bluuebunny/crossref_metadata_2025_split huggingface dataset:
A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal
Authors: Albertsen Mads , Hansen Lea Benedicte Skov , Saunders Aaron Marc , Nielsen Per Halkjær , Nielsen Kåre Lehmann 
Published: December 2011

Abstract
Enhanced biological phosphorus removal (EBPR) is widely used for removal of phosphorus from wastewater. In this study, a metagenome (18.2 Gb) was generated using Illumina sequencing from a full-scale EBPR plant to study the community structure and genetic potential. Quantitative fluorescence in situ hybridization (qFISH) was applied as an independent method to evaluate the community structure. The results were in qualitative agreement, but a DNA extraction bias against gram positive bacteria using standard extraction protocols was identified, which would not have been identified without the use of qFISH. The genetic potential for community function showed enrichment of genes involved in phosphate metabolism and biofilm formation, reflecting the selective pressure of the EBPR process. Most contigs in the assembled metagenome had low similarity to genes from currently sequenced genomes, underlining the need for more reference genomes of key EBPR species. Only the genome of ‘Candidatus Accumulibacter’, a genus of phosphorus-removing organisms, was closely enough related to the species present in the metagenome to allow for detailed investigations. Accumulibacter accounted for only 4.8% of all bacteria by qFISH, but the depth of sequencing enabled detailed insight into their microdiversity in the full-scale plant. Only 15% of the reads matching Accumulibacter had a high similarity (&gt;95%) to the sequenced Accumulibacter clade IIA strain UW-1 genome, indicating the presence of some microdiversity. The differences in gene complement between the Accumulibacter clades were limited to genes for extracellular polymeric substances and phage-related genes, suggesting a selective pressure from phages on the Accumulibacter diversity.
Heterotrophic organisms dominate nitrogen fixation in the South Pacific Gyre
Authors: Halm Hannah , Lam Phyllis , Ferdelman Timothy G , Lavik Gaute , Dittmar Thorsten , LaRoche Julie , D'Hondt Steven , Kuypers Marcel M M 
Published: December 2011

Abstract
Oceanic subtropical gyres are considered biological deserts because of the extremely low availability of nutrients and thus minimum productivities. The major source of nutrient nitrogen in these ecosystems is N2-fixation. The South Pacific Gyre (SPG) is the largest ocean gyre in the world, but measurements of N2-fixation therein, or identification of microorganisms involved, are scarce. In the 2006/2007 austral summer, we investigated nitrogen and carbon assimilation at 11 stations throughout the SPG. In the ultra-oligotrophic waters of the SPG, the chlorophyll maxima reached as deep as 200 m. Surface primary production seemed limited by nitrogen, as dissolved inorganic carbon uptake was stimulated upon additions of 15N-labeled ammonium and leucine in our incubation experiments. N2-fixation was detectable throughout the upper 200 m at most stations, with rates ranging from 0.001 to 0.19 nmn h−1. N2-fixation in the SPG may account for the production of 8–20% of global oceanic new nitrogen. Interestingly, comparable 15N2-fixation rates were measured under light and dark conditions. Meanwhile, phylogenetic analyses for the functional gene biomarker nifH and its transcripts could not detect any common photoautotrophic diazotrophs, such as, Trichodesmium, but a prevalence of γ-proteobacteria and the unicellular photoheterotrophic Group A cyanobacteria. The dominance of these likely heterotrophic diazotrophs was further verified by quantitative PCR. Hence, our combined results show that the ultra-oligotrophic SPG harbors a hitherto unknown heterotrophic diazotrophic community, clearly distinct from other oceanic gyres previously visited.
Verminephrobacter eiseniae type IV pili and flagella are required to colonize earthworm nephridia
Authors: Dulla Glenn F J , Go Ruth A , Stahl David A , Davidson Seana K 
Published: December 2011

Abstract
The bacterial symbiont Verminephrobacter eiseniae colonizes nephridia, the excretory organs, of the lumbricid earthworm Eisenia fetida. E. fetida transfers V. eisenia into the egg capsule albumin during capsule formation and V. eiseniae cells migrate into the earthworm nephridia during embryogenesis, where they bind and persist. In order to characterize the mechanistic basis of selective tissue colonization, methods for site-directed mutagenesis and colonization competence were developed and used to evaluate the consequences of individual gene disruptions. Using these newly developed tools, two distinct modes of bacterial motility were shown to be required for V. eiseniae colonization of nascent earthworm nephridia. Flagella and type IV pili mutants lacked motility in culture and were not able to colonize embryonic earthworms, indicating that both twitching and flagellar motility are required for entrance into the nephridia.
Freshwater bacterioplankton richness in oligotrophic lakes depends on nutrient availability rather than on species–area relationships
Authors: Logue Jürg Brendan , Langenheder Silke , Andersson Anders F , Bertilsson Stefan , Drakare Stina , Lanzén Anders , Lindström Eva S 
Published: December 2011

Abstract
A central goal in ecology is to grasp the mechanisms that underlie and maintain biodiversity and patterns in its spatial distribution can provide clues about those mechanisms. Here, we investigated what might determine the bacterioplankton richness (BR) in lakes by means of 454 pyrosequencing of the 16S rRNA gene. We further provide a BR estimate based upon a sampling depth and accuracy, which, to our knowledge, are unsurpassed for freshwater bacterioplankton communities. Our examination of 22 669 sequences per lake showed that freshwater BR in fourteen nutrient-poor lakes was positively influenced by nutrient availability. Our study is, thus, consistent with the finding that the supply of available nutrients is a major driver of species richness; a pattern that may well be universally valid to the world of both micro- and macro-organisms. We, furthermore, observed that BR increased with elevated landscape position, most likely as a consequence of differences in nutrient availability. Finally, BR decreased with increasing lake and catchment area that is negative species–area relationships (SARs) were recorded; a finding that re-opens the debate about whether positive SARs can indeed be found in the microbial world and whether positive SARs can in fact be pronounced as one of the few ‘laws’ in ecology.
Viral infections stimulate the metabolism and shape prokaryotic assemblages in submarine mud volcanoes
Authors: Corinaldesi Cinzia , Dell'Anno Antonio , Danovaro Roberto 
Published: December 2011

Abstract
Mud volcanoes are geological structures in the oceans that have key roles in the functioning of the global ecosystem. Information on the dynamics of benthic viruses and their interactions with prokaryotes in mud volcano ecosystems is still completely lacking. We investigated the impact of viral infection on the mortality and assemblage structure of benthic prokaryotes of five mud volcanoes in the Mediterranean Sea. Mud volcano sediments promote high rates of viral production (1.65–7.89 × 109 viruses g−1 d−1), viral-induced prokaryotic mortality (VIPM) (33% cells killed per day) and heterotrophic prokaryotic production (3.0–8.3 μgC g−1 d−1) when compared with sediments outside the mud volcano area. The viral shunt (that is, the microbial biomass converted into dissolved organic matter as a result of viral infection, and thus diverted away from higher trophic levels) provides 49 mgC m−2 d−1, thus fuelling the metabolism of uninfected prokaryotes and contributing to the total C budget. Bacteria are the dominant components of prokaryotic assemblages in surface sediments of mud volcanoes, whereas archaea dominate the subsurface sediment layers. Multivariate multiple regression analyses show that prokaryotic assemblage composition is not only dependant on the geochemical features and processes of mud volcano ecosystems but also on synergistic interactions between bottom-up (that is, trophic resources) and top-down (that is, VIPM) controlling factors. Overall, these findings highlight the significant role of the viral shunt in sustaining the metabolism of prokaryotes and shaping their assemblage structure in mud volcano sediments, and they provide new clues for our understanding of the functioning of cold-seep ecosystems.
A combined scanning tunneling microscope–atomic layer deposition tool
Authors: Mack James F. , Van Stockum Philip B. , Iwadate Hitoshi , Prinz Fritz B. 
Published: December 2011

We have built a combined scanning tunneling microscope–atomic layer deposition (STM-ALD) tool that performs in situ imaging of deposition. It operates from room temperature up to 200 °C, and at pressures from 1 × 10−6 Torr to 1 × 10−2 Torr. The STM-ALD system has a complete passive vibration isolation system that counteracts both seismic and acoustic excitations. The instrument can be used as an observation tool to monitor the initial growth phases of ALD in situ, as well as a nanofabrication tool by applying an electric field with the tip to laterally pattern deposition. In this paper, we describe the design of the tool and demonstrate its capability for atomic resolution STM imaging, atomic layer deposition, and the combination of the two techniques for in situ characterization of deposition.
Genotyping of Infectious Pancreatic Necrosis Virus Isolates from Mexico State
Authors: Barrera-Mejía Magda , Martínez Simón , Ortega César , Ulloa-Arvizu Raúl 
Published: December 2011

Abstract
The infectious pancreatic necrosis virus (IPNV; genus Aquabirnavirus) affects salmon and trout, causing high mortality in first-feeding fry. The classification of this virus includes nine serotypes and seven genogroups. In Mexico, two different isolates were identified in 2000 and 2008, respectively. Both isolates were classified into genogroup I according to the RNA genome of this virus. As Mexico is importing rainbow trout Oncorhynchus mykiss eggs from different countries, the aim of this study was to genotype IPNV isolates obtained from four rainbow trout producer regions within the state of Mexico. We utilized a fragment of the VP2* (outer capsid protein) gene sequence of Mexican IPNV isolates as a molecular marker to determine the genogroup to which they belong. Although all Mexican IPNV isolates were grouped into genogroup I, we identified genetic diversity among these isolates, and 14 unique nucleotide sequence types were associated with the four producer regions in Mexico State.
Received December 21, 2010; accepted July 27, 2011
A Randomized, Double-Blind, Placebo-Controlled Trial of Selective Digestive Decontamination Using Oral Gentamicin and Oral Polymyxin E for Eradication of Carbapenem-Resistant Klebsiella pneumoniae Carriage
Authors: Saidel-Odes Lisa , Polachek Hana , Peled Nehama , Riesenberg Klaris , Schlaeffer Francisc , Trabelsi Yafa , Eskira Seada , Yousef Baha , Smolykov Rozalia , Codish Shlomi , Borer Abraham 
Published: December 2011

Objective.To assess the effectiveness of selective digestive decontamination (SDD) for eradicating carbapenem-resistant Klebsiella pneumoniae (CRKP) oropharyngeal and gastrointestinal carriage.Design.A randomized, double-blind, placebo-controlled trial with 7 weeks of follow-up per patient.Setting.A 1,000-bed tertiary-care university hospital.Patients.Adults with CRKP-positive rectal swab cultures.Methods.Patients were blindly randomized (1:1) over a 20-month period. The SDD arm received oral gentamicin and polymyxin E gel (0.5 g 4 times per day) and oral solutions of gentamicin (80 mg 4 times per day) and polymyxin E (1 × 106 units 4 times per day for 7 days). The placebo arm received oral placebo gel 4 times per day and 2 placebo oral solutions 4 times per day for 7 days. Strict contact precautions were applied. Samples obtained from the throat, groin, and urine were also cultured.Results.Forty patients (mean age ± standard deviation, 71 ± 16 years; 65% male) were included. At screening, greater than or equal to 30% of oropharyngeal, greater than or equal to 60% of skin, and greater than or equal to 35% of urine cultures yielded CRKP isolates. All throat cultures became negative in the SDD arm after 3 days (P< .0001). The percentages of rectal cultures that were positive for CRKP were significandy reduced at 2 weeks. At that time, 16.1% of rectal cultures in the placebo arm and 61.1% in the SDD arm were negative (odds ratio, 0.13; 95% confidence interval, 0.02–0.74; P<.0016). A difference between the percentages in the 2 arms was still maintained at 6 weeks (33.3% vs 58.5%). Groin colonization prevalence did not change in either arm, and the prevalence of urine colonization increased in the placebo arm.Conclusions.This SDD regimen could be a suitable decolonization therapy for selected patients colonized with CRKP, such as transplant recipients or immunocompromised patients pending chemotherapy and patients who require major intestinal or oropharyngeal surgery. Moreover, in outbreaks caused by CRKP infections that are uncontrolled by routine infection control measures, SDD could provide additional infection containment.Infect Control Hosp Epidemiol 2012;33(1):14-19
Postdischarge Surgical Site Infection Surveillance Practices in Washington Acute Care Hospitals
Authors: Zarate Roxie , Birnbaum David 
Published: December 2011

Little is known about postdischarge surveillance practices currently in place among American hospitals. This survey describes practices used by acute care hospitals covered by Washington State's legislated mandate for public reporting of surgical site infections. While the vast majority of facilities use multiple techniques, wide variation in practices was discovered.Infect Control Hosp Epidemiol 2012;33(1):8
Relationships Between Simple Grain Quality Parameters for the Estimation of Sorghum and Maize Hardness in Commercial Hybrid Cultivars
Authors: Chiremba Constance , Rooney Lloyd W. , Taylor John R. N. 
Published: December 2011

ABSTRACTGrain hardness affects sorghum and maize processing properties especially for dry milling. A variety of simple grain quality parameters were assessed on 17 sorghum and 35 white maize hybrid cultivars grown in six and four locations, respectively, in South Africa. The purpose was to determine tests that can be used to distinguish hardness in commercial sorghum and maize. The grains were characterized by test weight (TW), thousand kernel weight (TKW), decortication with the tangential abrasive dehulling device (TADD), and kernel size. Maize was also characterized for susceptibility to breakage, stress cracking, and near‐infrared transmittance (NIT) milling index. Principal component analysis showed that, in nontannin and tannin sorghums, TADD hardness and TW were closely correlated (P < 0.001). In maize, TADD hardness was closely correlated (P < 0.001) with NIT milling index and TW. Hence, TADD hardness and NIT milling index or TADD hardness and TW would be suitable for maize hardness evaluation. A combination of TADD hardness, TW, TKW, and kernel size >3.35 mm can be used together to select sorghum grain for hardness. It thus appears that TADD hardness is an excellent method of estimating both sorghum and maize hardness that can be applied for routine batch analysis and cultivar evaluation.
Optimal Assessment of Paediatric IBD With MRI and Barium Follow‐through
Authors: Giles Edward , Hanci Ozan , McLean Alison , Power Niall , Cole Angela , Croft Nicholas M. , McDonald Kirsteen , Chippington Sam , Naik Sandhia 
Published: December 2011

ABSTRACTObjectives:The present UK criterion standard for assessing children with suspected inflammatory bowel disease (IBD) is upper endoscopy, ileocolonoscopy, and barium follow‐through (BaFT). Significant doses of radiation, unpalatable contrast, and volume intolerance are involved with BaFT. Practice in investigating Crohn disease (CD) is changing with the increasing use of magnetic resonance imaging (MRI). The aim of the present study was to compare BaFT and a new abdominal MRI protocol in a paediatric IBD population.Methods:All consecutive patients with a new diagnosis of IBD or requiring reassessment from September 2008 to December 2010 were investigated with both abdominal MRI and BaFT in accordance with a specific local paediatric IBD protocol. The studies were reported by nonblinded radiologists with an interest in gastrointestinal imaging. The reports were compared in conjunction with case note review.Results:Eighty‐seven patients underwent both BaFT and MRI abdomen. Thirty‐one percent of patients had additional pathology on MRI, not seen on the BaFT. Sixty‐seven percent of patients (n = 59) had an MRI finding equivalent to BaFT. Using histology as a criterion standard for detecting terminal ileal disease, BaFT had a sensitivity and specificity of 76% and 67%, and MRI had a sensitivity and specificity of 83% and 95%, respectively.Conclusions:This is the largest series of small bowel MRI in a paediatric population. MRI reports were at least equivalent to BaFT. MRI had higher sensitivity and, particularly, specificity in detecting terminal ileal pathology. These findings suggest that MRI should become the criterion standard investigation in children with IBD in centres with appropriate expertise, with zero radiation exposure being highly advantageous.
Rab11 is phosphorylated by classical and novel protein kinase C isoenzymes upon sustained phorbol ester activation
Authors: Pavarotti Martín , Capmany Anahí , Vitale Nicolas , Colombo María Isabel , Damiani María Teresa 
Published: December 2011

AbstractBackground informationRab11 is a small GTPase that controls diverse intracellular trafficking pathways. However, the molecular machinery that regulates the participation of Rab11 in those different transport events is poorly understood. In resting cells, Rab11 localizes at the endocytic recycling compartment (ERC), whereas the different protein kinase C (PKC) isoforms display a cytosolic distribution.ResultsSustained phorbol ester stimulation induces the translocation of the classical PKCα and PKCβII isoenzymes to the ERC enriched in Rab11, and results in transferrin recycling inhibition. In contrast, novel PKCε and atypical PKCζ isoenzymes neither redistribute to the perinucleus nor modify transferrin recycling transport after phorbol ester stimulation. Although several Rabs have been shown to be phosphorylated, there is to date no evidence indicating Rab11 as a kinase substrate. In this report, we show that Rab11 appears phosphorylated in vivo in phorbol ester‐stimulated cells. A bioinformatic analysis of Rab11 allowed us to identify several high‐probability Ser/Thr kinase phosphorylation sites. Our results demonstrate that classical PKC (PKCα and PKCβII but not PKCβI) directly phosphorylate Rab11 in vitro. In addition, novel PKCε and PKCη but not PKCδ isoenzymes also phosphorylate Rab11. Mass spectrometry analysis revealed that Ser 177 is the Rab11 residue to be phosphorylated in vitro by either PKCβII or PKCε. In agreement, the phosphomimetic mutant, Rab11 S177D, retains transferrin at the ERC in the absence of phorbol‐12‐myristate‐13‐acetate stimulus.ConclusionsThis report shows for the first time that Rab11 is differentially phosphorylated by distinct PKC isoenzymes and that this post‐translational modification might be a regulatory mechanism of intracellular trafficking.
TI‐VAMP/VAMP7 is the SNARE of secretory lysosomes contributing to ATP secretion from astrocytes
Authors: Verderio Claudia , Cagnoli Cinzia , Bergami Matteo , Francolini Maura , Schenk Ursula , Colombo Alessio , Riganti Loredana , Frassoni Carolina , Zuccaro Emanuela , Danglot Lydia , Wilhelm Claire , Galli Thierry , Canossa Marco , Matteoli Michela 
Published: December 2011

AbstractBackground informationATP is the main transmitter stored and released from astrocytes under physiological and pathological conditions. Morphological and functional evidence suggest that besides secretory granules, secretory lysosomes release ATP. However, the molecular mechanisms involved in astrocytic lysosome fusion remain still unknown.ResultsIn the present study, we identify tetanus neurotoxin‐insensitive vesicle‐associated membrane protein (TI‐VAMP, also called VAMP7) as the vesicular SNARE which mediates secretory lysosome exocytosis, contributing to release of both ATP and cathepsin B from glial cells. We also demonstrate that fusion of secretory lysosomes is triggered by slow and locally restricted calcium elevations, distinct from calcium spikes which induce the fusion of glutamate‐containing clear vesicles. Downregulation of TI‐VAMP/VAMP7 expression inhibited the fusion of ATP‐storing vesicles and ATP‐mediated calcium wave propagation. TI‐VAMP/VAMP7 downregulation also significantly reduced secretion of cathepsin B from glioma.ConclusionsGiven that sustained ATP release from glia upon injury greatly contributes to secondary brain damage and cathepsin B plays a critical role in glioma dissemination, TI‐VAMP silencing can represent a novel strategy to control lysosome fusion in pathological conditions.
MicroRNAs: critical regulators of epithelial to mesenchymal (EMT) and mesenchymal to epithelial transition (MET) in cancer progression
Authors: Bullock Marc D. , Sayan Abdulkadir E. , Packham Graham K. , Mirnezami Alex H. 
Published: December 2011

AbstractMicroRNAs (miRNAs) are a class of small highly conserved RNAs that provide widespread expressional control through the translational repression of mRNA. MiRNAs have fundamental roles in the regulation of intracellular processes, and their importance during malignant transformation and metastasis is becoming increasingly well recognized. An important event in the metastatic cascade is epithelial to mesenchymal transition (EMT), a reversible phenotypic switch over, which endows malignant epithelial cells with the capacity to break free from one another and invade the surrounding stroma. Our understanding of EMT has been significantly improved by the characterization of miRNAs that influence the signalling pathways and downstream events that define EMT on a molecular<?brk?> level.Here, we detail the role of miRNAs in EMT, and in doing so demonstrate their importance in the early stages of the metastatic cascade; we discuss a significant body of data that suggest new opportunities for drug development, and we highlight critical knowledge gaps that remain to be addressed.