binding sites are clustered at functional centers of the ribosome, such as the decoding center, the peptidyl transferase center, the GTPase center, the peptide exit tunnel, and the subunit interface spanning both subunits on the ribosome. Upon binding, the drugs interfere with the positioning and movement of substrates, products, and ribosomal components that are essential for protein synthesis. Ribosomal antibiotic resistance is due to the alteration of the antibiotic binding sites through either mutation or methylation. Our knowledge of antibiotic resistance mechanisms has increased, in particular due to the elucidation of the detailed structures of antibiotic-ribosome complexes and the components of the efflux systems. A number of mutations and methyltransferases conferring antibiotic resistance have been characterized. These developments are important for understanding and approaching the problems associated with antibiotic resistance, including design of antimicrobials that are impervious to known bacterial resistance mechanisms.
ATP Synthesis by Oxidative Phosphorylation
Authors: Vik Steven B.
Published: May 2014

The F
1
F
0
-ATP synthase (EC 3.6.1.34) is a remarkable enzyme that functions as a rotary motor. It is found in the inner membranes of
Escherichia coli
and is responsible for the synthesis of ATP in response to an electrochemical proton gradient. Under some conditions, the enzyme functions reversibly and uses the energy of ATP hydrolysis to generate the gradient. The ATP synthase is composed of eight different polypeptide subunits in a stoichiometry of α
3
β
3
γδε
ab
2
c
10
. Traditionally they were divided into two physically separable units: an F
1
that catalyzes ATP hydrolysis (α
3
β
3
γδε) and a membrane-bound F
0
sector that transports protons (
ab
2
c
10
). In terms of rotary function, the subunits can be divided into rotor subunits (γε
c
10
) and stator subunits (α
3
β
3
δ
ab
2
). The stator subunits include six nucleotide binding sites, three catalytic and three noncatalytic, formed primarily by the β and α subunits, respectively. The stator also includes a peripheral stalk composed of δ and
b
subunits, and part of the proton channel in subunit
a
. Among the rotor subunits, the
c
subunits form a ring in the membrane, and interact with subunit
a
to form the proton channel. Subunits γ and ε bind to the
c
-ring subunits, and also communicate with the catalytic sites through interactions with α and β subunits. The eight subunits are expressed from a single operon, and posttranscriptional processing and translational regulation ensure that the polypeptides are made at the proper stoichiometry. Recent studies, including those of other species, have elucidated many structural and rotary properties of this enzyme.
S
- and
N
-Oxide Reductases
Authors: Cheng Victor W. T. , Weiner Joel H.
Published: May 2014

Escherichia coli
is a versatile facultative anaerobe that can respire on a number of terminal electron acceptors, including oxygen, fumarate, nitrate, and
S
- and
N
-oxides. Anaerobic respiration using
S
- and
N
-oxides is accomplished by enzymatic reduction of these substrates by dimethyl sulfoxide reductase (DmsABC) and trimethylamine
N
-oxide reductase (TorCA). Both DmsABC and TorCA are membrane-associated redox enzymes that couple the oxidation of menaquinol to the reduction of
S
- and
N
-oxides in the periplasm. DmsABC is membrane bound and is composed of a membrane-extrinsic dimer with a 90.4-kDa catalytic subunit (DmsA) and a 23.1-kDa electron transfer subunit (DmsB). These subunits face the periplasm and are held to the membrane by a 30.8-kDa membrane anchor subunit (DmsC). The enzyme provides the scaffold for an electron transfer relay composed of a quinol binding site, five [4Fe-4S] clusters, and a molybdo-bis(molybdopterin guanine dinucleotide) (present nomenclature: Mo-bis-pyranopterin) (Mo-bisMGD) cofactor. TorCA is composed of a soluble periplasmic subunit (TorA, 92.5 kDa) containing a Mo-bis-MGD. TorA is coupled to the quinone pool via a pentaheme
c
subunit (TorC, 40.4 kDa) in the membrane. Both DmsABC and TorCA require system-specific chaperones (DmsD or TorD) for assembly, cofactor insertion, and/or targeting to the Tat translocon. In this chapter, we discuss the complex regulation of the
dmsABC
and
torCAD
operons, the poorly understood paralogues, and what is known about the assembly and translocation to the periplasmic space by the Tat translocon.
Solute and Ion Transport: Outer Membrane Pores and Receptors
Authors: Yamashita Satoshi , Buchanan Susan K.
Published: May 2014

Two membranes enclose Gram-negative bacteria-an inner membrane consisting of phospholipid and an outer membrane having an asymmetric structure in which the inner leaflet contains phospholipid and the outer leaflet consists primarily of lipopolysaccharide. The impermeable nature of the outer membrane imposes a need for numerous outer membrane pores and transporters to ferry substances in and out of the cell. These outer membrane proteins have structures distinct from their inner membrane counterparts and most often function without any discernable energy source. In this chapter, we review the structures and functions of four classes of outer membrane protein: general and specific porins, specific transporters, TonB-dependent transporters, and export channels. While not an exhaustive list, these classes exemplify small-molecule transport across the outer membrane and illustrate the diversity of structures and functions found in Gram-negative bacteria.
Hexose/Pentose and Hexitol/Pentitol Metabolism
Authors: Mayer Christoph , Boos Winfried
Published: May 2014

Escherichia coli
and
Salmonella enterica
serovar Typhimurium exhibit a remarkable versatility in the usage of different sugars as the sole source of carbon and energy, reflecting their ability to make use of the digested meals of mammalia and of the ample offerings in the wild. Degradation of sugars starts with their energy-dependent uptake through the cytoplasmic membrane and is carried on further by specific enzymes in the cytoplasm, destined finally for degradation in central metabolic pathways. As variant as the different sugars are, the biochemical strategies to act on them are few. They include phosphorylation, keto-enol isomerization, oxido/reductions, and aldol cleavage. The catabolic repertoire for using carbohydrate sources is largely the same in
E. coli
and in serovar Typhimurium. Nonetheless, significant differences are found, even among the strains and substrains of each species. We have grouped the sugars to be discussed according to their first step in metabolism, which is their active transport, and follow their path to glycolysis, catalyzed by the sugar-specific enzymes. We will first discuss the phosphotransferase system (PTS) sugars, then the sugars transported by ATP-binding cassette (ABC) transporters, followed by those that are taken up via proton motive force (PMF)-dependent transporters. We have focused on the catabolism and pathway regulation of hexose and pentose monosaccharides as well as the corresponding sugar alcohols but have also included disaccharides and simple glycosides while excluding polysaccharide catabolism, except for maltodextrins.
Catabolism of Hexuronides, Hexuronates, Aldonates, and Aldarates
Authors: Mandrand-Berthelot M.-A. , Condemine G. , Hugouvieux-Cotte-Pattat N.
Published: May 2014

Following elucidation of the regulation of the lactose operon in
Escherichia coli
, studies on the metabolism of many sugars were initiated in the early 1960s. The catabolic pathways of D-gluconate and of the two hexuronates, D-glucuronate and D-galacturonate, were investigated. The post genomic era has renewed interest in the study of these sugar acids and allowed the complete characterization of the D-gluconate pathway and the discovery of the catabolic pathways for L-idonate, D-glucarate, galactarate, and ketogluconates. Among the various sugar acids that are utilized as sole carbon and energy sources to support growth of
E. coli
, galacturonate, glucuronate, and gluconate were shown to play an important role in the colonization of the mammalian large intestine. In the case of sugar acid degradation, the regulators often mediate negative control and are inactivated by interaction with a specific inducer, which is either the substrate or an intermediate of the catabolism. These regulators coordinate the synthesis of all the proteins involved in the same pathway and, in some cases, exert crosspathway control between related catabolic pathways. This is particularly well illustrated in the case of hexuronide and hexuronate catabolism. The structural genes encoding the different steps of hexuronate catabolism were identified by analysis of numerous mutants affected for growth with galacturonate or glucuronate.
E. coli
is able to use the diacid sugars D-glucarate and galactarate (an achiral compound) as sole carbon source for growth. Pyruvate and 2-phosphoglycerate are the final products of the D-glucarate/galactarate catabolism.
Glycerol and Methylglyoxal Metabolism
Authors: Booth Ian R.
Published: May 2014

The metabolic connection between glycerol and methylglyoxal (MG) is principally that DHAP, which is an intermediate in the aerobic breakdown of glycerol, is also the major precursor of MG, being the substrate for methylglyoxal synthase (MGS). The synthesis of MG is a consequence of unbalanced metabolism related either to a limitation for phosphate or to excessive carbon flux through the pathways that have the capacity to generate significant pools of DHAP. Cells producing MG produce a poison as an intermediate strategy for survival of metabolic imbalance. Indeed the panoply of metabolic regulation in this sector of catabolism can be seen as a strategy to avoid death by self-poisoning. Glycerol entry into
Escherichia coli
and
Salmonella enterica
serovar Typhimurium is facilitated by the aquaglyceroporin, GlpF. A homologous protein in serovar Typhimurium, PduF, facilitates the entry of 1,2-propanediol (Ppd) and is part of the Ppd metabolic pathway. MGS catalyzes the elimination of phosphate from DHAP, forming an enzyme-bound enediol(ate) intermediate that is released from the enzyme, followed by release of inorganic phosphate. The enzyme is highly specific for DHAP. Multiple MG detoxification pathways are found in both
E. coli
and serovar Typhimurium, but the dominant pathway is the GSH-dependent glyoxalase III system. The KefB and KefC systems have evolved to provide protection during detoxification of electrophiles. KefB and KefC are GSH-gated K
+
efflux systems that are activated by the formation and binding of glutathione adducts that are generated during detoxification.
C
4
-Dicarboxylate Degradation in Aerobic and Anaerobic Growth
Authors: Unden Gottfried , Kleefeld Alexandra
Published: May 2014

C
4
-dicarboxylates, like succinate, fumarate,
L
- and
D
-malate, tartrate, and the C
4
-dicarboxylic amino acid aspartate, support aerobic and anaerobic growth of
Escherichia coli
and related bacteria and can serve as carbon and energy sources. In aerobic growth, the C
4
-dicarboxylates are oxidized in the citric acid cycle. Due to the interruption of the citric acid cycle under anaerobic conditions, anaerobic metabolism of the C
4
-dicarboxylates depends on fumarate reduction to succinate. In some related bacteria (e.g.,
Klebsiella
), degradation of C
4
-dicarboxylates, like tartrate, uses a different mechanism and pathway. It requires the functioning of an Na
+
-dependent and membrane-associated oxaloacetate decarboxylase. Due to the incomplete function of the citric acid cycle in anaerobic growth, succinate supports only aerobic growth of
E. coli
. This chapter describes the pathways of and differences in aerobic and anaerobic C
4
-dicarboxylate metabolism and the physiological consequences. The citric acid cycle, fumarate respiration, and fumarate reductase are discussed here only in the context of aerobic and anaerobic C
4
-dicarboxylate metabolism. Some recent aspects of C
4
-dicarboxylate metabolism, such as transport and sensing of C
4
-dicarboxylates, and their relationships are treated in more detail.
Glycolysis and Flux Control
Authors: Romeo Tony , Snoep Jacky L.
Published: May 2014

Central metabolism of carbohydrates uses the Embden-Meyerhof-Parnas (EMP), pentose phosphate (PP), and Entner-Doudoroff (ED) pathways. This review reviews the biological roles of the enzymes and genes of these three pathways of
E. coli
. Glucose, pentoses, and gluconate are primarily discussed as the initial substrates of the three pathways, respectively. The genetic and allosteric regulatory mechanisms of glycolysis and the factors that affect metabolic flux through the pathways are considered here. Despite the fact that a lot of information on each of the reaction steps has been accumulated over the years for
E. coli
, surprisingly little quantitative information has been integrated to analyze glycolysis as a system. Therefore, the review presents a detailed description of each of the catalytic steps by a systemic approach. It considers both structural and kinetic aspects. Models that include kinetic information of the reaction steps will always contain the reaction stoichiometry and therefore follow the structural constraints, but in addition to these also kinetic rate laws must be fulfilled. The kinetic information obtained on isolated enzymes can be integrated using computer models to simulate behavior of the reaction network formed by these enzymes. Successful examples of such approaches are the modeling of glycolysis in
S. cerevisiae
, the parasite
Trypanosoma brucei
, and the red blood cell. With the rapid developments in the field of Systems Biology many new methods have been and will be developed, for experimental and theoretical approaches, and the authors expect that these will be applied to
E. coli
glycolysis in the near future.
Anaerobic Formate and Hydrogen Metabolism
Authors: Sawers R. Gary , Blokesch Melanie , Böck August
Published: May 2014

During fermentative growth,
Escherichia coli
degrades carbohydrates via the glycolytic route into two pyruvate molecules. Pyruvate can be reduced to lactate or nonoxidatively cleaved by pyruvate formate lyase into acetyl-coenzyme A (acetyl-CoA) and formate. Acetyl-CoA can be utilized for energy conservation in the phosphotransacetylase (PTA) and acetate kinase (ACK) reaction sequence or can serve as an acceptor for reducing equivalents gathered during pyruvate formation, through the action of alcohol dehydrogenase (AdhE). Formic acid is strongly acidic and has a redox potential of −420 mV under standard conditions and therefore can be classified as a high-energy compound. Its disproportionation into CO
2
and molecular hydrogen (E

m
,7

−420 mV) via the formate hydrogenlyase (FHL) system is therefore of high selective value. The FHL reaction involves the participation of at least seven proteins, most of which are metalloenzymes, with requirements for iron, molybdenum, nickel, or selenium. Complex auxiliary systems incorporate these metals. Reutilization of the hydrogen evolved required the evolution of H
2
oxidation systems, which couple the oxidation process to an appropriate energy-conserving terminal reductase.
E. coli
has two hydrogen-oxidizing enzyme systems. Finally, fermentation is the "last resort" of energy metabolism, since it gives the minimal energy yield when compared with respiratory processes. Consequently, fermentation is used only when external electron acceptors are absent. This has necessitated the establishment of regulatory cascades, which ensure that the metabolic capability is appropriately adjusted to the physiological condition. Here we review the genetics, biochemistry, and regulation of hydrogen metabolism and its hydrogenase maturation system.
Amino Acid Metabolism and Fluxes
Authors: Hatfield G. Wesley
Published: May 2014

By the mid1960s, the pioneering work of Umbarger and Gerhart and Pardee had shown us that carbon flow through a biosynthetic pathway was controlled by allosteric inhibition of the first enzyme of the pathway by its end product; and, studies of the
lac
operon by Jacob and Monod had established that genes were controlled by an operator-repressor mechanism. During the intervening forty-plus years, knowledge and technologies have continued to explode in unanticipated ways. Today, we understand in great detail the molecular mechanisms of the many levels of metabolic and genetic regulation that control carbon flow through the amino acid biosynthetic pathways. Traditional experimental approaches are not sufficient for the integration and reconstruction of complex biological systems using data mostly generated by high-throughput experiments. Only with computational methods and adequate modeling tools will we be able to reconstruct and query these large and complicated systems. Due to complicated enzyme reaction mechanisms and the frequent lack of rate constant measurements needed for solving differential equations, most investigators have turned their attention to the development of abstract, top-down modeling tools. For example, Palsson and colleagues have used metabolic flux balance analysis (FBA) methods to simulate steady-state metabolite flux through
E. coli
pathways representing hundreds of enzyme steps. Recently, Yang et al. have developed a bottom-up, enzyme mechanism modeling language, kMech (kinetic mechanism), for the mathematical simulation of metabolic pathways.
Selenophosphate Synthetase
Authors: Wolfe Matt D.
Published: May 2014

Selenophosphate synthetase, the
selD
gene product from
Escherichia coli
, is one of the enzymes required for the synthesis and specific insertion of selenocysteine into proteins directed by the TGA codon. Selenophosphate synthetases have been isolated from or are thought to be present in most organisms; however, the best characterized selenophosphate synthetase is from
E. coli
, in which both in vivo and in vitro studies have been performed. Leinfelder and coworkers showed that an
E. coli
mutant lacking an intact
selD
gene fails to incorporate Se into both the selenocysteine-containing enzyme formate dehydrogenase (FDH) and tRNA species that normally contain 2-selenouridine residues at the wobble position. Thus, this study strongly implicated selenophosphate as playing a major role in
E. coli
selenium metabolic pathways. The selenophosphate synthetase reaction requires some form of reduced selenium such as hydrogen selenide (HSe
-
) and ATP as substrates to generate a stoichiometric amount of SePO
3
, AMP, and orthophosphate. Studies of selenophosphate inhibition have provided further insight into the mechanism of selenophosphate synthetase. An assay by which AMP formation is measured in the absence of selenide showed that selenophosphate synthetase catalyzes hydrolysis of ATP to AMP and two orthophosphates in an uncoupled reaction. The sequencing of selenophosphate synthetase genes from various organisms reveals several conserved regions in the gene product. Recent investigations into the mechanism of selenophosphate synthetase have revealed a property of selenophosphate synthetase not previously observed. In samples of purified selenophosphate synthetase, an unusual optical absorption spectrum is seen.