bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aggregate Size and Architecture Determine Microbial Activity Balance for One-Stage Partial Nitritation and Anammox
Authors: Vlaeminck Siegfried E. , Terada Akihiko , Smets Barth F. , De Clippeleir Haydée , Schaubroeck Thomas , Bolca Selin , Demeestere Lien , Mast Jan , Boon Nico , Carballa Marta , Verstraete Willy 
Published: December 2009

ABSTRACT
Aerobic ammonium-oxidizing bacteria (AerAOB) and anoxic ammonium-oxidizing bacteria (AnAOB) cooperate in partial nitritation/anammox systems to remove ammonium from wastewater. In this process, large granular microbial aggregates enhance the performance, but little is known about granulation so far. In this study, three suspended-growth oxygen-limited autotrophic nitrification-denitrification (OLAND) reactors with different inoculation and operation (mixing and aeration) conditions, designated reactors A, B, and C, were used. The test objectives were (i) to quantify the AerAOB and AnAOB abundance and the activity balance for the different aggregate sizes and (ii) to relate aggregate morphology, size distribution, and architecture putatively to the inoculation and operation of the three reactors. A nitrite accumulation rate ratio (NARR) was defined as the net aerobic nitrite production rate divided by the anoxic nitrite consumption rate. The smallest reactor A, B, and C aggregates were nitrite sources (NARR, >1.7). Large reactor A and C aggregates were granules capable of autonomous nitrogen removal (NARR, 0.6 to 1.1) with internal AnAOB zones surrounded by an AerAOB rim. Around 50% of the autotrophic space in these granules consisted of AerAOB- and AnAOB-specific extracellular polymeric substances. Large reactor B aggregates were thin film-like nitrite sinks (NARR, <0.5) in which AnAOB were not shielded by an AerAOB layer. Voids and channels occupied 13 to 17% of the anoxic zone of AnAOB-rich aggregates (reactors B and C). The hypothesized granulation pathways include granule replication by division and budding and are driven by growth and/or decay based on species-specific physiology and by hydrodynamic shear and mixing.
Archaeal and Bacterial Communities Respond Differently to Environmental Gradients in Anoxic Sediments of a California Hypersaline Lake, the Salton Sea
Authors: Swan Brandon K. , Ehrhardt Christopher J. , Reifel Kristen M. , Moreno Lilliana I. , Valentine David L. 
Published: December 2009

ABSTRACT

Sulfidic, anoxic sediments of the moderately hypersaline Salton Sea contain gradients in salinity and carbon that potentially structure the sedimentary microbial community. We investigated the abundance, community structure, and diversity of
Bacteria
and
Archaea
along these gradients to further distinguish the ecologies of these domains outside their established physiological range. Quantitative PCR was used to enumerate 16S rRNA gene abundances of
Bacteria
,
Archaea
, and
Crenarchaeota
. Community structure and diversity were evaluated by terminal restriction fragment length polymorphism (T-RFLP), quantitative analysis of gene (16S rRNA) frequencies of dominant microorganisms, and cloning and sequencing of 16S rRNA.
Archaea
were numerically dominant at all depths and exhibited a lesser response to environmental gradients than that of
Bacteria
. The relative abundance of
Crenarchaeota
was low (0.4 to 22%) at all depths but increased with decreased carbon content and increased salinity. Salinity structured the bacterial community but exerted no significant control on archaeal community structure, which was weakly correlated with total carbon. Partial sequencing of archaeal 16S rRNA genes retrieved from three sediment depths revealed diverse communities of
Euryarchaeota
and
Crenarchaeota
, many of which were affiliated with groups previously described from marine sediments. The abundance of these groups across all depths suggests that many putative marine archaeal groups can tolerate elevated salinity (5.0 to 11.8% [wt/vol]) and persist under the anaerobic conditions present in Salton Sea sediments. The differential response of archaeal and bacterial communities to salinity and carbon patterns is consistent with the hypothesis that adaptations to energy stress and availability distinguish the ecologies of these domains.
Alanine Mutagenesis of the Primary Antigenic Escape Residue Cluster, C1, of Apical Membrane Antigen 1
Authors: Dutta Sheetij , Dlugosz Lisa S. , Clayton Joshua W. , Pool Christopher D. , Haynes J. David , Gasser Robert A. , Batchelor Adrian H. 
Published: December 2009

ABSTRACTAntibodies against apical membrane antigen 1 (AMA1) inhibit invasion ofPlasmodiummerozoites into red cells, and a large number of single nucleotide polymorphisms on AMA1 allow the parasite to escape inhibitory antibodies. The availability of a crystal structure makes it possible to test protein engineering strategies to develop a monovalent broadly reactive vaccine. Previously, we showed that a linear stretch of polymorphic residues (amino acids 187 to 207), localized within the C1 cluster on domain 1, conferred the highest level of escape from inhibitory antibodies, and these were termed antigenic escape residues (AER). Here we test the hypothesis that immunodampening the C1 AER will divert the immune system toward more conserved regions. We substituted seven C1 AER of the FVO strainPlasmodium falciparumAMA1 with alanine residues (ALA). The resulting ALA protein was less immunogenic than the native protein in rabbits. Anti-ALA antibodies contained a higher proportion of cross-reactive domain 2 and domain 3 antibodies and had higher avidity than anti-FVO. No overall enhancement of cross-reactive inhibitory activity was observed when anti-FVO and anti-ALA sera were compared for their ability to inhibit invasion. Alanine mutations at the C1 AER had shifted the immune response toward cross-strain-reactive epitopes that were noninhibitory, refuting the hypothesis but confirming the importance of the C1 cluster as an inhibitory epitope. We further demonstrate that naturally occurring polymorphisms that fall within the C1 cluster can predict escape from cross-strain invasion inhibition, reinforcing the importance of the C1 cluster genotype for antigenic categorization and allelic shift analyses in future phase 2b trials.
Role of RpoS in Virulence of Pathogens
Authors: Dong Tao , Schellhorn Herb E. 
Published: December 2009

ABSTRACT

Understanding mechanisms of bacterial pathogenesis is critical for infectious disease control and treatment. Infection is a sophisticated process that requires the participation of global regulators to coordinate expression of not only genes coding for virulence factors but also those involved in other physiological processes, such as stress response and metabolic flux, to adapt to host environments. RpoS is a key response regulator to stress conditions in
E
scherichia coli
and many other proteobacteria. In contrast to its conserved well-understood role in stress response, effects of RpoS on pathogenesis are highly variable and dependent on species. RpoS contributes to virulence through either enhancing survival against host defense systems or directly regulating expression of virulence factors in some pathogens, while RpoS is dispensable, or even inhibitory, to virulence in others. In this review, we focus on the distinct and niche-dependent role of RpoS in virulence by surveying recent findings in many pathogens.
Global Regulation of Gene Expression and Cell Differentiation inCaulobacter crescentusin Response to Nutrient Availability
Authors: England Jennifer C. , Perchuk Barrett S. , Laub Michael T. , Gober James W. 
Published: December 2009

ABSTRACTIn a developmental strategy designed to efficiently exploit and colonize sparse oligotrophic environments,Caulobacter crescentuscells divide asymmetrically, yielding a motile swarmer cell and a sessile stalked cell. After a relatively fixed time period under typical culture conditions, the swarmer cell differentiates into a replicative stalked cell. Since differentiation into the stalked cell type is irreversible, it is likely that environmental factors such as the availability of essential nutrients would influence the timing of the decision to abandon motility and adopt a sessile lifestyle. We measured two different parameters in nutrient-limited chemostat cultures, biomass concentration and the ratio of nonstalked to stalked cells, over a range of flow rates and found that nitrogen limitation significantly extended the swarmer cell life span. The transcriptional profiling experiments described here generate the first comprehensive picture of the global regulatory strategies used by an oligotroph when confronted with an environment where key macronutrients are sparse. The pattern of regulated gene expression in nitrogen- and carbon-limited cells shares some features in common with most copiotrophic organisms, but critical differences suggest thatCaulobacter, and perhaps other oligotrophs, have evolved regulatory strategies to deal distinctly with their natural environments. We hypothesize that nitrogen limitation extends the swarmer cell lifetime by delaying the onset of a sequence of differentiation events, which when initiated by the correct combination of external environmental cues, sets the swarmer cell on a path to differentiate into a stalked cell within a fixed time period.
Characterization of an ATP Translocase Identified in the Destructive Plant Pathogen “
Candidatus
Liberibacter asiaticus”
Authors: Vahling Cheryl M. , Duan Yongping , Lin Hong 
Published: December 2009

ABSTRACT

ATP/ADP translocases transport ATP across a lipid bilayer, which is normally impermeable to this molecule due to its size and charge. These transport proteins appear to be unique to mitochondria, plant plastids, and obligate intracellular bacteria. All bacterial ATP/ADP translocases characterized thus far have been found in endosymbionts of protozoa or pathogens of higher-order animals, including humans. A putative ATP/ADP translocase was uncovered during the genomic sequencing of the intracellular plant pathogen “
Candidatus
Liberibacter asiaticus,” the causal agent of citrus huanglongbing. Bioinformatic analysis of the protein revealed 12 transmembrane helices and predicted an isoelectric point of 9.4, both of which are characteristic of this family of proteins. The “
Ca.
Liberibacter asiaticus” gene (
nttA
) encoding the translocase was subsequently expressed in
Escherichia coli
and shown to enable
E.
coli
to import ATP directly into the cell. Competition assays with the heterologous
E. coli
system demonstrated that the translocase was highly specific for ATP and ADP but that other nucleotides, if present in high concentrations, could also be taken up and/or block the ability of the translocase to import ATP. In addition, a protein homologous to NttA was identified in “
Ca.
Liberibacter solanacearum,” the bacterium associated with potato zebra chip disease. This is the first reported characterization of an ATP translocase from “
Ca.
Liberibacter asiaticus,” indicating that some intracellular bacteria of plants also have the potential to import ATP directly from their environment.
In
Salmonella enterica
, 2-Methylcitrate Blocks Gluconeogenesis
Authors: Rocco Christopher J. , Escalante-Semerena Jorge C. 
Published: December 2009

ABSTRACT

Strains of
Salmonella enterica
serovar Typhimurium LT2 lacking a functional 2-methylcitric acid cycle (2-MCC) display increased sensitivity to propionate. Previous work from our group indicated that this sensitivity to propionate is in part due to the production of 2-methylcitrate (2-MC) by the Krebs cycle enzyme citrate synthase (GltA). Here we report
in vivo
and
in vitro
data which show that a target of the 2-MC isomer produced by GltA (2-MC
GltA
) is fructose-1,6-bisphosphatase (FBPase), a key enzyme in gluconeogenesis. Lack of growth due to inhibition of FBPase by 2-MC
GltA
was overcome by increasing the level of FBPase or by micromolar amounts of glucose in the medium. We isolated an
fbp
allele encoding a single amino acid substitution in FBPase (S123F), which allowed a strain lacking a functional 2-MCC to grow in the presence of propionate. We show that the 2-MC
GltA
and the 2-MC isomer synthesized by the 2-MC synthase (PrpC; 2-MC
PrpC
) are not equally toxic to the cell, with 2-MC
GltA
being significantly more toxic than 2-MC
PrpC
. This difference in 2-MC toxicity is likely due to the fact that as a
si
-citrate synthase, GltA may produce multiple isomers of 2-MC, which we propose are not substrates for the 2-MC dehydratase (PrpD) enzyme, accumulate inside the cell, and have deleterious effects on FBPase activity. Our findings may help explain human inborn errors in propionate metabolism.
Function of Ech Hydrogenase in Ferredoxin-Dependent, Membrane-Bound Electron Transport in
Methanosarcina mazei
Authors: Welte Cornelia , Kallnik Verena , Grapp Marcel , Bender Gunes , Ragsdale Steve , Deppenmeier Uwe 
Published: December 2009

ABSTRACT

Reduced ferredoxin is an intermediate in the methylotrophic and aceticlastic pathway of methanogenesis and donates electrons to membrane-integral proteins, which transfer electrons to the heterodisulfide reductase. A ferredoxin interaction has been observed previously for the Ech hydrogenase. Here we present a detailed analysis of a
Methanosarcina mazei
Δ
ech
mutant which shows decreased ferredoxin-dependent membrane-bound electron transport activity, a lower growth rate, and faster substrate consumption. Evidence is presented that a second protein whose identity is unknown oxidizes reduced ferredoxin, indicating an involvement in methanogenesis from methylated C
1
compounds.
Genome Sequence of the Cellulosome-Producing Mesophilic Organism
Clostridium cellulovorans
743B
Authors: Tamaru Yutaka , Miyake Hideo , Kuroda Kouichi , Nakanishi Akihito , Kawade Yujiro , Yamamoto Kousuke , Uemura Masaaki , Fujita Yasuhiro , Doi Roy H. , Ueda Mitsuyoshi 
Published: December 2009

ABSTRACT

Clostridium cellulovorans
743B was isolated from a wood chip pile and is an anaerobic and mesophilic spore-forming bacterium. This organism degrades native substrates in soft biomass such as corn fiber and rice straw efficiently by producing an extracellular enzyme complex called the cellulosome. Here we report the genome sequence of
C. cellulovorans
743B.
‘I am in blood Stepp'd in so far…’: ethical dilemmas and the sports team doctor
Authors: Devitt Brian Meldan , McCarthy Conor 
Published: December 2009

There are many ethical dilemmas that are unique to sports medicine because of the unusual clinical environment of caring for players within the context of a team whose primary objective is to win. Many of these ethical issues arise because the traditional relationship between doctor and patient is distorted or absent. The emergence of a doctor–patient–team triad has created a scenario in which the team’s priority can conflict with or even replace the doctor’s primary obligation to player well-being. As a result, the customary ethical norms that provide guidelines for most forms of clinical practice, such as patient autonomy and confidentiality, are not easily translated in the field of sports medicine. Sports doctors are frequently under intense pressure, whether implicit or explicit, from management, coaches, trainers and agents, to improve performance of the athlete in the short term rather than considering the long-term sequelae of such decisions. A myriad of ethical dilemmas are encountered, and for many of these dilemmas there are no right answers. In this article, a number of ethical principles and how they relate to sports medicine are discussed. To conclude, a list of guidelines has been drawn up to offer some support to doctors facing an ethical quandary, the most important of which is ‘do not abdicate your responsibility to the individual player.’‘I am in blood Stepp’d in so far that,should I wade no more,Returning would be as tedious as to go o’er’—Macbeth: Act III, Scene IV, William Shakespeare
Catheter exchange technique for the Wingspan stent: technical note
Authors: Lesley W S , Rangaswamy R 
Published: December 2009

Background and purposeThe only Food and Drug Administration-approved implant for managing intracranial stenosis is the Wingspan stent. Modification of the standard Wingspan stent delivery procedure has not been previously reported.Material and methodsRetrospective, single-patient, technical report.ResultsFollowing uneventful balloon angioplasty, a symptomatic intracranial vertebral artery stenosis was inaccessible to Wingspan stent delivery using standard procedural protocol because of poor proximal guide catheter purchase. After placing a Renegade Hi-Flo microcatheter across the stenosis, the Wingspan stent was transferred to this catheter and advanced to the lesion using a Neuroform stabilizer. Unsheathing of the stent yielded uncomplicated, precise placement of the stent with a good clinical result.ConclusionThe Wingspan stent transfer technique can be used successfully in the management of intracranial stenotic disease.
Tandem duplication of thefabp1bgene and subsequent divergence of the tissue-specific distribution offabp1b.1andfabp1b.2transcripts in zebrafish (Danio rerio)
Authors: Karanth Santhosh , Denovan-Wright Eileen M. , Thisse Christine , Thisse Bernard , Wright Jonathan M. 
Published: December 2009

We describe a fatty acid-binding protein 1 (fabp1b.2) gene and its tissue-specific expression in zebrafish embryos and adults. The 3.5 kb zebrafish fabp1b.2 gene is the paralog of the previously described zebrafish fabp1a and fabp1b genes. Using the LN54 radiation hybrid mapping panel, we assigned the zebrafish fabp1b.2 gene to linkage group 8, the same linkage group to which fabp1b.1 was mapped. fabp1b.1 and fabp1b.2 appear to have arisen by a tandem duplication event. Whole-mount in situ hybridization of a riboprobe to embryos and larvae detected fabp1b.2 transcripts in the diencephalon and as spots in the periphery of the yolk sac. In adult zebrafish, in situ hybridization revealed fabp1b.2 transcripts in the anterior intestine and skin, and reverse transcription PCR (RT-PCR) detected fabp1b.2 transcripts in the intestine, brain, heart, ovary, skin, and eye. By contrast, fabp1b.1 transcripts were detected by RT-PCR in the liver, intestine, heart, testis, ovary, and gills. The tissue-specific distribution of transcripts for the tandemly duplicated fabp1b.1 and fabp1b.2 genes in adult tissues and during development suggests that the duplicated fabp1b genes of zebrafish have acquired additional functions compared with the ancestral fabp1 gene, i.e., by neofunctionalization. Furthermore, these functions were subsequently divided between fabp1b.1 and fabp1b.2 owing to subfunctionalization.
Theoretical investigation of the oxidation pathways of HO•-initiated reactions of acrolein, methacrolein, and trans-crotonaldehyde
Authors: El-Taher Sabry 
Published: December 2009

Ab initio molecular-orbital calculations have been performed to investigate the reaction mechanisms of the HO•-initiated reactions of the α,β-unsaturated aldehydes: acrolein (ACR), methacrolein (MACR), and trans-crotonaldehyde (CROT). All geometries were fully optimized at the MP2(Full)/6–31G(d,p) level. The correlation energy corrections were introduced by carrying out single-point calculations using both spin-projected second-order Møller–Plesset perturbation theory (PMP2) and coupled-cluster theory (CCSD(T)) using basis sets of different sizes. All reaction pathways studied proceed via a barrierless formation of a loosely bound pre-reactive complex in the entrance channel. The transition-state structures of the HO• additions to the terminal (β) and to the central (α) carbon atoms of the C=C double bond are found to be reactant-like structures. The lowest-energy barrier pathways are found to be the aldehydic H-atom abstraction. The β-addition pathways are found to be energetically more favored than the α-addition pathways. The HO• addition and aldehydic H-atom abstraction pathways are found to be highly exoergic, with the H-atom abstraction pathway being more exoergic than the addition pathways. Although the methyl substitution at the C=C double bond of methacrolein and crotonaldehyde lowers the energies of the transition-state structures of both α- and β-addition pathways, it destabilizes the energies of the transition-state structures of the corresponding aldehydic H-atom abstraction pathways, compared with that of acrolein.
A Childe Bibliography: A Hand-List of the Works of Vere Gordon Childe
Authors: Gathercole Peter , Irving Terry , Díaz-Andreu Margarita 
Published: December 2009

This hand-list is devoted to the published writings of Vere Gordon Childe (1892–1957). It was compiled for two reasons: the limitations of earlier lists of his works, and the changing needs of scholars studying Childe and the disciplines to which he contributed.The earliest and then most complete list of Childe’s writings was produced by Isobel Smith for the Childe festschrift published in the Proceedings of the Prehistoric Society 21(1956): 295–304. Both Bruce Trigger and Sally Green have added items missed by Smith to the bibliographies of their books on Childe. However, the present bibliography contains over twice as many published items by Childe as have appeared previously.
Gene expression profiling identifies emerging oncogenic pathways operating in extranodal NK/T-cell lymphoma, nasal type
Authors: Huang Yenlin , de Reyniès Aurélien , de Leval Laurence , Ghazi Bouchra , Martin-Garcia Nadine , Travert Marion , Bosq Jacques , Brière Josette , Petit Barbara , Thomas Emilie , Coppo Paul , Marafioti Teresa , Emile Jean-François , Delfau-Larue Marie-Hélène , Schmitt Christian , Gaulard Philippe 
Published: December 2009

Abstract
Biopsies and cell lines of natural killer/T-cell lymphoma, nasal type (NKTCL) were subject to combined gene expression profiling and array-based comparative genomic hybridization analyses. Compared with peripheral T-cell lymphoma, not otherwise specified, NKTCL had greater transcript levels for NK-cell and cytotoxic molecules, especially granzyme H. Compared with normal NKcells, tumors were closer to activated than resting cells and overexpressed several genes related to vascular biology, Epstein-Barr Virus–induced genes, and PDGFRA. Notably, platelet-derived growth factor receptor α and its phosphorylated form were confirmed at the protein level, and in vitro the MEC04 NKTCL cell line was sensitive to imatinib. Deregulation of the AKT, Janus kinase–signal transducers and activators of transcription, and nuclear factor-κB pathways was corroborated by nuclear expression of phosphorylated AKT, signal transducers and activators of transcription 3, and RelA in NKTCL, and several deregulated genes in these pathways mapped to regions of recurrent copy number aberrations (AKT3 [1q44], IL6R [1q21.3], CCL2 [17q12], TNFRSF21 [6p12.3]). Several features of NKTCL uncovered by this analysis suggest perturbation of angiogenic pathways. Integrative analysis also evidenced deregulation of the tumor suppressor HACE1 in the frequently deleted 6q21 region. This study highlights emerging oncogenic pathways in NKTCL and identifies novel diagnostic and therapeutic targets.