bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytoplasmic Histidine Kinase (HP0244)-Regulated Assembly of Urease with UreI, a Channel for Urea and Its Metabolites, CO
2
, NH
3
, and NH
4
+
, Is Necessary for Acid Survival of
Helicobacter pylori
Authors: Scott David R. , Marcus Elizabeth A. , Wen Yi , Singh Siddarth , Feng Jing , Sachs George 
Published: October 2009

ABSTRACT

Helicobacter pylori
colonizes the normal human stomach by maintaining both periplasmic and cytoplasmic pH close to neutral in the presence of gastric acidity. Urease activity, urea flux through the pH-gated urea channel, UreI, and periplasmic α-carbonic anhydrase are essential for colonization. Exposure to pH 4.5 for up to 180 min activates total bacterial urease threefold. Within 30 min at pH 4.5, the urease structural subunits, UreA and UreB, and the Ni
2+
insertion protein, UreE, are recruited to UreI at the inner membrane. Formation of this complex and urease activation depend on expression of the cytoplasmic sensor histidine kinase, HP0244. Its deletion abolishes urease activation and assembly, impairs cytoplasmic and periplasmic pH homeostasis, and depolarizes the cells, with an ∼7-log loss of survival at pH 2.5, even in 10 mM urea. Associated with this assembly, UreI is able to transport NH
3
, NH
4
+
, and CO
2
, as shown by changes in cytoplasmic pH following exposure to NH
4
Cl or CO
2
. To be able to colonize cells in the presence of the highly variable pH of the stomach, the organism expresses two pH-sensor histidine kinases, one, HP0165, responding to a moderate fall in periplasmic pH and the other, HP0244, responding to cytoplasmic acidification at a more acidic medium pH. Assembly of a pH-regulatory complex of active urease with UreI provides an advantage for periplasmic buffering.
Combined Genomic and Proteomic Approaches Identify Gene Clusters Involved in Anaerobic 2-Methylnaphthalene Degradation in the Sulfate-Reducing Enrichment Culture N47
Authors: Selesi Draženka , Jehmlich Nico , von Bergen Martin , Schmidt Frank , Rattei Thomas , Tischler Patrick , Lueders Tillmann , Meckenstock Rainer U. 
Published: October 2009

ABSTRACT

The highly enriched deltaproteobacterial culture N47 anaerobically oxidizes the polycyclic aromatic hydrocarbons naphthalene and 2-methylnaphthalene, with sulfate as the electron acceptor. Combined genome sequencing and liquid chromatography-tandem mass spectrometry-based shotgun proteome analyses were performed to identify genes and proteins involved in anaerobic aromatic catabolism. Proteome analysis of 2-methylnaphthalene-grown N47 cells resulted in the identification of putative enzymes catalyzing the anaerobic conversion of 2-methylnaphthalene to 2-naphthoyl coenzyme A (2-naphthoyl-CoA), as well as the reductive ring cleavage of 2-naphthoyl-CoA, leading to the formation of acetyl-CoA and CO
2
. The glycyl radical-catalyzed fumarate addition to the methyl group of 2-methylnaphthalene is catalyzed by naphthyl-2-methyl-succinate synthase (Nms), composed of α-, β-, and γ-subunits that are encoded by the genes
nmsABC
. Located upstream of
nmsABC
is
nmsD
, encoding the Nms-activating enzyme, which harbors the characteristic [Fe
4
S
4
] cluster sequence motifs of
S
-adenosylmethionine radical enzymes. The
bns
gene cluster, coding for enzymes involved in beta-oxidation reactions converting naphthyl-2-methyl-succinate to 2-naphthoyl-CoA, was found four intervening open reading frames further downstream. This cluster consists of eight genes (
bnsABCDEFGH
) corresponding to 8.1 kb, which are closely related to genes for enzymes involved in anaerobic toluene degradation within the denitrifiers “
Aromatoleum aromaticum
” EbN1,
Azoarcus
sp. strain T, and
Thauera aromatica
. Another contiguous DNA sequence harbors the gene for 2-naphthoyl-CoA reductase (
ncr
) and 16 additional genes that were found to be expressed in 2-methylnaphthalene-grown cells. These genes code for enzymes that were supposed to catalyze the dearomatization and ring cleavage reactions converting 2-naphthoyl-CoA to acetyl-CoA and CO
2
. Comparative sequence analysis of the four encoding subunits (
ncrABCD
) showed the gene product to have the closest similarity to the
Azoarcus
type of benzoyl-CoA reductase. The present work provides the first insight into the genetic basis of anaerobic 2-methylnaphthalene metabolism and delivers implications for understanding contaminant degradation.
Benzo[a]pyrene-induced neurobehavioral function and neurotransmitter alterations in coke oven workers
Authors: Niu Qiao , Zhang Hongmei , Li Xin , Li Meiqin 
Published: October 2009

ObjectiveTo study alterations in neurobehavioral function and neurotransmitter levels in coke oven workers occupationally exposed to benzo[a]pyrene (B[a]P) and explore possible biomarkers of B[a]P neurotoxicity.Methods176 coke oven workers occupationally exposed to B[a]P and 48 warehouse workers (controls) were investigated by questionnaire. Emotional and cognitive function was investigated using the WHO/NCTB. B[a]P concentrations in the working environment, concentrations of monoamine and amino acid neurotransmitters, and levels of urinary 1-hydroxypyrene (1-OH-Py) were assayed by HPLC. Spectrophotometry was used to determine choline neurotransmitter concentrations.ResultsAirborne B[a]P concentrations were higher in the coke oven plant than in the controls' workplace, and 1-OH-Py levels were significantly increased in coke workers compared to controls (p=0.000). Digital span and order digital span scores indicated that learning and memory were significantly decreased in coke oven workers (p=0.006). Concentrations of norepinephrine (NE), dopamine, 5-hydroxytryptamine and homovanillic acid were lower, while levels of 5-hydroxyindoleacetic acid were higher in the exposed group compared to controls; the difference in NE was significant (p=0.000). Aspartic acid and gamma-aminobutyric acid levels were significantly decreased in coke oven workers compared to controls (p=0.004 and p=0.004). Acetylcholine (Ach) concentration was four- to fivefold greater in coke oven workers than in controls, while acetylcholine esterase (AchE) activity was significantly decreased (p=0.000 and p=0.012). Statistical analysis showed that digital span and order digital span scores were negatively correlated to Ach and positively correlated to AchE.ConclusionOccupational B[a]P exposure may reduce coke oven workers' neurobehavioral function and monoamine, amino acid and choline neurotransmitter levels. Moreover, Ach and AchE correlated with neurobehavioral function; AchE has poor specificity, but Ach is a potential biomarker of B[a]P neurotoxicity in coke oven workers.
Yam (Dioscorea pseudojaponicaYamamoto) Ameliorates Cognition Deficit and Attenuates Oxidative Damage in Senescent Mice Induced by D-Galactose
Authors: Chiu Chuan-Sung , Deng Jeng-Shyan , Hsieh Ming-Tsuen , Fan Ming-Jen , Lee Min-Min , Chueh Fu-Shin , Han Chien-Kuo , Lin Ying-Chih , Peng Wen-Huang 
Published: October 2009

This study attempted to access the neuroprotective effect of yam (Dioscorea pseudojaponica Yamamoto) on the senescent mice induced by D-gal. The mice in the experiments were administered orally with yam (20, 100 or 500 mg/kg for 4 weeks, from the sixth week). The learning and memory abilities of the mice in Morris water maze test and the mechanisms involved in the neuroprotective effect of yam on the mice brain tissue were investigated. The content of diosgenin in the yam was also detected by using HPLC.Mice treated with yam were found to significantly improve their learning and memory abilities in Morris water maze test compared to those treated with D-gal (200 mg/kg for 10 weeks). In addition, yam was also found to increase the activities of superoxide dismutase (SOD) and glutathione peroxidase (GPx) and decrease the malondialdehyde (MDA) level on the brains of D-gal treated mice. Finally, the amount of diosgenin in the yam was 5.49 mg/g extract.To sum up, these results indicate that yam had the potential to be a useful treatment for cognitive impairment in TCM. Its beneficial effect may be partly mediated via enhancing endogenous antioxidant enzymatic activities.
VASOMOTION SPECTRA AND PRINCIPAL COMPONENTS OF POOLED MEASURES PREDICT DIABETES IN MONKEYS
Authors: TIGNO X. T. , HANSEN B. C. , ALBANO A. M. 
Published: October 2009

Diabetic neuropathy may be a result of disturbed vasomotion, the spontaneous rhythmic oscillations of vessel diameter, flow, or pressure in the microcirculation. To examine the differences in vasomotion prior to overt diabetes and with diagnosed diabetes, metabolic and blood flow measurements were obtained from three metabolically distinct groups of nonhuman primates: normoglycemic, metabolic syndrome/prediabetic, and overtly diabetic. Three of these indices characterize spectral properties of microcirculatory vasomotion: (1) the fraction of spectral power in a band around 2.0 Hz, (2) the ratio of spectral power in a band around 1.0 Hz to that around 2.0 Hz, (3) the Hurst exponent. The rest were more traditional measures including (4) fasting plasma Glucose (FPG), (5) glycosylated hemoglobin level (HbA1c), (6) fasting insulin levels (IRI), (7) average systolic blood pressure, and (8) average diastolic blood pressure. We found that the mean fraction of the spectral power of the vasomotion in the 2 Hz band is significantly greater in the nondiabetic than in the diabetic group. Similarly, the ratio of the spectral power in the 1.0 Hz band to that in the 2.0 Hz band was significantly higher among the diabetic subjects than in the nondiabetic and prediabetic subjects. Principal component analysis (PCA) of the ensemble of eight measures revealed that values of the first principal component in the diabetic group were highly and significantly different from those of the normal and prediabetic groups, which are also significantly different from each other. Furthermore, the spectral measures of vasomotion offered a distinct advantage over the traditional physiological variables in distinguishing the normal subjects from the prediabetic group, and are likely to reflect very early autonomic dysfunction.
Transient Environmental Sensitivities of Explicitly Simulated Tropical Convection
Authors: Tulich Stefan N. , Mapes Brian E. 
Published: October 2009

Abstract
A three-dimensional cloud-resolving model, maintained in a statistically steady convecting state by tropics-like forcing, is subjected to sudden (10 min) stimuli consisting of horizontally homogeneous temperature and/or moisture sources with various profiles. Ensembles of simulations are used to increase the statistical robustness of the results and to assess the deterministic nature of the model response for domain sizes near contemporary global model resolution. The response to middle- and upper-tropospheric perturbations is predominantly local in the vertical: convection damps the imposed stimulus over a few hours. Low-level perturbations are similarly damped, but also produce a vertically nonlocal response: enhancement or suppression of new deep convective clouds extending above the perturbed level. Experiments show that the “effective inhibition layer” for deep convection is about 4 km deep, far deeper than traditional convective inhibition defined for undilute lifted parcels. Both the local and nonlocal responses are remarkably linear but can be highly stochastic, especially if deep convection is only intermittently present (small domains, weak forcing). Quantitatively, temperature-versus-moisture perturbations in a ratio corresponding to adiabatic vertical displacements produce responses of roughly equal magnitude. However, moisture perturbations seem to provoke the nonlocal (upward spreading) type of response more effectively. This nonlocal part of the response is also more effective when background forcing intensity is weak. Only at very high intensity does the response approach the limits of purely local damping and pure determinism that would be most convenient for theory and parameterization.
A Conductivity Sensor for Nearbed Sediment Concentration Profiling
Authors: Puleo Jack A. , Faries Joe , Davidson Michael , Hicks Betsy 
Published: October 2009

Abstract
A new sensor that measures the vertical profile of nearbed sediment concentration is described. The conductivity-based sensor is composed of eight electrode pairs separated in the vertical by 2.5 × 10−3 m. Electrode pairs are sampled at 16 Hz, with higher rates achievable. Each electrode pair response is linear over the range of conductivity tested from 0.2 to 0.65 mS cm−1 that exceeds the range of conductivity values corresponding to sediment–water mixtures from clear water to the packed bed limit of 0.65 m3 m−3. A laboratory test over a planar sloping beach indicates the capability of the sensor to simultaneously quantify sediment concentration profiles from roughly 0.01 m below to 0.1 m above the at-rest bed. The data indicate that the upper few millimeters of the bed are highly mobile and that bed dilation and sediment mobility vary considerably over a swash cycle.
Molecular and functional analysis of the stem cell compartment of chronic myelogenous leukemia reveals the presence of a CD34− cell population with intrinsic resistance to imatinib
Authors: Lemoli Roberto M. , Salvestrini Valentina , Bianchi Elisa , Bertolini Francesco , Fogli Miriam , Amabile Marilina , Tafuri Agostino , Salati Simona , Zini Roberta , Testoni Nicoletta , Rabascio Cristina , Rossi Lara , Martin-Padura Ines , Castagnetti Fausto , Marighetti Paola , Martinelli Giovanni , Baccarani Michele , Ferrari Sergio , Manfredini Rossella 
Published: October 2009

Abstract
We show the molecular and functional characterization of a novel population of lineage-negative CD34-negative (Lin−CD34−) hematopoietic stem cells from chronic myelogenous leukemia (CML) patients at diagnosis. Molecular karyotyping and quantitative analysis of BCR-ABL transcript demonstrated that approximately one-third of CD34− cells are leukemic. CML Lin−CD34− cells showed kinetic quiescence and limited clonogenic capacity. However, stroma-dependent cultures induced CD34 expression on some cells and cell cycling, and increased clonogenic activity and expression of BCR-ABL transcript. Lin−CD34− cells showed hematopoietic cell engraftment rate in 2 immunodeficient mouse strains similar to Lin-CD34+ cells, whereas endothelial cell engraftment was significantly higher. Gene expression profiling revealed the down-regulation of cell-cycle arrest genes and genes involved in antigen presentation and processing, while the expression of genes related to tumor progression, such as angiogenic factors, was strongly up-regulated compared with normal counterparts. Phenotypic analysis confirmed the significant down-regulation of HLA class I and II molecules in CML Lin−CD34− cells. Imatinib mesylate did not reduce fusion transcript levels, BCR-ABL kinase activity, and clonogenic efficiency of CML Lin−CD34− cells in vitro. Moreover, leukemic CD34− cells survived exposure to BCR-ABL inhibitors in vivo. Thus, we identified a novel CD34− leukemic stem cell subset in CML with peculiar molecular and functional characteristics.
Anticoagulant and antithrombotic properties of platelet protease nexin-1
Authors: Boulaftali Yacine , Adam Frédéric , Venisse Laurence , Ollivier Véronique , Richard Benjamin , Taieb Sabrina , Monard Denis , Favier Rémi , Alessi Marie-Christine , Bryckaert Marijke , Arocas Véronique , Jandrot-Perrus Martine , Bouton Marie-Christine 
Published: October 2009

AbstractProtease nexin–1 (PN-1) is a serpin that inhibits plasminogen activators, plasmin, and thrombin. PN-1 is barely detectable in plasma but is expressed by platelets. Here, we studied platelet PN-1 in resting and activated conditions and its function in thrombosis. Studies on human platelets from healthy donors and from patients with a Gray platelet syndrome demonstrate that PN-1 is present both at the platelet surface and in α-granules. The role of PN-1 was investigated in vitro using human platelets incubated with a blocking antibody and using platelets from PN-1–deficient mice. Both approaches indicate that platelet PN-1 is active on thrombin and urokinase-type plasminogen activator. Blockade and deficiency of platelet PN-1 result in accelerated and increased tissue factor-induced thrombin generation as indicated by calibrated automated thrombography. Moreover, platelets from PN-1–deficient mice respond to subthreshold doses of thrombin, as assessed by P-selectin expression and platelet aggregation. Thrombus formation, induced ex vivo by collagen in blood flow conditions and in vivo by FeCl3-induced injury, is significantly increased in PN-1–deficient mice, demonstrating the antithrombotic properties of platelet PN-1. Platelet PN-1 is thus a key player in the thrombotic process, whose negative regulatory role has been, up to now, markedly underestimated.
An insight into the role of phosphotransacetylase (pta) and the acetate/acetyl-CoA node in Escherichia coli
Authors: Castaño-Cerezo Sara , Pastor José M , Renilla Sergio , Bernal Vicente , Iborra José L , Cánovas Manuel 
Published: October 2009

Abstract

Background
Acetate metabolism in Escherichia coli plays an important role in the control of the central metabolism and in bioprocess performance. The main problems related to the use of E. coli as cellular factory are i) the deficient utilization of carbon source due to the excretion of acetate during aerobic growth, ii) the inhibition of cellular growth and protein production by acetate and iii) the need for cofactor recycling (namely redox coenzymes and free CoASH) to sustain balanced growth and cellular homeostasis.

Results
This work analyzes the effect of mutations in the acetate excretion/assimilation pathways, acetyl-CoA synthethase (acs) and phosphotransacetylase (pta), in E. coli BW25113 grown on glucose or acetate minimal media. Biomass and metabolite production, redox (NADH/NAD+) and energy (ATP) state, enzyme activities and gene expression profiles related to the central metabolism were analyzed. The knock-out of pta led to a more altered phenotype than that of acs. Deletion of pta reduced the ability to grow on acetate as carbon source and strongly affected the expression of several genes related to central metabolic pathways.

Conclusion
Results showed that pta limits biomass yield in aerobic glucose cultures, due to acetate production (overflow metabolism) and its inefficient use during glucose starvation. Deletion of pta severely impaired growth on acetate minimal medium and under anaerobiosis due to decreased acetyl-coenzyme A synthethase, glyoxylate shunt and gluconeogenic activities, leading to lower growth rate. When acetate is used as carbon source, the joint expression of pta and acs is crucial for growth and substrate assimilation, while pta deletion severely impaired anaerobic growth. Finally, at an adaptive level, pta deficiency makes the strain more sensitive to environmental changes and de-regulates the central metabolism.
Co-transfection of plasmid DNA and laser-generated gold nanoparticles does not disturb the bioactivity of GFP-HMGB1 fusion protein
Authors: Petersen Svea , Soller Jan T , Wagner Siegfried , Richter Andreas , Bullerdiek Jörn , Nolte Ingo , Barcikowski Stephan , Escobar Hugo Murua 
Published: October 2009

Abstract
Ultrashort pulsed laser ablation in liquids represents a powerful tool for the generation of pure gold nanoparticles (AuNPs) avoiding chemical precursors and thereby making them especially interesting for biomedical applications. However, because of their electron accepting properties, laser-generated AuNPs might affect biochemical properties of biomolecules, which often adsorb onto the nanoparticles. We investigated possible effects of such laser-generated AuNPs on biological functionality of DNA molecules. We tested four differently sized and positively charged AuNPs by incubating them with recombinant eGFP-C1-HMGB1 DNA expression plasmids that code for eGFP fusion proteins and contain the canine architectural transcription factor HMGB1. We were able to show that successfully transfected mammalian cells are still able to synthesize and process the fusion proteins. Our observations revealed that incubation of AuNP with the plasmid DNA encoding the recombinant canine HMGB1 neither prevented the mediated uptake of the vector through the plasma membrane in presence of a transfection reagent nor had any effect on the transport of the synthesized fusion proteins to the nuclei. Biological activity of the recombinant GFP-HMGB1 fusion protein appears to have not been affected either, as a strong characteristic protein accumulation in the nucleus could be observed. We also discovered that transfection efficiencies depend on the size of AuNP. In conclusion, our data indicate that laser-generated AuNPs present a good alternative to chemically synthesized nanoparticles for use in biomedical applications.
The transplant iron score as a predictor of stem cell transplant survival
Authors: Storey Jonathan A , Connor Rebecca F , Lewis Zachary T , Hurd David , Pomper Gregory , Keung Yi K , Grover Manisha , Lovato James , Torti Suzy V , Torti Frank M , Molnár István 
Published: October 2009

Abstract
Recent studies have suggested that the presence of iron overload prior to stem cell transplantation is associated with decreased survival. Within these studies, the criteria used to define iron overload have varied considerably. Given the lack of consensus regarding the definition of iron overload in the transplant setting, we sought to methodically examine iron status among transplant patients. We studied 78 consecutive patients at risk for transfusion-related iron overload (diagnoses included AML, ALL, MDS, and aplastic anemia) who received either autologous or allogeneic stem cell transplant. Multiple measures of iron status were collected prior to transplantation and examined for their association with survival. Using this data, three potentially prognostic iron measures were identified and incorporated into a rational and unified scoring system. The resulting Transplant Iron Score assigns a point for each of the following variables: (1) greater than 25 red cell units transfused prior to transplantation; (2) serum ferritin > 1000 ng/ml; and (3) a semi-quantitative bone marrow iron stain of 6+. In our cohort, the score (range 0 to 3) was more closely associated with survival than any available single iron parameter. In multivariate analysis, we observed an independent effect of iron overload on transplant survival (p = 0.01) primarily attributable to an increase in early treatment-related deaths (p = 0.02) and lethal infections. In subgroup analysis, the predictive power of the iron score was most pronounced among allogeneic transplant patients, where a high score (≥ 2) was associated with a 50% absolute decrease in survival at one year. In summary, our results lend further credence to the notion that iron overload prior to transplant is detrimental and suggest iron overload may predispose to a higher rate of lethal infections.