bluuebunny/crossref_metadata_2025_split huggingface dataset:
Citrate Uptake in Exchange with Intermediates in the Citrate Metabolic Pathway in
Lactococcus lactis
IL1403
Authors: Pudlik Agata M. , Lolkema Juke S. 
Published: November 2010

ABSTRACT

Carbohydrate/citrate cometabolism in
Lactococcus lactis
results in the formation of the flavor compound acetoin. Resting cells of strain IL1403(pFL3) rapidly consumed citrate while producing acetoin when substoichiometric concentrations of glucose or
l
-lactate were present. A proton motive force was generated by electrogenic exchange of citrate and lactate catalyzed by the citrate transporter CitP and proton consumption in decarboxylation reactions in the pathway. In the absence of glucose or
l
-lactate, citrate consumption was biphasic. During the first phase, hardly any citrate was consumed. In the second phase, citrate was converted rapidly, but without the formation of acetoin. Instead, significant amounts of the intermediates pyruvate and α-acetolactate, and the end product acetate, were excreted from the cells. It is shown that the intermediates and acetate are excreted in exchange with the uptake of citrate catalyzed by CitP. The availability of exchangeable substrates in the cytoplasm determines both the rate of citrate consumption and the end product profile. It follows that citrate metabolism in
L. lactis
IL1403(pFL3) splits up in two routes after the formation of pyruvate, one the well-characterized route yielding acetoin and the other a new route yielding acetate. The flux distribution between the two branches changes from 85:15 in the presence of
l
-lactate to 30:70 in the presence of pyruvate. The proton motive force generated was greatest in the presence of
l
-lactate and zero in the presence of pyruvate, suggesting that the pathway to acetate does not generate proton motive force.
Leprosy and the Human Genome
Authors: Misch Elizabeth A. , Berrington William R. , Vary James C. , Hawn Thomas R. 
Published: November 2010

SUMMARYDespite the availability of effective treatment for several decades, leprosy remains an important medical problem in many regions of the world. Infection withMycobacterium lepraecan produce paucibacillary disease, characterized by well-formed granulomas and a Th1 T-cell response, or multibacillary disease, characterized by poorly organized cellular infiltrates and Th2 cytokines. These diametric immune responses confer states of relative resistance or susceptibility to leprosy, respectively, and have well-defined clinical manifestations. As a result, leprosy provides a unique opportunity to dissect the genetic basis of humanin vivoimmunity. A series of studies over the past 40 years suggests that host genes influence the risk of leprosy acquisition and the predilection for different clinical forms of the disease. However, a comprehensive, cellular, and molecular view of the genes and variants involved is still being assembled. In this article, we review several decades of human genetic studies of leprosy, including a number of recent investigations. We emphasize genetic analyses that are validated by the replication of the same phenotype in independent studies or supported by functional experiments demonstrating biological mechanisms of action for specific polymorphisms. Identifying and functionally exploring the genetic and immunological factors that underlie human susceptibility to leprosy have yielded important insights intoM. lepraepathogenesis and are likely to advance our understanding of the immune response to other pathogenic mycobacteria. This knowledge may inform new treatment or vaccine strategies for leprosy or tuberculosis.
Folded DNA in Action: Hairpin Formation and Biological Functions in Prokaryotes
Authors: Bikard David , Loot Céline , Baharoglu Zeynep , Mazel Didier 
Published: November 2010

SUMMARY
Structured forms of DNA with intrastrand pairing are generated in several cellular processes and are involved in biological functions. These structures may arise on single-stranded DNA (ssDNA) produced during replication, bacterial conjugation, natural transformation, or viral infections. Furthermore, negatively supercoiled DNA can extrude inverted repeats as hairpins in structures called cruciforms. Whether they are on ssDNA or as cruciforms, hairpins can modify the access of proteins to DNA, and in some cases, they can be directly recognized by proteins. Folded DNAs have been found to play an important role in replication, transcription regulation, and recognition of the origins of transfer in conjugative elements. More recently, they were shown to be used as recombination sites. Many of these functions are found on mobile genetic elements likely to be single stranded, including viruses, plasmids, transposons, and integrons, thus giving some clues as to the manner in which they might have evolved. We review here, with special focus on prokaryotes, the functions in which DNA secondary structures play a role and the cellular processes giving rise to them. Finally, we attempt to shed light on the selective pressures leading to the acquisition of functions for DNA secondary structures.
Nitrogen Fixation and Hydrogen Metabolism in Cyanobacteria
Authors: Bothe Hermann , Schmitz Oliver , Yates M. Geoffrey , Newton William E. 
Published: November 2010

SUMMARYThis review summarizes recent aspects of (di)nitrogen fixation and (di)hydrogen metabolism, with emphasis on cyanobacteria. These organisms possess several types of the enzyme complexes catalyzing N2fixation and/or H2formation or oxidation, namely, two Mo nitrogenases, a V nitrogenase, and two hydrogenases. The two cyanobacterial Ni hydrogenases are differentiated as either uptake or bidirectional hydrogenases. The different forms of both the nitrogenases and hydrogenases are encoded by different sets of genes, and their organization on the chromosome can vary from one cyanobacterium to another. Factors regulating the expression of these genes are emerging from recent studies. New ideas on the potential physiological and ecological roles of nitrogenases and hydrogenases are presented. There is a renewed interest in exploiting cyanobacteria in solar energy conversion programs to generate H2as a source of combustible energy. To enhance the rates of H2production, the emphasis perhaps needs not to be on more efficient hydrogenases and nitrogenases or on the transfer of foreign enzymes into cyanobacteria. A likely better strategy is to exploit the use of radiant solar energy by the photosynthetic electron transport system to enhance the rates of H2formation and so improve the chances of utilizing cyanobacteria as a source for the generation of clean energy.
Fold–thrust belts: overlooked provinces or justifiably avoided?
Authors: Goffey Graham P. , Craig Jonathan , Needham Tim , Scott Robert 
Published: November 2010

Abstract
This volume results from a conference intended to assess the exploration and exploitation primarily of onshore fold–thrust belts. These are commonly perceived as ‘difficult’ places to explore and therefore are often avoided by companies. However, fold–thrust belts host large oil and gas fields and barriers to effective exploration mean that substantial resources may remain.
This volume shows how evaluation techniques have developed over time. It is possible in certain circumstances to achieve good 3D seismic data. Structural restoration techniques have moved into the 3D domain and simple thermal constraints can be enhanced by using more sophisticated palaeo-thermal indicators to more accurately model burial and uplift evolution of source and reservoirs. Awareness of the influence of pre-thrust structure and stratigraphy and of hybrid thick and thin-skinned deformation styles is supplementing the simplistic thin-skinned fault-bend and fault propagation models employed in earlier exploration.
The ‘learning curve’ in fold–thrust belt exploration has not been steep and further improvement seems likely to be a slow, expensive and iterative process with information from outcrop, well penetration and slowly improving seismic data. Industry and academia need together to develop and continually improve the necessary understanding of subsurface geometries, reservoir and charge evolution and timing.
Spontaneous fluid emissions in the Northern Apennines: geochemistry, structures and implications for the petroleum system
Authors: Capozzi Rossella , Picotti Vincenzo 
Published: November 2010

Abstract
Natural seeps in the Northern Apennines document a variability of fluids and reservoirs in terms of origin, age and evolution. Their spatial distribution appears controlled by the presence or absence of the tectonic overburden provided by the Ligurian nappe. The general trend of deepening of the Mesozoic basement toward the internal part of the thrust belt is reflected by the nature of the seeps, characterized by thermogenic methane and oil at the foothills, whereas the innermost seeps show occurrence of dry thermogenic gas suggesting overcooking of the residual oil. At the front of the Ligurian nappe, or in places never covered by it, the seepages are associated with biogenic methane related to bacterial degradation of the organic-rich intervals occurring in the Pliocene and Pleistocene marine succession. The coupling of geochemical and structural analysis allows reconstructing the tectono-thermal evolution of the belt, improving our knowledge on the processes acting within the reservoir and controlling important parameters of the petroleum system, such as the reservoir porosity and its modifications, and the migration patterns.
Deepwater folding and thrusting offshore NW Borneo, SE Asia
Authors: Hesse S. , Back S. , Franke D. 
Published: November 2010

Abstract
The slope and deepwater portion of the offshore NW Borneo continental margin hosts a number of proven hydrocarbon accumulations. Reprocessed and post-stack depth-migrated regional 2D seismic data reveal the occurrence of an extensive series of deepwater folds located at the leading edges of imbricate thrusts. Typical thrust-top folds include (1) anticlines characterized by large interlimb angles that lack a sea-floor expression; (2) anticlines with medium interlimb angles that show a clear sea-floor expression and normal faulting in the crest; and (3) anticlines with small to medium interlimb angles, a clear sea-floor expression and intensive crestal faulting associated with partial crestal failure. The different fold types occur at specific locations within the fold–thrust system, the widest and youngest anticlines near the present-day thrust front, and the narrowest and oldest folds in the most landward parts of the fold–thrust belt. Geometric restoration of the deepwater fold–thrust system along six regional shelf-to-basin cross sections provides incremental measurements of fault- and fold-related shortening for the time between the Miocene and present day in deepwater NW Borneo. Across the study area, the main thrust and fold activity appears to be largely of Pliocene–Holocene age. An apparent maximum of both incremental and total shortening is located in the central part of the study area. This location coincides with the maximum width of the fold–thrust belt and the preferential location for the development of the most recent deepwater anticlines.
High Levels of Systemic Myeloperoxidase Are Associated With Coronary Plaque Erosion in Patients With Acute Coronary Syndromes
Authors: Ferrante Giuseppe , Nakano Masataka , Prati Francesco , Niccoli Giampaolo , Mallus Maria T. , Ramazzotti Vito , Montone Rocco A. , Kolodgie Frank D. , Virmani Renu , Crea Filippo 
Published: November 2010

Background—
Systemic levels of myeloperoxidase predict prognosis in patients with acute coronary syndromes and are considered a marker of plaque vulnerability. It is not known whether myeloperoxidase is associated with different coronary morphologies (ie, rupture or erosion of the culprit lesion) in patients with acute coronary syndrome.

Methods and Results—

Twenty-five consecutive patients (aged 67±11 years; 15 men [60%]; 13 [52%] with non–ST-segment elevation acute coronary syndrome and 12 [48%] with acute ST-segment elevation myocardial infarction) were enrolled. Optical coherence tomography classified the culprit lesion as ruptured in 18 (72%) or eroded in 7 patients (28%) and detected intraluminal thrombus in 89% of ruptured plaques and 100% of eroded plaques. Baseline systemic levels of serum myeloperoxidase were significantly higher in patients with an eroded plaque than in those with a ruptured plaque (median, 2500 ng/mL; 25th to 75th percentile, 1415 to 2920 versus median, 707 ng/mL; 25th to 75th percentile, 312 to 943;
P
=0.001), whereas C-reactive protein levels did not differ significantly (median, 11.3 mg/L; 25th to 75th percentile, 1.3 to 28.5 versus median, 3.9 mg/L; 25th to 75th percentile, 1.3 to 17.8;
P
=0.76, respectively). In addition, the density of myeloperoxidase-positive cells within thrombi overlying plaques in postmortem coronary specimens retrieved from sudden coronary death victims was significantly higher in lesions with erosion (n=11) than ruptures (n=11) (median, 1584; 25th to 75th percentile, 1088 to 2135 cells/mm
2
versus median, 579; 25th to 75th percentile, 442 to 760 cells/mm
2
;
P
=0.0012).

Conclusions—
Systemic myeloperoxidase levels are significantly elevated in patients with acute coronary syndrome presenting with eroded culprit plaque compared with patients presenting with ruptured culprit plaque. Consistently, in postmortem coronary specimens, luminal thrombi superimposed on eroded plaques contain a higher density of myeloperoxidase-positive cells than thrombi superimposed on ruptured plaques. This study supports the concept that elevations in selective inflammatory biomarkers reflect specific acute complications of coronary atherosclerosis.
Myocardial Steatosis and Biventricular Strain and Strain Rate Imaging in Patients With Type 2 Diabetes Mellitus
Authors: Ng Arnold C.T. , Delgado Victoria , Bertini Matteo , van der Meer Rutger W. , Rijzewijk Luuk J. , Hooi Ewe See , Siebelink Hans-Marc , Smit Johannes W.A. , Diamant Michaela , Romijn Johannes A. , de Roos Albert , Leung Dominic Y. , Lamb Hildo J. , Bax Jeroen J. 
Published: November 2010

Background—
Magnetic resonance spectroscopy can quantify myocardial triglyceride content in type 2 diabetic patients. Its relation to alterations in left (LV) and right (RV) ventricular myocardial functions is unknown.

Methods and Results—

A total of 42 men with type 2 diabetes mellitus were recruited. Exclusion criteria included hemoglobin A
1c
>8.5, known cardiovascular disease, diabetes-related complications, or blood pressure >150/85 mm Hg. Myocardial ischemia was excluded by a negative dobutamine stress test. LV and RV volumes and ejection fraction were quantified by magnetic resonance imaging. LV global longitudinal and RV free wall longitudinal strain, systolic strain rate, and diastolic strain rate were quantified by echocardiographic speckle tracking analyses. Myocardial triglyceride content was quantified by magnetic resonance spectroscopy and dichotomized on the basis of the median value of 0.76. The median age was 59 years (25th and 75th percentiles, 54 and 62 years). Median diabetes diagnosis duration was 4 years, and median glycohemoglobin level was 6.2 (25th and 75th percentiles, 5.9 and 6.8). There were no differences in LV and RV end-diastolic and end-systolic volume indexes and ejection fraction between patients with high (≥0.76) and those with low (<0.76) myocardial triglyceride content. However, patients with high myocardial triglyceride content had greater impairment of LV and RV myocardial strain and strain rate. The myocardial triglyceride content was an independent correlate of LV and RV longitudinal strain, systolic strain rate, and diastolic strain rate.

Conclusions—
High myocardial triglyceride content is associated with more pronounced impairment of LV and RV functions in men with uncomplicated type 2 diabetes mellitus.
Improving Predictions of Water and Heat Fluxes by Assimilating MODIS Land Surface Temperature Products into the Common Land Model
Authors: Xu Tongren , Liu Shaomin , Liang Shunlin , Qin Jun 
Published: November 2010

AbstractFour data assimilation scheme combinations derived from two strategies and two optimization algorithms [the ensemble Kalman filter (EnKF) and the shuffled complex evolution method developed at The University of Arizona (SCE-UA)] are developed based on the Common Land Model (CLM) to improve predictions of water and heat fluxes. The first strategy is constructed through adjusting the soil temperature, while the second strategy adjusts the soil moisture. Moderate Resolution Imaging Spectroradiometer (MODIS) land surface temperature (LST) products are compared with ground-measured surface temperature, and assimilated into the CLM. The relationship equation between the MODIS LST products and CLM surface temperature is taken as the observation operator and the root-mean-square error (RMSE) is applied as the observation error. The assimilation results are validated by measurements from six observation sites located in Germany, the United States, and China. Results indicate that the developed data assimilation schemes can improve estimates of water and heat fluxes. Overall, strategy 2 is superior to strategy 1 when using the same optimization algorithm. The EnKF algorithm performs slightly better than the SCE-UA algorithm when using the same strategy. Strategy 2 combined with the EnKF algorithm performs best for water and heat fluxes, and the reductions in the RMSE are found to be 24.0 and 15.2 W m−2 for sensible and latent heat fluxes, respectively. The joint assimilation of the MODIS LST and soil moisture observations can produce better results for strategy 2 with the SCE-UA. Since preprocessing model parameters are used in this study, the uncertainties in the model parameters may have resulted in suboptimal assimilation results. Therefore, model calibrations should be conducted in the future.
Diabetes Oral Medication Initiation and Intensification
Authors: Grant Richard W. , Pabon-Nau Lina , Ross Kaile M. , Youatt Emily J. , Pandiscio Jennifer C. , Park Elyse R. 
Published: November 2010

Purpose The purpose of this study was to compare patient perceptions about medication management with principles underlying American Diabetes Association (ADA) published treatment algorithms. Methods Six focus groups (4 English and 2 Spanish) were conducted with 50 patients with type 2 diabetes. Patients were asked about their prior experiences with initiating and changing oral medicines. They were also shown a medication plan for a hypothetical patient depicting future potential changes to achieve glycemic control. Coded responses were mapped to 3 concepts implicit in the ADA recommended treatment algorithm: (1) prescribing medicines to achieve A1c goal is beneficial, (2) medical regimens are generally intensified, and (3) intensification should be timely. Results Patient perceptions contrasted markedly with the treatment algorithm: (1) most patients had negative perceptions of medication initiation, viewing this event as evidence of personal failure and an increased burden; (2) patients equated medication intensification with increased risk for diabetes-related complications (rather than a step to reduce future risk) and viewed de-escalation as a primary goal; and (3) no patients expressed concerns about delays in medication intensification. Patients responded very favorably to an individualized medication plan depicting future potential changes. Conclusions Patients in this study described a conceptual model for medication therapy that contrasted in critical ways from the principles of current treatment guidelines. Underscoring the key role of patient-provider communication, the results suggest that effective counseling should also include an informed discussion of future medication intensification.
Anticipation in familial hematologic malignancies
Authors: Tegg Elizabeth M. , Thomson Russell J. , Stankovich Jim M. , Banks Annette , Marsden Katherine A. , Lowenthal Ray M. , Foote Simon J. , Dickinson Joanne L. 
Published: November 2010

AbstractWe describe a collection of 11 families with ≥ 2 generations of family members whose condition has been diagnosed as a hematologic malignancy. In 9 of these families there was a significant decrease in age at diagnosis in each subsequent generation (anticipation). The mean age at diagnosis in the first generation was 67.8 years, 57.1 years in the second, and 41.8 years in the third (P < .0002). This was confirmed in both direct parent-offspring pairs with a mean reduction of 19 years in the age at diagnosis (P = .0087) and when the analysis was repeated only including cases of mature B-cell neoplasm (P = .0007). We believe that these families provide further insight into the nature of the underlying genetic mechanism of predisposition in these families.
Global genome analysis of the shikimic acid pathway reveals greater gene loss in host-associated than in free-living bacteria
Authors: Zucko Jurica , Dunlap Walter C , Shick J Malcolm , Cullum John , Cercelet François , Amin Bijal , Hammen Lena , Lau Timothy , Williams Jamal , Hranueli Daslav , Long Paul F 
Published: November 2010

Abstract

Background
A central tenet in biochemistry for over 50 years has held that microorganisms, plants and, more recently, certain apicomplexan parasites synthesize essential aromatic compounds via elaboration of a complete shikimic acid pathway, whereas metazoans lacking this pathway require a dietary source of these compounds. The large number of sequenced bacterial and archaean genomes now available for comparative genomic analyses allows the fundamentals of this contention to be tested in prokaryotes. Using Hidden Markov Model profiles (HMM profiles) to identify all known enzymes of the pathway, we report the presence of genes encoding shikimate pathway enzymes in the hypothetical proteomes constructed from the genomes of 488 sequenced prokaryotes.

Results
Amongst free-living prokaryotes most Bacteria possess, as expected, genes encoding a complete shikimic acid pathway, whereas of the culturable Archaea, only one was found to have a complete complement of recognisable enzymes in its predicted proteome. It may be that in the Archaea, the primary amino-acid sequences of enzymes of the pathway are highly divergent and so are not detected by HMM profiles. Alternatively, structurally unrelated (non-orthologous) proteins might be performing the same biochemical functions as those encoding recognized genes of the shikimate pathway. Most surprisingly, 30% of host-associated (mutualistic, commensal and pathogenic) bacteria likewise do not possess a complete shikimic acid pathway. Many of these microbes show some degree of genome reduction, suggesting that these host-associated bacteria might sequester essential aromatic compounds from a parasitised host, as a 'shared metabolic adaptation' in mutualistic symbiosis, or obtain them from other consorts having the complete biosynthetic pathway. The HMM results gave 84% agreement when compared against data in the highly curated BioCyc reference database of genomes and metabolic pathways.

Conclusions
These results challenge the conventional belief that the shikimic acid pathway is universal and essential in prokaryotes. The possibilities that non-orthologous enzymes catalyse reactions in this pathway (especially in the Archaea), or that there exist specific uptake mechanisms for the acquisition of shikimate intermediates or essential pathway products, warrant further examination to better understand the precise metabolic attributes of host-beneficial and pathogenic bacteria.