bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-Resolution Crystal Structure of the Subclass B3 Metallo-β-Lactamase BJP-1: Rational Basis for Substrate Specificity and Interaction with Sulfonamides
Authors: Docquier Jean-Denis , Benvenuti Manuela , Calderone Vito , Stoczko Magdalena , Menciassi Nicola , Rossolini Gian Maria , Mangani Stefano 
Published: August 2010

ABSTRACT

Metallo-β-lactamases (MBLs) are important enzymatic factors in resistance to β-lactam antibiotics that show important structural and functional heterogeneity. BJP-1 is a subclass B3 MBL determinant produced by
Bradyrhizobium japonicum
that exhibits interesting properties. BJP-1, like CAU-1 of
Caulobacter vibrioides
, overall poorly recognizes β-lactam substrates and shows an unusual substrate profile compared to other MBLs. In order to understand the structural basis of these properties, the crystal structure of BJP-1 was obtained at 1.4-Å resolution. This revealed significant differences in the conformation and locations of the active-site loops, determining a rather narrow active site and the presence of a unique N-terminal helix bearing Phe-31, whose side chain binds in the active site and represents an obstacle for β-lactam substrate binding. In order to probe the potential of sulfonamides (known to inhibit various zinc-dependent enzymes) to bind in the active sites of MBLs, the structure of BJP-1 in complex with 4-nitrobenzenesulfonamide was also obtained (at 1.33-Å resolution), thereby revealing the mode of interaction of these molecules in MBLs. Interestingly, sulfonamide binding resulted in the displacement of the side chain of Phe-31 from its hydrophobic binding pocket, where the benzene ring of the molecule is now found. These data further highlight the structural diversity shown by MBLs but also provide interesting insights in the structure-function relationships of these enzymes. More importantly, we provided the first structural observation of MBL interaction with sulfonamides, which might represent an interesting scaffold for the design of MBL inhibitors.
Discovery and Analysis of 4
H
-Pyridopyrimidines, a Class of Selective Bacterial Protein Synthesis Inhibitors
Authors: Ribble Wendy , Hill Walter E. , Ochsner Urs A. , Jarvis Thale C. , Guiles Joseph W. , Janjic Nebojsa , Bullard James M. 
Published: August 2010

ABSTRACT

Bacterial protein synthesis is the target for numerous natural and synthetic antibacterial agents. We have developed a poly(U) mRNA-directed aminoacylation/translation protein synthesis system composed of phenyl-tRNA synthetases, ribosomes, and ribosomal factors from
Escherichia coli
. This system, utilizing purified components, has been used for high-throughput screening of a small-molecule chemical library. We have identified a series of compounds that inhibit protein synthesis with 50% inhibitory concentrations (IC
50
s) ranging from 3 to 14 μM. This series of compounds all contained the same central scaffold composed of tetrahydropyrido[4,3-
d
]pyrimidin-4-ol (e.g., 4
H
-pyridopyrimidine). All analogs contained an
ortho
pyridine ring attached to the central scaffold in the 2 position and either a five- or a six-member ring tethered to the 6-methylene nitrogen atom of the central scaffold. These compounds inhibited the growth of
E. coli
,
Staphylococcus aureus
,
Streptococcus pneumoniae
,
Haemophilus influenzae
, and
Moraxella catarrhalis
, with MICs ranging from 0.25 to 32 μg/ml. Macromolecular synthesis (MMS) assays with
E. coli
and
S. aureus
confirmed that antibacterial activity resulted from specific inhibition of protein synthesis. Assays were developed for the steps performed by each component of the system in order to ascertain the target of the compounds, and the ribosome was found to be the site of inhibition.
The Development of Ciprofloxacin Resistance in
Pseudomonas aeruginosa
Involves Multiple Response Stages and Multiple Proteins
Authors: Su Hsun-Cheng , Ramkissoon Kevin , Doolittle Janet , Clark Martha , Khatun Jainab , Secrest Ashley , Wolfgang Matthew C. , Giddings Morgan C. 
Published: August 2010

ABSTRACT

Microbes have developed resistance to nearly every antibiotic, yet the steps leading to drug resistance remain unclear. Here we report a multistage process by which
Pseudomonas aeruginosa
acquires drug resistance following exposure to ciprofloxacin at levels ranging from 0.5× to 8× the initial MIC. In stage I, susceptible cells are killed
en masse
by the exposure. In stage II, a small, slow to nongrowing population survives antibiotic exposure that does not exhibit significantly increased resistance according to the MIC measure. In stage III, exhibited at 0.5× to 4× the MIC, a growing population emerges to reconstitute the population, and these cells display heritable increases in drug resistance of up to 50 times the original level. We studied the stage III cells by proteomic methods to uncover differences in the regulatory pathways that are involved in this phenotype, revealing upregulation of phosphorylation on two proteins, succinate-semialdehyde dehydrogenase (SSADH) and methylmalonate-semialdehyde dehydrogenase (MMSADH), and also revealing upregulation of a highly conserved protein of unknown function. Transposon disruption in the encoding genes for each of these targets substantially dampened the ability of cells to develop the stage III phenotype. Considering these results in combination with computational models of resistance and genomic sequencing results, we postulate that stage III heritable resistance develops from a combination of both genomic mutations and modulation of one or more preexisting cellular pathways.
Comparative Biochemical and Computational Study of the Role of Naturally Occurring Mutations at Ambler Positions 104 and 170 in GES β-Lactamases
Authors: Kotsakis Stathis D. , Miriagou Vivi , Tzelepi Eva , Tzouvelekis Leonidas S. 
Published: August 2010

ABSTRACT
In GES-type β-lactamases, positions 104 and 170 are occupied by Glu or Lys and by Gly, Asn, or Ser, respectively. Previous studies have indicated an important role of these amino acids in the interaction with β-lactams, although their precise role, especially that of residue 104, remains uncertain. In this study, we constructed GES-1 (Glu104, Gly170), GES-2 (Glu104, Asn170), GES-5 (Glu104, Ser170), GES-6 (Lys104, Ser170), GES-7 (Lys104, Gly170), and GES-13 (Lys104, Asn170) by site-specific mutagenesis and compared their hydrolytic properties. Isogenic comparisons of β-lactam resistance levels conferred by these GES variants were also performed. Data indicated the following patterns: (i) Lys104-containing enzymes exhibited enhanced hydrolysis of oxyimino-cephalosporins and reduced efficiency against imipenem in relation to enzymes possessing Glu104, (ii) Asn170-containing enzymes showed reduced hydrolysis rates of penicillins and older cephalosporins, (iii) Ser170 enabled GES to hydrolyze cefoxitin efficiently, and (iv) Asn170 and Ser170 increased the carbapenemase character of GES enzymes but reduced their activity against ceftazidime. Molecular dynamic simulations of GES apoenzyme models, as well as construction of GES structures complexed with cefoxitin and an achiral ceftazidime-like boronic acid, provided insights into the catalytic behavior of the studied mutants. There were indications that an increased stability of the hydrogen bonding network of Glu166-Lys73-Ser70 and an altered positioning of Trp105 correlated with the substrate spectra, especially with acylation of GES by imipenem. Furthermore, likely effects of Ser170 on GES interactions with cefoxitin and of Lys104 on interactions with oxyimino-cephalosporins were revealed. Overall, the data unveiled the importance of residues 104 and 170 in the function of GES enzymes.
Toll-Like Receptor 2 Deficiency Results in Impaired Antibody Responses and Septic Shock during
Borrelia hermsii
Infection
Authors: Dickinson Gregory S. , Piccone Heather , Sun Guizhi , Lien Egil , Gatto Louis , Alugupalli Kishore R. 
Published: August 2010

ABSTRACT

Overwhelming bacteremia is a leading cause of death. To understand the mechanisms involved in protective antibody and pathological inflammatory responses during bacteremia, we have been studying the murine model of
Borrelia hermsii
infection. Toll-like receptor (TLR) signaling plays an important role in generating the rapid anti-
B. hermsii
antibody responses required for the resolution of bacteremia. Using NF-κB reporter assays, we found that
B. hermsii
activates TLR2 and TLR9. However, TLR2
−/−
TLR9
−/−
mice exhibited an impairment in anti-
B. hermsii
antibody responses similar to that of TLR2
−/−
mice. Moreover, the impairment in the antibody responses of TLR2
−/−
mice or TLR2
−/−
TLR9
−/−
mice coincides with an order-of-magnitude-higher bacteremia, and death results from septic shock, as evidenced by a dysregulated systemic cytokine response and characteristic organ pathology. Since TLR2 appears to be the major extracellular sensor stimulated by
B. hermsii
, we hypothesized that during elevated bacteremia the activation of intracellular sensors of bacteria triggers dysregulated inflammation in TLR2
−/−
mice. Indeed, blocking the internalization of
B. hermsii
prevented the induction of inflammatory cytokine responses in TLR2-deficient cells. Furthermore, we found that
B. hermsii
activates the cytoplasmic sensor nucleotide-binding oligomerization domain 2 (NOD2). Macrophages deficient in both TLR2 and NOD2 have impaired cytokine responses to
B. hermsii
compared to cells lacking TLR2 alone, and
B. hermsii
-infected TLR2
−/−
NOD2
−/−
mice exhibited improved survival compared to TLR2
−/−
mice. These data demonstrate that TLR2 is critical for protective immunity and suggest that, during heightened bacteremia, recognition of bacterial components by intracellular sensors can lead to pathological inflammatory responses.
Arachidonic Acid Metabolism Regulates
Escherichia coli
Penetration of the Blood-Brain Barrier
Authors: Zhu Longkun , Maruvada Ravi , Sapirstein Adam , Malik Kafait U. , Peters-Golden Marc , Kim Kwang Sik 
Published: August 2010

ABSTRACT

Escherichia coli
K1 meningitis occurs following penetration of the blood-brain barrier, but the underlying mechanisms involved in
E. coli
penetration of the blood-brain barrier remain incompletely understood. We have previously shown that host cytosolic phospholipase A
2
α (cPLA
2
α) contributes to
E. coli
invasion of human brain microvascular endothelial cells (HBMEC), which constitute the blood-brain barrier, but the underlying mechanisms remain unclear. cPLA
2
α selectively liberates arachidonic acid from membrane phospholipids. Here, we provide the first direct evidence that host 5-lipoxygenase and lipoxygenase products of arachidonic acid, cysteinyl leukotrienes (LTs), contribute to
E. coli
K1 invasion of HBMEC and penetration into the brain, and their contributions involve protein kinase C alpha (PKCα). These findings demonstrate that arachidonic acid metabolism regulates
E. coli
penetration of the blood-brain barrier, and studies are needed to further elucidate the mechanisms involved with metabolic products of arachidonic acid for their contribution to
E. coli
invasion of the blood-brain barrier.
Specific and Nonspecific B-Cell Function in the Small Intestines of Patients with Whipple's Disease
Authors: Geelhaar Anika , Moos Verena , Schinnerling Katina , Allers Kristina , Loddenkemper Christoph , Fenollar Florence , LaScola Bernard , Raoult Didier , Schneider Thomas 
Published: August 2010

ABSTRACTWhipple's disease is a chronic multisystemic infection caused byTropheryma whippleithat is characterized by arthritis, weight loss, and diarrhea. The immunological defects in the duodenal mucosa, the site of major replication of the agent underlying the pathogenesis of Whipple's disease, are poorly understood. Mucosal immunoglobulins are essential for the defense against intestinal pathogens; therefore, we analyzed the B-cell response in duodenal specimens and sera of Whipple's disease patients. Whereas systemic immunoglobulin production was affected only marginally, duodenal biopsy specimens of Whipple's disease patients contained reduced numbers of immunoglobulin-positive plasma cells and secreted less immunoglobulin compared to healthy controls but showed a weak secretory IgA response towardT. whipplei.ThisT. whipplei-specific intestinal immune response was not observed in controls. Thus, we were able to demonstrate that general mucosal immunoglobulin production in Whipple's disease patients is impaired. However, this deficiency does not completely abolishT. whipplei-specific secretory IgA production that nonetheless does not protect from chronic infection.
Enterococcal Biofilm Formation and Virulence in an Optimized Murine Model of Foreign Body-Associated Urinary Tract Infections
Authors: Guiton Pascale S. , Hung Chia S. , Hancock Lynn E. , Caparon Michael G. , Hultgren Scott J. 
Published: August 2010

ABSTRACTCatheter-associated urinary tract infections (CAUTIs) constitute the majority of nosocomial UTIs and pose significant clinical challenges. Enterococcal species are among the predominant causative agents of CAUTIs. However, very little is known about the pathophysiology ofEnterococcus-mediated UTIs. We optimized a murine model of foreign body-associated UTI in order to mimic conditions of indwelling catheters in patients. In this model, the presence of a foreign body elicits major histological changes and induces the expression of several proinflammatory cytokines in the bladder. In addition, in contrast to naïve mice, infection of catheter-implanted mice withEnterococcus faecalisinduced the specific expression of interleukin 1β (IL-1β) and macrophage inflammatory protein 1α (MIP-1α) in the bladder. These responses resulted in a favorable niche for the development of persistentE. faecalisinfections in the murine bladders and kidneys. Furthermore, biofilm formation on the catheter implantin vivocorrelated with persistent infections. However, the enterococcal autolytic factors GelE and Atn (also known as AtlA), which are important in biofilm formationin vitro, are dispensablein vivo. In contrast, the housekeeping sortase A (SrtA) is critical for biofilm formation and virulence in CAUTIs. Overall, this murine model represents a significant advance in the understanding of CAUTIs and underscores the importance of urinary catheterization duringE. faecalisuropathogenesis. This model is also a valuable tool for the identification of virulence determinants that can serve as potential antimicrobial targets for the treatment of enterococcal infections.
HIERARCHIES OF PIECEWISE TESTABLE LANGUAGES
Authors: KLÍMA ONDŘEJ , POLÁK LIBOR 
Published: August 2010

The classes of languages which are Boolean combinations of languages of the form [Formula: see text] for a fixed k ≥ 0, form a natural hierarchy within piecewise testable languages and have been studied by Simon, Blanchet-Sadri, Volkov and others. The main issues were the existence of finite bases of identities for the corresponding pseudovarieties of monoids and monoids generating these pseudovarieties. Here we deal with similar questions concerning the finite unions and positive Boolean combinations of the languages of the form above. In the first case the corresponding pseudovarieties are given by a single identity, in the second case there are finite bases for k equals to 1 and 2 and there is no finite basis for k ≥ 4 (the case k = 3 remains open). All the pseudovarieties are generated by a single algebraic structure.
Loss of miR-200c Expression Induces an Aggressive, Invasive, and Chemoresistant Phenotype in Non–Small Cell Lung Cancer
Authors: Ceppi Paolo , Mudduluru Giridhar , Kumarswamy Regalla , Rapa Ida , Scagliotti Giorgio V. , Papotti Mauro , Allgayer Heike 
Published: August 2010

AbstractThe development of metastases is the main reason for cancer-related death in non–small cell lung cancer (NSCLC). The initiation of metastasis involves an increase in cell motility mediated by the loss of cell-cell adhesion caused by E-cadherin repression, in a process commonly known as epithelial-to-mesenchymal transition. A role for microRNA-200 family members in regulating epithelial-to-mesenchymal transition has recently been indicated but data about their expression in lung tumors is still unavailable. The present study investigated the expression of miR-200c in a panel of NSCLC cell lines (n = 9), and a strong inverse correlation with invasion was detected. Reintroduction of miR-200c into highly invasive/aggressive NSCLC cells induced a loss of the mesenchymal phenotype by restoring E-cadherin and reducing N-cadherin expression, and inhibited in vitro cell invasion as well as in vivo metastasis formation. Moreover, miR-200c overexpression restored the sensitivity of NCI-H1299 cells to cisplatin and cetuximab. Hypermethylation of the promoter region was found to be responsible for the loss of miR-200c in invasive cells, as evaluated by 5-aza-2′-deoxycytidine treatment, methylation-specific PCR, and bisulfite sequencing. In primary tumor specimens obtained from 69 patients with consecutively resected NSCLC, lower miR-200c expression levels were found to be associated with a poor grade of differentiation (P = 0.04), a higher propensity to lymph node metastases (P &lt; 0.01), and with a lower E-cadherin expression (P = 0.01). These data indicate that the loss of miR-200c expression induces an aggressive, invasive, and chemoresistant phenotype, and that assessment of its expression could contribute to a better clinicopathologic definition of patients with NSCLC. Mol Cancer Res; 8(9); 1207–16. ©2010 AACR.
Dynamical Diagnosis: A Comparison of Quasigeostrophy and Ertel Potential Vorticity
Authors: Nielsen-Gammon John W. , Gold David A. 
Published: August 2010

Abstract
Advances in computer power, new forecasting challenges, and new diagnostic techniques have brought about changes in the way atmospheric development and vertical motion are diagnosed in an operational setting. Many of these changes, such as improved model skill, model resolution, and ensemble forecasting, have arguably been detrimental to the ability of forecasters to understand and respond to the evolving atmosphere. The use of nondivergent wind in place of geostrophic wind would be a step in the right direction, but the advantages of potential vorticity suggest that its widespread adoption as a diagnostic tool on the west side of the Atlantic is overdue. Ertel potential vorticity (PV), when scaled to be compatible with pseudopotential vorticity, is generally similar to pseudopotential vorticity, so forecasters accustomed to quasigeostrophic reasoning through the height tendency equation can transfer some of their intuition into the Ertel-PV framework. Indeed, many of the differences between pseudopotential vorticity and Ertel potential vorticity are consequences of the choice of definition of quasigeostrophic PV and are not fundamental to the quasigeostrophic system. Thus, at its core, PV thinking is consistent with commonly used quasigeostrophic diagnostic techniques.
Finescale Radar Observations of a Dryline during the International H2O Project (IHOP_2002)
Authors: Weiss Christopher C. , Bluestein Howard B. , Pazmany Andrew L. , Geerts Bart 
Published: August 2010

Abstract
A case study of a double dryline on 22 May 2002 is presented. Mobile, 3-mm-wavelength Doppler radars from the University of Massachusetts and the University of Wyoming (Wyoming cloud radar) were used to collect very fine resolution vertical-velocity data in the vicinity of each of the moisture gradients associated with the drylines. Very narrow (50–100 m wide) channels of strong upward vertical velocity (up to 8 m s–1) were measured in the convergence zone of the easternmost dryline, larger in magnitude than reported with previous drylines. Distinct areas of descending motion were evident to the east and west of both drylines. Radar data are interpreted in the context of other observational platforms available during the International H2O Project (IHOP-2002). a variational ground-based mobile radar data processing technique was developed and applied to pseudo-dual-Doppler data collected during a rolling range-height indicator deployment. It was found that there was a secondary (vertical) circulation normal to the easternmost moisture gradient; the circulation comprised an easterly component near-surface flow to the east, a strong upward vertical component in the convergence zone, a westerly return, flow above the convective boundary layer, and numerous regions of descending motion, the most prominent approximately 3–5 km to the east of the surface convergence zone.
Linking Weather and Climate
Authors: Dole Randall M. 
Published: August 2010

Abstract
Historically, the atmospheric sciences have tended to treat problems of weather and climate separately. The real physical system, however, is a continuum, with short-term (minutes to days) “weather” fluctuations influencing climate variations and change, and, conversely, more slowly varying aspects of the system (typical time scales of a season or longer) affecting the weather that is experienced. While this past approach has served important purposes, it is becoming increasingly apparent that in order to make progress in addressing many socially important problems, an improved understanding of the connections between weather and climate is required.
This overview summarizes the progress over the last few decades in the understanding of the phenomena and mechanisms linking weather and climate variations. The principal emphasis is on developments in understanding key phenomena and processes that bridge the time scales between synoptic-scale weather variability (periods of approximately 1 week) and climate variations of a season or longer. Advances in the ability to identify synoptic features, improve physical understanding, and develop forecast skill within this time range are reviewed, focusing on a subset of major, recurrent phenomena that impact extratropical wintertime weather and climate variations over the Pacific–North American region. While progress has been impressive, research has also illuminated areas where future gains are possible. This article concludes with suggestions on near-term directions for advancing the understanding and capabilities to predict the connections between weather and climate variations.
An Empirical Perspective on Cold Fronts
Authors: Kessler Edwin 
Published: August 2010

Abstract
Oklahoma Mesonetwork data are used to illustrate important atmospheric features that are not well shown by the usual synoptic data. For example, some shifts of wind from south to north that are shown as cold fronts on synoptic charts are not cold fronts by any plausible definition. As previously discussed by Fred Sanders and others, such errors in analysis can be reduced by knowledge of the wide variety of weather phenomena that actually exists, and by more attention to temperatures at the earth's surface as revealed by conventional synoptic data. Mesoscale data for four cases reinforce previous discussions of the ephemeral nature of fronts and deficiencies in the usual analyses of cold fronts. One type of misanalyzed case involves post-cold-frontal boundary layer air that is warmer than the prefrontal air. A second type is usually nocturnal, with a rise of local temperature during disruption of an inversion and a wind shift with later cooling that accompanies advection of a climatological gradient of temperature.