bluuebunny/crossref_metadata_2025 huggingface dataset:
Minimally invasive (laparoscopic and robot‐assisted) approach for solid pseudopapillary tumor of the distal pancreas: a single‐center experience
Authors: Kang Chang Moo , Choi Sung Hoon , Hwang Ho Kyoung , Lee Woo Jung , Chi Hoon Sang
Published: July 2010

Background/purpose

A single‐institutional experiences of solid pseudopapillary tumor (SPT) in the distal pancreas were retrospectively reviewed with special reference to a minimally invasive approach.

Methods

Thirty‐five patients with SPT of the distal pancreas treated during the past 20 years were retrospectively evaluated. We divided the patients into 2 groups based on the surgical approach: the laparoscopic/robot‐assisted surgery (LR) group and the conventional open surgery (O) group. We reviewed the chronological changes and characteristics of SPT. A comparative analysis of the two groups (LR vs. O) was conducted in terms of perioperative surgical outcomes.

Results

The discovery of relatively small SPTs without symptoms seemed to be increasing (p < 0.05). Eleven of the 35 patients were assigned to the LR group. Ten patients were female and 1 was male, and they had a median age of 32 years (range 24–62 years) and a median tumor size of 3.6 cm (range 1–8.5 cm). Eight patients underwent laparoscopic distal pancreatectomy with or without splenectomy, and the remaining 3 underwent robot‐assisted central pancreatectomy with pancreaticogastrostomy. In the comparative analysis of the LR and O groups, smaller tumor size, earlier oral intake, and shorter hospital stay, without increasing morbidity, were noted in the LR group (p < 0.05).

Conclusions

A minimally invasive (laparoscopic/robot‐assisted) approach for SPT of the distal pancreas is thought to be more appropriate than and preferable to conventional open surgery in well‐selected patients.
Fixation of subtrochanteric extending/derotational femoral osteotomies with the Locking Compression Plate in ambulatory neuro-orthopaedic patients
Authors: Haefeli Mathias , Huber Hanspeter , Dierauer Stefan , Ramseier Leonhard E.
Published: July 2010

Purpose

Patients with neuro-orthopaedic disorders often develop hip flexion contractures or rotational hip deformities. Increasing deformities impair the already diminished walking abilities and proximal femoral osteotomies are often performed to maintain/improve walking abilities. Fixation of the osteotomies with condylar plates has been successfully used but does often not allow immediate postoperative full weight bearing. To avoid a substantial postoperative rehabilitation deficit and additional bone loss due to inactivity, a postoperative treatment with full weight bearing is, therefore, wishful. Newer fixed-angled implants with stronger anchoring in osteopenic bone might fit these demands. The objective of this study was to evaluate bone healing and the complication rate after proximal extending and/or derotational femoral osteotomy fixed with 3.5/4.5 Locking Compression Plate (LCP; Synthes®) and postoperative full weight bearing in ambulatory neuro-orthopaedic patients.

Methods

Fifteen ambulatory neuro-orthopaedic patients (12 cerebral palsy [CP], 1 trisomy 21, 2 hemiparesis) with a mean age of 13.7 years (range 7–22) with hip flexion contractures and/or rotational deformities underwent subtrochanteric ( n = 26) osteotomy between July 2004 and October 2007. All patients were allowed to bear their full weight postoperatively. We investigated the fusion rate, implant failure, and general complication rate until union had occurred.

Results

Fourteen patients (mean weight 42.0 kg [range 21.8–59]) uneventfully achieved solid fusion. One patient (19 years of age, 73 kg) needed revision surgery due to implant failure with consecutive varus deformity and achieved solid fusion after the second intervention. Besides one superficial wound infection, no other complications occurred.

Conclusions

Subtrochanteric extending and/or derotational osteotomies fixed with an LCP are a reliable procedure in neuro-orthopaedic patients. Most patients can be treated with early postoperative full weight bearing. However, in heavier patients, possible implant failure must be considered.
Assessing the Extent of Substitution Rate Variation of Retrotransposon Long Terminal Repeat Sequences in Oryza sativa and Oryza glaberrima
Authors: Zuccolo Andrea , Sebastian Aswathy , Yu Yeisoo , Jackson Scott , Rounsley Steve , Billheimer Dean , Wing Rod A.
Published: July 2010

Long Terminal Repeat retrotransposons (LTR-RTs) are a major component of several plant genomes. Important insights into the evolutionary dynamics of these elements in a genome are provided by the comparative study of their insertion times. These can be inferred by the comparison of pairs of LTRs flanking intact LTR-RTs in combination with an estimated substitution rate. Over the past several years, different substitution rates have been proposed for LTRs in crop plants. However, very little is known about the extent of substitution rate variation and the factors contributing to this variation, so the rates currently used are generally considered rough estimators of actual rates. To evaluate the extent of substitution rate variation in LTRs, we identified 70 orthologous LTRs on the short arms of chromosome 3 of both Oryza sativa and Oryza glaberrima, species that diverged ∼0.64 Ma. Since these orthologous sequences were present in a common ancestor prior to species divergence, nucleotide differences identified in comparing these regions must correspond to mutations accumulated post-speciation, thereby giving us the opportunity to study LTR substitution rate variation in different elements across these short arms. As a control, we analyzed a similar amount of non-repeat-related sequences collected near the orthologous LTRs. Our analysis showed that substitution rate variation in LTRs is greater than 5-fold, is positively correlated with G+C content, and tends to increase near centromeric regions. We confirmed that in the vast majority of cases, LTRs mutate faster than their corresponding non-repeat-related neighboring sequences.
Vom Anforderungsprofil zum Interventionsansatz
Authors: Achter Mathias , Stoll Oliver
Published: July 2010

Zusammenfassung. Die zunehmende Relevanz sportpsychologischer Arbeit im Spitzensport macht die Entwicklung sportartspezifischer Betreuungskonzepte notwendig. Der vorliegende Artikel zeigt überblicksartig die Entwicklung einer sportpsychologischen Expertise für die vier Fachsparten (Wasserspringen/Schwimmen/Synchronschwimmen/Wasserball) des Deutschen Schwimm-Verbandes e.V. (DSV). Auf Wunsch des Sportdirektors des DSV, Herrn Buschkow, und durch die finanzielle Unterstützung des Bundesinstituts für Sportwissenschaft (BISp) konnte die Umsetzung der Expertise realisiert werden. Trainer/innen und Sportpsychologen/innen wurden in Einzelinterviews zu den für die Leistung wichtigsten psychologischen und sozialen Fertigkeiten der Athleten/innen befragt. Eine qualitative Inhaltsanalyse diente als Basis für die Erstellung eines spezifischen psychologischen Anforderungsprofils für die jeweilige Fachsparte. Die Profile bilden die empfehlende Grundlage für spezifische sportpsychologische Betreuungskonzepte, welche speziell für jede einzelne Fachsparte anwendbar sind.
Occipitofrontal Switching for Simultaneous Correction of Synostotic Frontal and Occipital Plagiocephaly: A Novel Surgical Technique
Authors: Kim Peter Chanwoo , Kim Yong Don , Park Dae Hwan
Published: July 2010

Plagiocephaly has traditionally been corrected by unilateral or bilateral frontal bone advancement or rotation using bone-molding forceps and distraction devices. Complete symmetrical correction of deformed frontal bones is considered almost impossible because the curvature of each frontal bone varies. We evaluated the feasibility of measuring the optimal curvature of frontal and occipital bones using a plaster skull model and applying these measurements to “switch” them for simultaneous correction of frontal and occipital plagiocephaly. A 2-year-old girl suffering from unifrontal flattening visited our clinic. Unilateral coronal synostosis was observed. The 3-D rapid prototype model and skull replica method using thin paper clay were used for preplanned virtual surgery. The triangular bone was harvested from the contralateral bulging side of the occipital bone (“occipitofrontal switching”) for the best optimal curvature in the affected frontal bone. Another triangular bone was harvested from the ipsilateral flattened side of the frontal bone, and bones were switched with each other. Further bending of the frontal or occipital segment was not necessary for optimal curvature. Symmetrical correction was made by switching the triangular bone of the frontal area with that of the contralateral occipital area. Revision has not been necessary, and infection was not observed at 1-year follow-up. Our novel technique of preplanning surgery using a 3-D plaster model for simultaneous correction of frontal and occipital plagiocephaly is effective and time-saving.
Stress coping stimulates hippocampal neurogenesis in adult monkeys
Authors: Lyons David M. , Buckmaster Paul S. , Lee Alex G. , Wu Christine , Mitra Rupshi , Duffey Lauren M. , Buckmaster Christine L. , Her Song , Patel Paresh D. , Schatzberg Alan F.
Published: July 2010

Coping with intermittent social stress is an essential aspect of living in complex social environments. Coping tends to counteract the deleterious effects of stress and is thought to induce neuroadaptations in corticolimbic brain systems. Here we test this hypothesis in adult squirrel monkey males exposed to intermittent social separations and new pair formations. These manipulations simulate conditions that typically occur in male social associations because of competition for limited access to residency in mixed-sex groups. As evidence of coping, we previously confirmed that cortisol levels initially increase and then are restored to prestress levels within several days of each separation and new pair formation. Follow-up studies with exogenous cortisol further established that feedback regulation of the hypothalamic-pituitary-adrenal axis is not impaired. Now we report that exposure to intermittent social separations and new pair formations increased hippocampal neurogenesis in squirrel monkey males. Hippocampal neurogenesis in rodents contributes to spatial learning performance, and in monkeys we found that spatial learning was enhanced in conditions that increased hippocampal neurogenesis. Corresponding changes were discerned in the expression of genes involved in survival and integration of adult-born granule cells into hippocampal neural circuits. These findings support recent indications that stress coping stimulates hippocampal neurogenesis in adult rodents. Psychotherapies designed to promote stress coping potentially have similar effects in humans with major depression.
Ribosomal protein L7Ae is a subunit of archaeal RNase P
Authors: Cho I-Ming , Lai Lien B. , Susanti Dwi , Mukhopadhyay Biswarup , Gopalan Venkat
Published: July 2010

To the mounting evidence of nonribosomal functions for ribosomal proteins, we now add L7Ae as a subunit of archaeal RNase P, a ribonucleoprotein (RNP) that catalyzes 5′-maturation of precursor tRNAs (pre-tRNAs). We first demonstrate that L7Ae coelutes with partially purified
Methanococcus maripaludis
(
Mma
) RNase P activity. After establishing in vitro reconstitution of the single RNA with four previously known protein subunits (POP5, RPP21, RPP29, and RPP30), we show that addition of L7Ae to this RNase P complex increases the optimal reaction temperature and
k
cat
/
K

m

(by ∼360-fold) for pre-tRNA cleavage to those observed with partially purified native
Mma
RNase P. We identify in the
Mma
RNase P RNA a putative kink-turn (K-turn), the structural motif recognized by L7Ae. The large stimulatory effect of
Mma
L7Ae on RNase P activity decreases to ≤ 4% of wild type upon mutating either the conserved nucleotides in this K-turn or amino acids in L7Ae shown to be essential for K-turn binding. The critical, multifunctional role of archaeal L7Ae in RNPs acting in tRNA processing (RNase P), RNA modification (H/ACA, C/D snoRNPs), and translation (ribosomes), especially by employing the same RNA-recognition surface, suggests coevolution of various translation-related functions, presumably to facilitate their coordinate regulation.
Ideal MHD stability limits of the PROTO-SPHERA configuration
Authors: Micozzi P. , Alladio F. , Mancuso A. , Rogier F.
Published: July 2010

The PROTO-SPHERA experiment (under construction in Frascati inside the START vacuum vessel) aims to study the properties of a spherical torus (ST), where a hydrogen force-free screw pinch (SP, with open field lines and fed by electrodes) replaces the central rod of the standard spherical tokamak experiments: PROTO-SPHERA, with a central screw pinch current I
e = 60 kA, aims at producing a spherical torus (with closed field lines) of diameter 2R
sph = 70 cm, and aspect ratio R/a = A = 1.2–1.3, carrying a toroidal current I
p = 120–240 kA. Such a configuration is an evolution of the flux core spheromak (FCS) concept, first proposed by Taylor. The formation mechanism of the configuration will be the one successfully developed by the TS-3 team at the University of Tokyo. The spherical torus toroidal current should be sustained by helicity injection from the screw pinch, therefore some level of resistive instability with toroidal mode numbers n = 1 and/or n = 2 is requested after the formation and during the sustainment phase; nevertheless, the configuration should be operated such as to maintain it stable from an ideal MHD point of view. The ideal MHD stability limits of PROTO-SPHERA have been analysed by a numerical code able to handle magnetic configurations endowed with both closed and open magnetic field lines. The results of such an analysis are presented in terms of the main parameter, which is the ratio between the currents in the spherical torus and in the central screw pinch, I
p/I
e, and of other relevant parameters of the ST (elongation, aspect ratio, total beta and the toroidal plasma current profile). A comparison with the TS-3 results is also shown.
Effects of α particles on the resistive wall mode stability in ITER
Authors: Liu Yueqiang
Published: July 2010

The effects of the fusion born α particles on the stability of the RWM are numerically investigated for one of the advanced steady state scenarios in ITER. The α contribution is found to be generally stabilizing, compared with the thermal particle kinetic contribution alone. The same conclusion is achieved following both a perturbative and self-consistent approach. The latter generally predicts less stabilization than the former. At high enough plasma pressure, the self-consistent approach predicts two unstable branches for the ITER plasma studied here. The stabilizing effect from α particles is found to be generally weak, in particular in terms of the modification of the stability boundary. The effect is more pronounced only at fast enough plasma rotation frequency, roughly matching the α precession frequency, which is in the order of a few per cent of the toroidal Alfvén frequency for ITER. A simple, energy principle based, fishbone-like dispersion relation is proposed to gain a qualitative understanding of the numerical results.
Particle transport in low core turbulence Tore-Supra plasmas
Authors: Guirlet R. , Sirinelli A. , Parisot T. , Sabot R. , Artaud J.F. , Bourdelle C. , Garbet X. , Hennequin P. , Hoang G.T. , Imbeaux F. , Ségui J.L. , Mazon D. , Villegas D.
Published: July 2010

Electron and impurity transport has been studied in sawtoothing plasmas in the Tore-Supra tokamak. High time and space resolution measurements of the electron density reveal the existence of a flat profile region encompassing the q = 1 surface, on which is superimposed a density peak building up between sawtooth relaxations. For the first time in this regime, we have determined the underlying transport of both nickel and electrons independently of the effect of sawteeth in the central part of the plasma. Electron transport is consistent with the neoclassical expectations only in the close vicinity of the magnetic axis. Further out, it exceeds the neoclassical values as calculated with the NCLASS code, although the turbulence level is very low in the whole central region region. In contrast, nickel transport is in good agreement with the neoclassical calculations in the same region. The neoclassical effect on trapped particles of a persisting mode due to incomplete reconnection of the magnetic surfaces is consistent with these observations.
When the collective acts on its components: economic crisis autocatalytic percolation
Authors: Cantono S , Solomon S
Published: July 2010

Agent-based models have improved the standards for empirical support and validation criteria in social, biological, cognitive and human sciences. Yet, the inclusion, in these models, of vertical interactions between various aggregation levels remains a challenge. We study analytically, numerically and by simulation the generic consequences of interactions between the collective and its individual components:

 the appearance of an autocatalytic loop between the dynamics of the collective and its components;

 the system, which is dominated by a limited number of factors amplified by this collective↔individuals autocatalytic loop;

 the microscopic features, which are not involved in the autocatalytic loop and are irrelevant at the systemic level; and

 how the above clarify the interplay between macroscopic predictable features and the ones dependent on random unpredictable individual events.

Using the social and market percolation framework, we study the dramatic effects of the collective↔individuals autocatalytic loop on economic crisis propagation:

  the percolation transition becomes discontinuous;

 there are a few relevant regions and regimes corresponding to a quite diverse range of response policy options;

 there are stability ranges where appropriate policies can help to avoid macroscopic crisis percolation; and

  beyond those regions the systemic crisis might become unstoppable.
Relations of serum phosphorus levels to echocardiographic left ventricular mass and incidence of heart failure in the community
Authors: Dhingra Ravi , Gona Philimon , Benjamin Emelia J. , Wang Thomas J. , Aragam Jayashri , D'Agostino Ralph B. , Kannel William B. , Vasan Ramachandran S.
Published: July 2010

Aims

To evaluate the association of serum phosphorus with cardiac structure/function and incident heart failure.

Methods and results

We related serum phosphorus to echocardiographic left ventricular (LV) measurements cross‐sectionally, and to incident heart failure prospectively in 3300 participants (mean age 44 years, 51% women) free of heart failure, myocardial infarction, and chronic kidney disease (estimated glomerular filtration rate [eGFR]<60 mL/min/1.73 m2). Cross‐sectionally, serum phosphorus was related positively to LV mass, internal dimensions, and systolic dysfunction. On follow‐up (mean 17.4 years), 157 individuals developed heart failure. In models adjusting for established risk factors as time‐varying covariates, each mg/dL increment in serum phosphorus was associated with a 1.74‐fold risk of heart failure [95% confidence intervals (CI) 1.17–2.59]. Individuals in the highest serum phosphorus quartile experienced a two‐fold (95% CI 1.28–3.40) risk of heart failure compared with participants in the lowest quartile. These relations were maintained upon additional adjustment for LV mass/dimensions and systolic dysfunction. In analyses restricted to individuals with eGFR >90 mL/min/1.73 m2, no proteinuria and serum phosphorus <4.5 mg/dL, the association of serum phosphorus with heart failure remained robust.

Conclusion

In our community‐based sample, higher serum phosphorus was associated with greater LV mass cross‐sectionally, and with an increased risk of heart failure prospectively.
Cardiac remodelling and myocardial recovery: lost in translation?
Authors: Mann Douglas L. , Bogaev Roberta , Buckberg Gerald D.
Published: July 2010

The insight that decreases in left ventricular (LV) volume and mass occur secondary to the recovery of the myocardium at the cellular and molecular level has engendered a wider appreciation of the importance of LV remodelling as a mechanism for worsening heart failure. Despite these recent insights into the recognition of the importance of LV reverse remodelling in heart failure, many clinicians do not consider simple measurements of LV structure (i.e. LV volume) in their routine clinical decision‐making process, preferring instead to rely on measurements of LV function [e.g. ejection fraction (EF)] when making decisions about medical and surgical treatment options. Although there are probably multiple reasons of why the use of LV volumes has not gained wider acceptance in day‐to‐day clinical management of heart failure patients, the most likely reason is that clinicians remain extremely comfortable using the LVEF to assess their heart failure patients. Importantly, LV volumes predict outcome more reliably than does the EF. Moreover, knowledge regarding LV volumes is extremely useful in optimizing patient selection for surgical and device therapies. Based on the foregoing arguments, we suggest that it is time to begin developing individualized clinical strategies based upon a consideration of the important role that LV remodelling plays in the pathogenesis of heart failure, and that we begin to incorporate measurements of LV volume and mass into the clinical decision‐making process.
Current state of knowledge on aetiology, diagnosis, management, and therapy of peripartum cardiomyopathy: a position statement from the Heart Failure Association of the European Society of Cardiology Working Group on peripartum cardiomyopathy
Authors: Sliwa Karen , Hilfiker‐Kleiner Denise , Petrie Mark C. , Mebazaa Alexandre , Pieske Burkert , Buchmann Eckhart , Regitz‐Zagrosek Vera , Schaufelberger Maria , Tavazzi Luigi , van Veldhuisen Dirk J. , Watkins Hugh , Shah Ajay J. , Seferovic Petar M. , Elkayam Uri , Pankuweit Sabine , Papp Zoltan , Mouquet Frederic , McMurray John J.V.
Published: July 2010

Peripartum cardiomyopathy (PPCM) is a cause of pregnancy‐associated heart failure. It typically develops during the last month of, and up to 6 months after, pregnancy in women without known cardiovascular disease. The present position statement offers a state‐of‐the‐art summary of what is known about risk factors for potential pathophysiological mechanisms, clinical presentation of, and diagnosis and management of PPCM. A high index of suspicion is required for the diagnosis, as shortness of breath and ankle swelling are common in the peripartum period. Peripartum cardiomyopathy is a distinct form of cardiomyopathy, associated with a high morbidity and mortality, but also with the possibility of full recovery. Oxidative stress and the generation of a cardiotoxic subfragment of prolactin may play key roles in the pathophysiology of PPCM. In this regard, pharmacological blockade of prolactin offers the possibility of a disease‐specific therapy.
A randomized trial of the effects of exercise training in Chagas cardiomyopathy
Authors: Lima Márcia M.O. , Rocha Manoel Otávio C. , Nunes Maria Carmo P. , Sousa Lidiane , Costa Henrique S. , Alencar Maria Clara N. , Britto Raquel R. , Ribeiro Antonio Luiz P.
Published: July 2010

Aims

The effects of exercise training in chronic heart failure are well established, however, they have not been evaluated in Chagas cardiomyopathy (ChC). We sought to determine the effects of exercise training on functional capacity, health‐related quality of life (HQoL), and brain natriuretic peptide (BNP) levels in patients with ChC.

Methods and results

This randomized, controlled, single‐blind trial included 40 patients with ChC (age 49.5 ± 7.8 years, 57.5% male) who did not practice regular exercise. All patients were assessed, at baseline and at the end of the study, by exercise test (VO2 and exercise time), six‐minute walk test (6MWT), Goldman Specific Activity Scale (SAS), HQoL, and BNP levels. Patients were randomized to inactive control group (ICG = 19) or exercise training group (ETG = 21). Exercise training group patients underwent 12 weeks of exercise training: walking for up to 30 min (intensity 50–70% HR reserve + HR at rest) and warm‐up and cooling‐down exercising, three times a week. The data were analysed for delta values (Δ= end − baseline). After intervention, compared with the ICG, the ETG had significant increases in functional parameters including, ΔVO2 (6.5 vs. 2.8 mL/kg/min, P = 0.001), Δ exercise time (2.9 vs.1.1 min, P < 0.001), Δ6MWT distance (83.5 vs. 2.0 m, P = 0.001) improved ΔSAS (8 vs. 1 patient, P = 0.008), and HQoL: Δ domains vitality (7.5 vs. 0 points, P = 0.013), Δ emotional aspects (16.7 vs. 0 points, P = 0.012), and Δ mental health (16.1 vs. 0 points, P = 0.031). There was no difference in BNP levels.

Conclusion

In patients with ChC, exercise training was associated with a major improvement in functional capacity and HQoL without any adverse effects.
Streptococcus porcorum sp. nov., isolated from domestic and wild pigs
Authors: Vela A. I. , Sánchez V. , Mentaberre G. , Lavín S. , Domínguez L. , Fernández-Garayzábal J. F.
Published: July 2010

Seven isolates of an unidentified Gram-stain-positive, catalase-negative, coccus-shaped organism isolated from domestic and wild pigs were characterized by phenotypic and molecular-genetic methods. Based on cellular morphology and biochemical criteria, the isolates were tentatively assigned to the genus Streptococcus, although the organisms did not appear to correspond to any recognized species. Comparative 16S rRNA gene sequencing showed that the unknown bacterium was phylogenetically closely related to, but distinct from, Streptococcus suis (97.5 % 16S rRNA gene sequence similarity to the type strain). rpoB and sodA sequence analysis showed minimum interspecies divergence from phylogenetically close 16S rRNA gene sequence-based relatives of 13.8 and 18.6 %, respectively. DNA–DNA hybridization of a strain of the unidentified organism demonstrated 8–18 % reassociation with S. suis NCTC 10234T. The novel bacterium could be distinguished from S. suis and other Streptococcus species using biochemical tests. On the basis of phenotypic and phylogenetic evidence, it is proposed that the unknown isolates from domestic and wild animals be assigned to a novel species of the genus Streptococcus, Streptococcus porcorum sp. nov. The type strain is 682-03T ( = CCUG 58479T  = CECT 7593T).
Primorskyibacter sedentarius gen. nov., sp. nov., a novel member of the class Alphaproteobacteria from shallow marine sediments
Authors: Romanenko Lyudmila A. , Tanaka Naoto , Svetashev Vasily I. , Mikhailov Valery V.
Published: July 2010

Two Gram-negative, aerobic, non-pigmented, non-motile, rod-shaped bacteria, strains KMM 9015 and KMM 9018T, were isolated from a sample of shallow sediment collected from the Sea of Japan. An analysis of the nearly complete 16S rRNA gene sequences showed that the isolates were very close to each other phylogenetically (99.9 % sequence similarity) and their close relatives wereMarinovum algicolaFF3T(95.8 and 95.9 %, respectively) and members of the generaLeisingera(95.7–95.1 and 95.8–95.2 %),Phaeobacter(95.0–94.2 and 95.1–94.2 %) andThalassobius(96.3–94.8 and 96.2–94.7 %) of the classAlphaproteobacteria. In phylogenetic trees based on 16S rRNA gene sequences, strains KMM 9015 and KMM 9018Twere positioned as a distinct phylogenetic line adjacent toMarinovum algicola. The major isoprenoid quinone was Q-10, the polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown lipid and the major fatty acid was C18 : 1ω7c, followed by 11-methyl C18 : 1ω7c, in both strains. The DNA G+C contents of strains KMM 9015 and KMM 9018Twere 60.2 and 61.9 mol%, respectively. Based on distinctive phenotypic characteristics and phylogenetic analysis, strains KMM 9015 and KMM 9018Trepresent a novel species in a novel genus, for which the namePrimorskyibacter sedentariusgen. nov., sp. nov. is proposed. The type strain ofPrimorskyibacter sedentariusis strain KMM 9018T( = NRIC 0784T = JCM 16874T).
Nf2/Merlin controls progenitor homeostasis and tumorigenesis in the liver
Authors: Benhamouche Samira , Curto Marcello , Saotome Ichiko , Gladden Andrew B. , Liu Ching-Hui , Giovannini Marco , McClatchey Andrea I.
Published: July 2010

The molecular signals that control the maintenance and activation of liver stem/progenitor cells are poorly understood, and the role of liver progenitor cells in hepatic tumorigenesis is unclear. We report here that liver-specific deletion of the neurofibromatosis type 2 (Nf2) tumor suppressor gene in the developing or adult mouse specifically yields a dramatic, progressive expansion of progenitor cells throughout the liver without affecting differentiated hepatocytes. All surviving mice eventually developed both cholangiocellular and hepatocellular carcinoma, suggesting that Nf2−/− progenitors can be a cell of origin for these tumors. Despite the suggested link between Nf2 and the Hpo/Wts/Yki signaling pathway in Drosophila, and recent studies linking the corresponding Mst/Lats/Yap pathway to mammalian liver tumorigenesis, our molecular studies suggest that Merlin is not a major regulator of YAP in liver progenitors, and that the overproliferation of Nf2−/− liver progenitors is instead driven by aberrant epidermal growth factor receptor (EGFR) activity. Indeed, pharmacologic inhibition of EGFR blocks the proliferation of Nf2−/− liver progenitors in vitro and in vivo, consistent with recent studies indicating that the Nf2-encoded protein Merlin can control the abundance and signaling of membrane receptors such as EGFR. Together, our findings uncover a critical role for Nf2/Merlin in controlling homeostasis of the liver stem cell niche.
The bHLH Transcription Factor POPEYE Regulates Response to Iron Deficiency inArabidopsisRoots
Authors: Long Terri A. , Tsukagoshi Hironaka , Busch Wolfgang , Lahner Brett , Salt David E. , Benfey Philip N.
Published: July 2010

Global population increases and climate change underscore the need for better comprehension of how plants acquire and process nutrients such as iron. Using cell type–specific transcriptional profiling, we identified a pericycle-specific iron deficiency response and a bHLH transcription factor, POPEYE (PYE), that may play an important role in this response. Functional analysis of PYE suggests that it positively regulates growth and development under iron-deficient conditions. Chromatin immunoprecipitation-on-chip analysis and transcriptional profiling reveal that PYE helps maintain iron homeostasis by regulating the expression of known iron homeostasis genes and other genes involved in transcription, development, and stress response. PYE interacts with PYE homologs, including IAA–Leu Resistant3 (ILR3), another bHLH transcription factor that is involved in metal ion homeostasis. Moreover, ILR3 interacts with a third protein, BRUTUS (BTS), a putative E3 ligase protein, with metal ion binding and DNA binding domains, which negatively regulates the response to iron deficiency. PYE and BTS expression is also tightly coregulated. We propose that interactions among PYE, PYE homologs, and BTS are important for maintaining iron homeostasis under low iron conditions.
Identification of Novel Methane-, Ethane-, and Propane-Oxidizing Bacteria at Marine Hydrocarbon Seeps by Stable Isotope Probing
Authors: Redmond Molly C. , Valentine David L. , Sessions Alex L.
Published: July 2010

Marine hydrocarbon seeps supply oil and gas to microorganisms in sediments and overlying water. We used stable isotope probing (SIP) to identify aerobic bacteria oxidizing gaseous hydrocarbons in surface sediment from the Coal Oil Point seep field located offshore of Santa Barbara, California. After incubating sediment with
13
C-labeled methane, ethane, or propane, we confirmed the incorporation of
13
C into fatty acids and DNA. Terminal restriction fragment length polymorphism (T-RFLP) analysis and sequencing of the 16S rRNA and particulate methane monooxygenase (
pmoA
) genes in
13
C-DNA revealed groups of microbes not previously thought to contribute to methane, ethane, or propane oxidation. First,
13
C methane was primarily assimilated by
Gammaproteobacteria
species from the family
Methylococcaceae
,
Gammaproteobacteria
related to
Methylophaga
, and
Betaproteobacteria
from the family
Methylophilaceae
. Species of the latter two genera have not been previously shown to oxidize methane and may have been cross-feeding on methanol, but species of both genera were heavily labeled after just 3 days.
pmoA
sequences were affiliated with species of
Methylococcaceae
, but most were not closely related to cultured methanotrophs. Second,
13
C ethane was consumed by members of a novel group of
Methylococcaceae
. Growth with ethane as the major carbon source has not previously been observed in members of the
Methylococcaceae
; a highly divergent
pmoA
-like gene detected in the
13
C-labeled DNA may encode an ethane monooxygenase. Third,
13
C propane was consumed by members of a group of unclassified
Gammaproteobacteria
species not previously linked to propane oxidation. This study identifies several bacterial lineages as participants in the oxidation of gaseous hydrocarbons in marine seeps and supports the idea of an alternate function for some
pmoA
-like genes.
The Chitinolytic Activity ofListeria monocytogenesEGD Is Regulated by Carbohydrates but Also by the Virulence Regulator PrfA
Authors: Larsen M. H. , Leisner J. J. , Ingmer H.
Published: July 2010

Chitin, an insoluble polymer ofN-acetyl-d-glucosamine (GlcNAc), is one of the most abundant carbohydrate polymers in marine and terrestrial environments. Chitin hydrolysis byListeria monocytogenesdepends on two chitinase-encoding genes,chiAandchiB, and the aim of this study was to investigate their regulation. Chitin induces the expression of both chitinases in late exponential growth phase, andchiAbut notchiBis furthermore induced by the monomer GlcNAc. Furthermore, their expression is subjected to catabolite control. Chitinases expressed by bacterial pathogens have proven to be important not only for nutrient acquisition and environmental survival but also for infecting animals and humans. Interestingly, the centralL. monocytogenesvirulence gene regulator, PrfA, is required for the chitinolytic phenotype, as chitinase activity was significantly reduced inprfAmutant cells compared to its level in wild-type cells. In agreement with this, Northern blot analysis showed that the amounts ofchiAandchiBtranscripts upon induction by chitin were significantly lower in theprfAmutant than in the wild type. The chitinolytic activity andchiAandchiBexpression were reduced in the absence of thesigBgene, indicating that σBis also important for the production of chitinases. ThechiA,chiB, andchiA chiBmutants were not impaired forin vitroadhesion and invasion in epithelial cell lines, but thechiA chiBdouble mutant showed less survival ability in a chitin-enriched medium. The regulation of chitinolytic activity inL. monocytogenesis complex, and taken together, the results indicate that the biological role of this activity may not be limited to the external environment.
Interaction of
Mycobacterium ulcerans
with Mosquito Species: Implications for Transmission and Trophic Relationships
Authors: Wallace John R. , Gordon Matthew C. , Hartsell Lindsey , Mosi Lydia , Benbow M. Eric , Merritt Richard W. , Small Pamela L. C.
Published: July 2010

Mycobacterium ulcerans
is the causative agent of Buruli ulcer, a severe necrotizing skin disease that causes significant morbidity in Africa and Australia. Person-to-person transmission of Buruli ulcer is rare. Throughout Africa and Australia infection is associated with residence near slow-moving or stagnant water bodies. Although
M. ulcerans
DNA has been detected in over 30 taxa of invertebrates, fish, water filtrate, and plant materials and one environmental isolate cultured from a water strider (Gerridae), the invertebrate taxa identified are not adapted to feed on humans, and the mode of transmission for Buruli ulcer remains an enigma. Recent epidemiological reports from Australia describing the presence of
M. ulcerans
DNA in adult mosquitoes have led to the hypothesis that mosquitoes play an important role in the transmission of
M. ulcerans.
In this study we have investigated the potential of mosquitoes to serve as biological or mechanical vectors or as environmental reservoirs for
M. ulcerans
. Here we show that
Aedes aegypti
,
A. albopictus
,
Ochlerotatus triseriatus
, and
Culex restuans
larvae readily ingest wild-type
M. ulcerans
, isogenic toxin-negative mutants, and
Mycobacterium marinum
isolates and remain infected throughout larval development. However, the infections are not carried over into the pupae or adult mosquitoes, suggesting an unlikely role for mosquitoes as biological vectors. By following
M. ulcerans
through a food chain consisting of primary (mosquito larvae), secondary (predatory mosquito larva from
Toxorhynchites rutilus septentrionalis
), and tertiary (
Belostoma
species) consumers, we have shown that
M. ulcerans
can be productively maintained in an aquatic food web.
Characterization of Three
mnp
Genes of
Fomitiporia mediterranea
and Report of Additional Class II Peroxidases in the Order Hymenochaetales
Authors: Morgenstern Ingo , Robertson Deborah L. , Hibbett David S.
Published: July 2010

We report the sequence-based characterization and expression patterns of three manganese peroxidase genes from the white rot fungus and grape vine pathogen
Fomitiporia mediterranea
(Agaricomycotina, Hymenochaetales), termed
Fmmnp1
,
Fmmnp2
, and
Fmmnp3
. The predicted open reading frames (ORFs) are 1,516-, 1,351-, and 1,345-bp long and are interrupted by seven, four, and four introns, respectively. The deduced amino acid sequences encode manganese peroxidases (EC 1.11.1.13) containing 371, 369, and 371 residues, respectively, and are similar to the manganese peroxidases of the model white rot organism
Phanerochaete chrysosporium
. The expression of the genes is most likely differentially regulated, as revealed by real-time PCR analysis. Phylogenetic analysis reveals that other members of the order Hymenochaetales harbor
mnp
genes encoding proteins that are related only distantly to those of
F. mediterranea
. Furthermore, multiple partial
lip
- and
mnp
-like sequences obtained for
Pycnoporus cinnabarinus
(Agaricomycotina, Polyporales) suggest that lignin degradation by white rot taxa relies heavily on ligninolytic peroxidases and is not efficiently achieved by laccases only.
Construction of Self-Transmissible Green Fluorescent Protein-Based Biosensor Plasmids and Their Use for Identification ofN-Acyl Homoserine-Producing Bacteria in Lake Sediments
Authors: Lumjiaktase Putthapoom , Aguilar Claudio , Battin Tom , Riedel Kathrin , Eberl Leo
Published: July 2010

Many bacteria utilize quorum sensing (QS) systems to communicate with each other by means of the production, release, and response to signal molecules.N-Acyl homoserine lactone (AHL)-based QS systems are particularly widespread among theProteobacteria, in which they regulate various functions. It has become evident that AHLs can also serve as signals for interspecies communication. However, knowledge on the impact of AHLs for the ecology of bacteria in their natural habitat is scarce, due mainly to the lack of tools that allow the study of QS in bacterial communitiesin situ. Here, we describe the construction of self-mobilizable green fluorescent protein (GFP)-based AHL sensors that utilize the conjugation and replication properties of the broad-host-range plasmid RP4. We show that these novel AHL sensor plasmids can be easily transferred to different bacterial species by biparental mating and that they give rise to green fluorescent cells in case the recipient is an AHL producer. We also demonstrate that these sensor plasmids are capable of self-spreading within mixed biofilms and are a suitable tool for the identification of AHL-producing bacteria in lake sediment.
Phenotypic Characterization of
Shewanella oneidensis
MR-1 under Aerobic and Anaerobic Growth Conditions by Using Fourier Transform Infrared Spectroscopy and High-Performance Liquid Chromatography Analyses
Authors: Wang Hui , Hollywood Katherine , Jarvis Roger M. , Lloyd Jonathan R. , Goodacre Royston
Published: July 2010

Shewanella oneidensis
is able to conserve energy for growth by reducing a wide variety of terminal electron acceptors during anaerobic respiration, including several environmentally hazardous pollutants. This bacterium employs various electron transfer mechanisms for anaerobic respiration, including cell-bound reductases and secreted redox mediators. The aim of this study was to develop rapid tools for profiling the key metabolic changes associated with these different growth regimes and physiological responses. Initial experiments focused on comparing cells grown under aerobic and anaerobic conditions. Fourier transform infrared (FT-IR) spectroscopy with cluster analysis showed that there were significant changes in the metabolic fingerprints of the cells grown under these two culture conditions. FT-IR spectroscopy clearly differentiated cells of
S. oneidensis
MR-1 cultured at various growth points and cells grown using different electron acceptors, resulting in different phenotypic trajectories in the cluster analysis. This growth-related trajectory analysis is applied successfully for the first time, here with FT-IR spectroscopy, to investigate the phenotypic changes in contrasting
S. oneidensis
cells. High-performance liquid chromatography (HPLC) was also used to quantify the concentrations of flavin compounds, which have been identified recently as extracellular redox mediators released by a range of
Shewanella
species. The partial least-squares regression (PLSR) multivariate statistical technique was combined with FT-IR spectroscopy to predict the concentrations of the flavins secreted by cells of
S. oneidensis
MR-1, suggesting that this combination could be used as a rapid alternative to conventional chromatographic methods for analysis of flavins in cell cultures. Furthermore, coupling of the FT-IR spectroscopy and HPLC techniques appears to offer a potentially useful tool for rapid characterization of the
Shewanella
cell metabolome in various process environments.
Adaptation of Methanogenic Communities to the Cofermentation of Cattle Excreta and Olive Mill Wastes at 37°C and 55°C
Authors: Goberna Marta , Gadermaier Maria , García Carlos , Wett Bernhard , Insam Heribert
Published: July 2010

The acclimatization of methanogens to two-phase olive mill wastes (TPOMW) was investigated in pilot fermenters started up with cattle excreta (37°C) and after changing their feed to excreta plus TPOMW (37°C or 55°C) or TPOMW alone (37°C) until a steady state was reached (28 days). Methanogenic diversity was screened using a phylogenetic microarray (AnaeroChip), and positive targets were quantified by real-time PCR. Results revealed high phylogenetic richness, with representatives of three out of the four taxonomic orders found in digesters.
Methanosarcina
dominated in the starting excreta (>96% of total 16S rRNA gene copies; over 45 times more abundant than any other methanogen) at high acetate (0.21 g liter
−1
) and ammonia N concentrations (1.3 g liter
−1
). Codigestion at 37°C induced a 6-fold increase of
Methanosarcina
numbers, correlated with CH
4
production (
r
Pearson
= 0.94;
P
= 0.02). At 55°C, the rise in temperature and H
2
partial pressure induced a burst of
Methanobacterium
,
Methanoculleus
,
Methanothermobacter
, and a group of uncultured archaea. The digestion of excreta alone resulted in low but constant biogas production despite certain oscillations in the methanogenic biomass. Unsuccessful digestion of TPOMW alone was attributed to high Cu levels inducing inhibition of methanogenic activity. In conclusion, the versatile
Methanosarcina
immediately adapted to the shift from excreta to excreta plus TPOMW and was responsible for the stimulated CH
4
production at 37°C. Higher temperatures (55°C) fostered methanogenic diversity by promoting some H
2
scavengers while yielding the highest CH
4
production. Further testing is needed to find out whether there is a link between increased methanogenic diversity and reactor productivity.
Restoration of Growth Phenotypes of
Escherichia coli
DH5α in Minimal Media through Reversal of a Point Mutation in
purB
Authors: Jung Suk-Chae , Smith Chris L. , Lee Ki-Sung , Hong Min-Eui , Kweon Dae-Hyuk , Stephanopoulos Gregory , Jin Yong-Su
Published: July 2010

A point mutation (E115K) resulting in slower growth of
E
scherichia
coli
DH5α and XL1-Blue in minimal media was identified in the
purB
gene, coding for adenylosuccinate lyase (ASL), through complementation with an
E. coli
K-12 genomic library and serial subcultures. Chromosomal modification reversing the mutation to the wild type restored growth phenotypes in minimal media.
Functional Characterization of Three Leishmania Poly(A) Binding Protein Homologues with Distinct Binding Properties to RNA and Protein Partners
Authors: da Costa Lima Tamara D. , Moura Danielle M. N. , Reis Christian R. S. , Vasconcelos J. Ronnie C. , Ellis Louise , Carrington Mark , Figueiredo Regina C. B. Q. , de Melo Neto Osvaldo P.
Published: July 2010

Trypanosomatid protozoans are reliant on posttranscriptional processes to control gene expression. Regulation occurs at the levels of mRNA processing, stability, and translation, events that may require the participation of the poly(A) binding protein (PABP). Here, we have undertaken a functional study of the three distinct
Leishmania major
PABP (
Lm
PABP) homologues: the previously described
Lm
PABP1;
Lm
PABP2, orthologous to the PABP described from
Trypanosoma
species; and
Lm
PABP3, unique to
Leishmania
. Sequence identity between the three PABPs is no greater than 40%. In assays measuring binding to A-rich sequences,
Lm
PABP1 binding was poly(A) sensitive but heparin insensitive;
Lm
PABP2 binding was heparin sensitive and less sensitive to poly(A), compatible with unique substitutions observed in residues implicated in poly(A) binding; and
Lm
PABP3 displayed intermediate properties. All three homologues are simultaneously expressed as abundant cytoplasmic proteins in
L. major
promastigotes, but only
Lm
PABP1 is present as multiple isoforms. Upon transcription inhibition,
Lm
PABP2 and -3 migrated to the nucleus, while
Lm
PABP1 remained predominantly cytoplasmic. Immunoprecipitation assays showed an association between
Lm
PABP2 and -3. Although the three proteins bound to a
Leishmania
homologue of the translation initiation factor eukaryotic initiation factor 4G (eIF4G) (
Lm
EIF4G3)
in vitro
,
Lm
PABP1 was the only one to copurify with native
Lm
EIF4G3 from cytoplasmic extracts. Functionality was tested using RNA interference (RNAi) in
Trypanosoma brucei
, where both orthologues to
Lm
PABP1 and -2 are required for cellular viability. Our results indicate that these homologues have evolved divergent functions, some of which may be unique to the trypanosomatids, and reinforces a role for
Lm
PABP1 in translation through its interaction with the eIF4G homologue.