bluuebunny/crossref_metadata_2025_split huggingface dataset:
A wild-type Botrytis cinerea strain co-infected by double-stranded RNA mycoviruses presents hypovirulence-associated traits
Authors: Potgieter Christiaan A , Castillo Antonio , Castro Miguel , Cottet Luis , Morales Angélica 
Published: July 2013

Abstract

Background

Botrytis cinerea CCg378 is a wild-type strain infected with two types of double-stranded RNA (dsRNA) mycoviruses and which presents hypovirulence-associated traits. The objectives of the present study were to characterize the mycoviruses and investigate their relationship with the low virulence degree of the fungal host.

Results

B. cinerea CCg378 contains five dsRNA molecules that are associated with two different types of isometric viral particles of 32 and 23 nm in diameter, formed by structural polypeptides of 70-kDa and 48-kDa, respectively.
The transfection of spheroplasts of a virus-free strain, B. cinerea CKg54, with viral particles purified from the CCg378 strain revealed that the 2.2-kbp dsRNAs have no dependency on the smaller molecules for its stable maintenance in the fungal cytoplasm, because a fungal clone that only contains the 2.2-kbp dsRNAs associated with the 32-nm particles was obtained, which we named B. cinerea CKg54vi378. One of the 2.2 kbpdsRNA segments (2219 bp) was sequenced and corresponds to the gene encoding the capsid protein of B. cinerea CCg378 virus 1 (Bc378V1), a putative new member of the Partitiviridae family.
Furthermore, physiological parameters related to the degree of virulence of the fungus, such as the sporulation rate and laccase activity, were lower in B. cinerea CCg378 and B. cinerea CKg54vi378 than in B. cinerea CKg54. Additionally, bioassays performed on grapevine leaves showed that the CCg378 and CKg54vi378 strains presented a lower degree of invasiveness on the plant tissue than the CKg54 strain.

Conclusions
The results show that B. cinerea CCg378 is coinfected by two mycoviruses and that the 2.2-kbp dsRNAs correspond to the 32-nm mycovirus genome, which would be a new member of the Partitiviridae family as it has the typical pattern of partitiviruses. On the other hand, the results suggest that the hypovirulence of B. cinerea CCg378 could be conferred by both mycoviruses, since the fungal clone B. cinerea CKg54vi378 presents an intermediate virulence between the CKg54 and CCg378 strains. Therefore, the putative partitivirus would be partially contributing to the hypovirulence phenotype of the CCg378 strain.
Dual organism design cycle reveals small subunit substitutions that improve [NiFe] hydrogenase hydrogen evolution
Authors: Yonemoto Isaac T , Matteri Christopher W , Nguyen Thao Amy , Smith Hamilton O , Weyman Philip D 
Published: July 2013

Abstract

Background
Photosynthetic microorganisms that directly channel solar energy to the production of molecular hydrogen are a potential future biofuel system. Building such a system requires installation of a hydrogenase in the photosynthetic organism that is both tolerant to oxygen and capable of hydrogen production. Toward this end, we have identified the [NiFe] hydrogenase from the marine bacterium Alteromonas macleodii “Deep ecotype” that is able to be heterologously expressed in cyanobacteria and has tolerance to partial oxygen. The A. macleodii enzyme shares sequence similarity with the uptake hydrogenases that favor hydrogen uptake activity over hydrogen evolution. To improve hydrogen evolution from the A. macleodii hydrogenase, we examined the three Fe-S clusters found in the small subunit of many [NiFe] uptake hydrogenases that presumably act as a molecular wire to guide electrons to or from the active site of the enzyme. Studies by others altering the medial cluster of a Desulfovibrio fructosovorans hydrogenase from 3Fe-4S to 4Fe-4S resulted in two-fold improved hydrogen evolution activity.

Results
We adopted a strategy of screening for improved hydrogenase constructs using an Escherichia coli expression system before testing in slower growing cyanobacteria. From the A. macleodii enzyme, we created a mutation in the gene encoding the hydrogenase small subunit that in other systems is known to convert the 3Fe-4S medial cluster to 4Fe-4S. The medial cluster substitution did not improve the hydrogen evolution activity of our hydrogenase. However, modifying both the medial cluster and the ligation of the distal Fe-S cluster improved in vitro hydrogen evolution activity relative to the wild type hydrogenase by three- to four-fold. Other properties of the enzyme including thermostability and tolerance to partial oxygen did not appear to be affected by the substitutions.

Conclusions
Our results show that substitution of amino acids altering the ligation of Fe-S clusters in the A. macleodii [NiFe] uptake hydrogenase resulted in increased hydrogen evolution activity. This activity can be recapitulated in multiple host systems and with purified protein. These results validate the approach of using an E. coli-cyanobacteria shuttle system for enzyme expression and improvement.
The use of HE4, CA125 and CA72-4 biomarkers for differential diagnosis between ovarian endometrioma and epithelial ovarian cancer
Authors: Anastasi Emanuela , Granato Teresa , Falzarano Renato , Storelli Paola , Ticino Adele , Frati Luigi , Panici Pierluigi Benedetti , Porpora Maria Grazia 
Published: July 2013

AbstractBackgroundEndometriosis is frequently associated with high levels of CA125. This marker is therefore not useful for discriminating ovarian endometrioma from ovarian malignancy. The aim of this study was to establish a panel of complementary biomarkers that could be helpful in the differential diagnosis between ovarian endometriosis or other ovarian benign masses and ovarian cancer.MethodsBlood samples from 50 healthy women, 17 patients with benign ovarian tumors, 57 patients with ovarian endometrioma and 39 patients with ovarian cancer were analyzed and serum values were measured for the following biomarkers: CA125, HE4 and CA72-4.ResultsSerum CA125 concentration was elevated in both patients with ovarian endometriosis and ovarian cancer but not in patients with other benign ovarian masses. HE4 was never increased in patients with endometriosis or benign masses whereas it was significantly higher in all patients with ovarian cancer (p < 0.05). A marked difference in CA72-4 values was observed between women with ovarian cancer (67%) and those with endometriosis (p < 0.05).ConclusionsThe results of the study suggest that HE4 and CA72-4 determination is the best approach to confirm the benign nature of ovarian endometrioma in women with high CA125 levels.
Analysis of hairpin RNA transgene-induced gene silencing in Fusarium oxysporum
Authors: Schumann Ulrike , Smith Neil A , Kazan Kemal , Ayliffe Michael , Wang Ming-Bo 
Published: July 2013

Abstract

Background
Hairpin RNA (hpRNA) transgenes can be effective at inducing RNA silencing and have been exploited as a powerful tool for gene function analysis in many organisms. However, in fungi, expression of hairpin RNA transcripts can induce post-transcriptional gene silencing, but in some species can also lead to transcriptional gene silencing, suggesting a more complex interplay of the two pathways at least in some fungi. Because many fungal species are important pathogens, RNA silencing is a powerful technique to understand gene function, particularly when gene knockouts are difficult to obtain. We investigated whether the plant pathogenic fungus Fusarium oxysporum possesses a functional gene silencing machinery and whether hairpin RNA transcripts can be employed to effectively induce gene silencing.

Results
Here we show that, in the phytopathogenic fungus F. oxysporum, hpRNA transgenes targeting either a β-glucuronidase (Gus) reporter transgene (hpGus) or the endogenous gene Frp1 (hpFrp) did not induce significant silencing of the target genes. Expression analysis suggested that the hpRNA transgenes are prone to transcriptional inactivation, resulting in low levels of hpRNA and siRNA production. However, the hpGus RNA can be efficiently transcribed by promoters acquired either by recombination with a pre-existing, actively transcribed Gus transgene or by fortuitous integration near an endogenous gene promoter allowing siRNA production. These siRNAs effectively induced silencing of a target Gus transgene, which in turn appeared to also induce secondary siRNA production. Furthermore, our results suggested that hpRNA transcripts without poly(A) tails are efficiently processed into siRNAs to induce gene silencing. A convergent promoter transgene, designed to express poly(A)-minus sense and antisense Gus RNAs, without an inverted-repeat DNA structure, induced consistent Gus silencing in F. oxysporum.

Conclusions
These results indicate that F. oxysporum possesses functional RNA silencing machineries for siRNA production and target mRNA cleavage, but hpRNA transgenes may induce transcriptional self-silencing due to its inverted-repeat structure. Our results suggest that F. oxysporum possesses a similar gene silencing pathway to other fungi like fission yeast, and indicate a need for developing more effective RNA silencing technology for gene function studies in this fungal pathogen.
The role of viruses in autoreactive B cell activation within tertiary lymphoid structures in autoimmune diseases
Authors: Lucchesi Davide , Bombardieri Michele 
Published: June 2013

ABSTRACTTLS, characterized by the formation of ectopic B/T cell follicles with FDCs supporting an ectopic GC response, have been described in the target organs of several autoimmune diseases, including MS, RA, SS, and autoimmune thyroiditis. These structures represent functional niches, whereby autoreactive B cells undergo in situ affinity maturation and differentiation to autoantibody-producing cells, thus contributing to the progression and persistence of autoimmunity. Increasing evidence demonstrates that TLS can also develop in the context of cancer, as well as chronic infections. In this review, we collect recent evidences that highlights the relationship between persistent viral infection and the development of ectopic lymphoid structures in animal models and patients. Furthermore, we shall discuss the concept that whereas in physiological conditions, inducible TLS are critical for viral clearance and the establishment of protective immunity, but in the context of susceptible individuals, persistent viral infections may contribute, directly or indirectly, to the development of breach of tolerance against self-antigens and the development of autoimmunity through the formation of TLS.
Analysis of Molecular Motion of Proton-conductive Imidazolium Hydrogen Succinate Crystal Using Solid-state NMR
Authors: Umiyama Tsuyoshi , Ohashi Ryutaro , Ida Tomonori , Mizuno Motohiro 
Published: July 2013

Abstract
The dynamics of imidazolium ion and its influence on proton conductivity were investigated for imidazolium hydrogen succinate crystal using solid-state 2H and 13C NMR. A 180° flip and libration (rotational vibration) of the imidazolium ion were observed from 2H NMR broad line spectra, quadrupole Carr–Purcell–Meiboom–Gill (QCPMG) spectra and high-resolution 13C NMR spectra. From a comparison of the rates of these motions and proton transfer, the libration of imidazolium ion is important for the proton conductive process.
Heterogeneous Enantioselective Hydrogenation: pH Dependence and Interplay between Catalytic Efficacy and Surface Composition
Authors: Osawa Tsutomu , Kizawa Tomoko , Ikeda Shinji , Kitamura Takayuki , Inoue Yoshihisa , Borovkov Victor 
Published: July 2013

Abstract
The performance of a catalytic system consisting of metallic Ni powder, tartaric acid (TA), and NaBr in the enantioselective hydrogenation of methyl acetoacetate was strongly influenced by the pH of TA solution upon chiral modification, which is attributable to the pH-induced change in the surface composition of Ni catalyst as unambiguously confirmed by X-ray photoelectron spectroscopy for the first time.
Modelling and Simulation of Gas–liquid Hydrodynamics in a Rectangular Air-lift Reactor
Authors: Scargiali Francesca , Busciglio Antonio , Cipollina Andrea , Grisafi Franco , Micale Giorgio , Tamburini Alessandro , Vella Giuseppa , Brucato Alberto 
Published: July 2013

AbstractComputational Fluid Dynamics is a quite well established tool for carrying out realistic simulations of process apparatuses. However, as a difference from single phase systems, for multiphase systems the development of CFD models is still in progress. Among the two-phase systems, gas–liquid systems are characterised by an additional complexity level, related to the fact that bubble sizes are not known in advance, being rather the result of formation and breakage-coalescence dynamics and therefore of complex phenomena related to flow dynamics and interfacial effects. In the present work, Euler–Euler Reynolds-averaged flow simulations of an air-lift reactor are reported. All bubbles are assumed to share the same size, and a simplified approach is adopted for modelling inter-phase momentum exchange, that involves bubble terminal velocity as the sole parameter needed. Good agreement between simulation results and literature experimental data is found for all the gas flow rates simulated. This result implies that, despite the many simplifications that have to be adopted in order to make them viable, fully predictive CFD simulations of gas–liquid systems can give rise to reasonably accurate predictions of reactor fluid dynamics.
PAX8 is expressed in anaplastic thyroid carcinoma diagnosed by fine-needle aspiration: a study of three cases with histological correlates
Authors: Bellevicine Claudio , Iaccarino Antonino , Malapelle Umberto , Sasso Ferdinando Carlo , Biondi Bernardette , Troncone Giancarlo 
Published: June 2013

ObjectiveIt is difficult to diagnose anaplastic thyroid carcinoma (ATC) in a fine-needle aspiration (FNA) sample because, given the loss of morphological and immunophenotypical follicular thyroid features, its cytology resembles that of other undifferentiated neoplasms. Recent studies have shown that immunostaining for paired box gene 8 (PAX8), a transcription factor expressed in normal thyroid, is effective for diagnosing ATCs on histology. The aim of this study was to evaluate whether PAX8 could be used to identify ATCs on cytology also.Design and methodsWe selected three PAX8-immunostained undifferentiated FNA samples previously diagnosed as suspected ATCs, whose cell block had been negative for the expression of TGB and thyroid transcription factor-1. Matched histological samples, available in two cases, were also processed for PAX8 immunohistochemistry.ResultsAll three FNA samples were PAX8 positive. Two samples that had an epithelioid pattern showed a diffuse, intense nuclear signal. The third sample, which had a spindle-cell pattern, showed less intense and more patchy staining. Matched histology yielded overlapping results.ConclusionsPAX8 immunocytochemistry can help cytopathologists to diagnose ATCs.
Roux-en-Y gastric bypass and calorie restriction induce comparable time-dependent effects on thyroid hormone function tests in obese female subjects
Authors: Lips Mirjam A , Pijl Hanno , van Klinken Jan B , de Groot Gerrit H , Janssen Ignace M , Van Ramshorst Bert , Van Wagensveld Bart A , Swank Dingeman J , Van Dielen Fracois , Smit Johannes W A 
Published: June 2013

ObjectiveObesity and weight loss influence thyroid hormone physiology. The effects of weight loss by calorie restriction vs Roux-en-Y gastric bypass (RYGB) in obese subjects have not been studied in parallel. We hypothesized that differences in transient systemic inflammation and catabolic state between the intervention types could lead to differential effects on thyroid hormone physiology.Design and methodsWe recruited 12 lean and 27 obese females with normal fasting glucose (normal glucose tolerant (NGT)) and 27 obese females with type 2 diabetes mellitus (T2DM) for this study. Weight loss was achieved by restrictive treatment (gastric banding or high-protein-low-calorie diet) or by RYGB. Fasting serum leptin, TSH, triiodothyronine (T3), reverse T3(rT3), and free thyroxine (fT4) concentrations were measured at baseline and 3 weeks and 3 months after the start of the interventions.ResultsObesity was associated with higher TSH, T3, and rT3levels and normal fT4levels in all the subjects when compared with the controls. After 3 weeks, calorie restriction and RYGB induced a decline in TSH levels and a rise in rT3and fT4levels. The increase in rT3levels correlated with serum interleukin 8 (IL8) and IL6 levels. After 3 months, fT4and rT3levels returned to baseline levels, whereas TSH and T3levels were persistently decreased when compared with baseline levels. No differences in the effects on thyroid hormone parameters between the interventions or between NGT and T2DM subjects were observed at any time point.ConclusionsIn summary, weight loss directly influences thyroid hormone regulation, independently of the weight loss strategy used. The effects may be explained by a combination of decreased leptin levels and transient changes in peripheral thyroid hormone metabolism.
Effect of Continuous, Trapped, and Flowing Gas on Performance of Alkaline Surfactant Polymer ASP Flooding
Authors: Farajzadeh R.. , Ameri A.. , Faber M. J. , Van Batenburg D. W. , Boersma D. M. , Bruining J.. 
Published: July 2013

Abstract
Alkali Surfactant Polymer (ASP) flooding has traditionally been considered in tertiary mode, i.e., after a reservoir has been sufficiently water flooded. In screening studies experiments are usually conducted under two-phase flow conditions, i.e., in the absence of a gas phase in the rock.
In practice, oil reservoirs might contain some gas. In areas in the world, where gas flaring is not allowed and an infrastructure for gas transportation is not present, re-injection of produced gas is a common practice. Moreover, when the reservoir is depressurized below bubble point a gas phase will be created.
To the best of our knowledge, there are no data in the literature concerning the influence of in-situ gas phase (continuous or trapped) on the performance of ASP floods. The main objective of this paper is to evaluate how the presence of a free (non-dissolved) gas phase affects ASP flood performance. To this end, several experiments were carried out to evaluate different conditions, where free gas was present, either flowing or trapped.
We found that the ultimate residual oil saturation in most experiments is similar to the case without gas. When free gas is present in the porous medium, the oil-bank production occurs earlier, because a large fraction of the gas remains trapped and therefore the "effective" pore volume for liquid flow is reduced. When the gas and the ASP solution are co-injected, the oil is mostly produced in emulsion form as gas enhances mixing of the in-situ fluids. Trapped gas could lead to an efficient oil recovery, depending on the amount of trapped gas: the lower the trapped gas saturation the better the oil recovery.
Laboratory Investigation of Factors Affecting CO2 Enhanced Oil and Gas Recovery
Authors: Liu Keyu , Clennell Ben , Honari Abdolvahab , Sayem Taschfeen , Rashid Abdul , Wei Xiaofang , Saeedi Ali 
Published: July 2013

Abstract
A series of laboratory investigation on factors affecting Enhanced Oil and Gas Recovery and CO&lt;sub&gt;2&lt;/sub&gt; geo-sequestration were conducted. The coreflooding experiments were done using a relatively heavy crude oil (18& API), a number of brines of 0.18%-2.5% NaCl and varieties of cores with a range porosity and permeability from 15% and 17 mD to 19% and 330 mD under some typical reservoir pressure-temperature condition of 1164-3300 psi and 50-83 &C. Factors affecting CO&lt;sub&gt;2&lt;/sub&gt; enhanced oil and gas recovery including the effects of the petrophysical properties of the reservoir rocks, formation water salinity, reservoir pressure, the Minimum Miscibility Pressure (MMP), total volume (PV) injected and injection rate and gravity segregation.
Excellent recovery factors in the range of 27%-34% Original Oil In Place (OOIP) and almost 100% gas recovery were achieved through immiscible and miscible CO&lt;sub&gt;2&lt;/sub&gt; flooding. Some of the coreflooding experiments were monitored with a medical CT in real time. The coreflooding experiments have shown that (1) reservoir petrophysical properties with permeability difference of up to an order of magnitude do not affect the CO&lt;sub&gt;2&lt;/sub&gt; EOR factor; (2) variable EOR can be achieved both at reservoir pressures below or above the CO&lt;sub&gt;2&lt;/sub&gt;-oil MMP; (3) Incremental oil recovery is proportional to the pore volume (PV) of CO&lt;sub&gt;2&lt;/sub&gt; injected up to 3PV; (4) No significant additional recovery was observed beyond the MMP; (5) CO&lt;sub&gt;2&lt;/sub&gt;-Water alternating gas (WAG) flooding can be quite effective in EOR in terms of the less amount of CO&lt;sub&gt;2&lt;/sub&gt; injected as compared to that for the single CO&lt;sub&gt;2&lt;/sub&gt;-water flooding to achieve the same EOR; (6) there is no benefit to use low-salinity CO&lt;sub&gt;2&lt;/sub&gt; WAG flooding; (7) the optimum injection rate in the laboratory is around 1 cc/minute. These finding may provide some useful insight and guide for the field application of CO&lt;sub&gt;2&lt;/sub&gt; enhanced oil and gas recovery; (8) During enhanced gas recovery using supercritical CO&lt;sub&gt;2&lt;/sub&gt;, gravity segregation may occur in some porous-permeable reservoir with denser supercritical CO&lt;sub&gt;2&lt;/sub&gt; preferentially enter through the bottom of the reservoir.
Enhancing Value of Polymer Flood Project with Proactive Well and Reservoir Management
Authors: Choudhuri Biswajit , Kalbani Ali , Cherukupalli Pradeep Kumar , Ravula Chakravarthi , Hashmi Khalid , Jaspers Henri 
Published: July 2013

Summary
In viscous oil reservoirs, Polymer flooding is often used to improve oil recovery either after a short period of waterflooding or as a tertiary recovery process following extensive period of waterflood. After six years of water flooding in a major reservoir in Sultanate of Oman having viscous oil (90cp), a field development plan was developed to implement polymer flooding in this reservoir with anticipated incremental oil recovery of around 10% over and above that of waterflood. Necessary facilities were constructed, injection and production wells were drilled, completed, converted and the polymer flood project was initiated and ongoing since the last three years through 27 polymer injectors. By implementing proactive Well and Reservoir Management (WRM) strategies, the actual oil recoveries have been better than predicted levels so far. It is demonstrated here that proactive well and reservoir management through proper well and reservoir surveillance and dynamic adjustment of injection and production rates play a very important role in improving the performance of polymer floods as in waterfloods.
Well and Reservoir Management (WRM) principles in case of a polymer flood are similar to that of high mobility ratio waterfloods with some additional aspects that are specific to a polymer flood scenario. Polymer chemical costs, its higher viscosity and non Newtonian fluid flow behavior all create unique conditions that are nonexistent in normal waterfloods. This, in turn, dictates the strategies and methods employed to optimize polymer flood performance. This paper details successful implementation of proactive WRM strategy that has played a key role in sustaining production from this polymer flood field to date. It describes the pattern management processes to optimize pattern wise polymer injection and oil recoveries, conformance control measures implemented to increase sweep and oil recovery, innovative surveillance techniques to monitor fracture growth in polymer injection wells and for evaluation and optimization of production/injection profiles. Production wells and facilities issues arising from polymer breakthrough are being addressed to mitigate any adverse effects.