bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlates of gut community composition across an ant species (Cephalotes varians) elucidate causes and consequences of symbiotic variability
Authors: Hu Yi , Łukasik Piotr , Moreau Corrie S. , Russell Jacob A.
Published: November 2013

Insect guts are often colonized by multispecies microbial communities that play integral roles in nutrition, digestion and defence. Community composition can differ across host species with increasing dietary and genetic divergence, yet gut microbiota can also vary between conspecific hosts and across an individual's lifespan. Through exploration of such intraspecific variation and its correlates, molecular profiling of microbial communities can generate and test hypotheses on the causes and consequences of symbioses. In this study, we used 454 pyrosequencing and TRFLP to achieve these goals in an herbivorous ant, Cephalotes varians, exploring variation in bacterial communities across colonies, populations and workers reared on different diets. C. varians bacterial communities were dominated by 16 core species present in over two‐thirds of the sampled colonies. Core species comprised multiple genotypes, or strains and hailed from ant‐specific clades containing relatives from other Cephalotes species. Yet three were detected in environmental samples, suggesting the potential for environmental acquisition. In spite of their prevalence and long‐standing relationships with Cephalotes ants, the relative abundance and genotypic composition of core species varied across colonies. Diet‐induced plasticity is a likely cause, but only pollen‐based diets had consistent effects, altering the abundance of two types of bacteria. Additional factors, such as host age, genetics, chance or natural selection, must therefore shape natural variation. Future studies on these possibilities and on bacterial contributions to the use of pollen, a widespread food source across Cephalotes, will be important steps in developing C. varians as a model for studying widespread social insect‐bacteria symbioses.
The broad bacterial blight resistance of rice line CBB23 is triggered by a novel transcription activator‐like (TAL) effector of Xanthomonas oryzae pv. oryzae
Authors: Wang Chun‐Lian , Qin Teng‐Fei , Yu Hong‐Man , Zhang Xiao‐Ping , Che Jin‐Ying , Gao Ying , Zheng Chong‐Ke , Yang Bing , Zhao Kai‐Jun
Published: November 2013

Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is not only a disease devastating rice production worldwide, but also an ideal model system for the study of the interaction between plants and their bacterial pathogens. The rice near‐isogenic line (NIL) CBB23, derived from a cross between a wild rice Oryza rufipogon accession (RBB16) and a susceptible indica rice variety (Jingang 30), is highly resistant to all field Xoo strains tested so far. Although the BB resistance of CBB23 has been widely used in rice breeding programmes, the mechanism of its extremely broad‐spectrum resistance remains unknown. Here, we report the molecular cloning of an avirulence gene, designated as avrXa23, from Xoo strain PXO99A. We validate that AvrXa23, a novel transcription activator‐like effector, specifically triggers the broad‐spectrum BB resistance in CBB23. The prevalence of avrXa23 in all 38 Xoo strains surveyed may explain the broad‐spectrum feature of BB resistance in CBB23. The results will significantly facilitate the molecular cloning of the corresponding resistance (R) gene in the host, and provide new insights into our understanding of the molecular mechanism for broad‐spectrum disease resistance in plants.
A survey of 165 sporotrichosis cases examined in Nagasaki prefecture from 1951 to 2012
Authors: Takenaka Motoi , Yoshizaki Asako , Utani Atushi , Nishimoto Katsutaro
Published: November 2013

A total of 165 sporotrichosis cases occurring in Nagasaki prefecture, and examined at Nagasaki University Hospital, were evaluated. Both males and females were equally affected, with no significant differences in the affected body regions. Lesions were frequently seen on the face (49 cases, 29.5%) and upper limbs (101 cases, 60.9%). The localised cutaneous type of sporotrichosis (105 cases, 62.9%) was much more frequent than the lymphocutaneous type (62 cases, 37.1%). The infection rate in patients over 50 years of age was 73.1%. The most frequent occupation among the patients was farming (52 cases, 37.4%), and 34 patients had a history of injury. Regarding the geographical distribution of sporotrichosis, 48 cases occurred in the Shimabara peninsula (31.2%) and this is much higher than expected for the population size. Before 1994, almost all sporotrichosis cases (112 cases, 96.5%) were treated with potassium iodide (KI). After 1995, the number of patients treated with KI decreased (nine cases, 23.1%), and itraconazole (ITZ) was used in 21 cases (59.0%) and terbinafine in six cases (15.3%). The time between ITZ and KI treatment and cure was 13.8 weeks and 12.5 weeks, respectively. All 116 cases, for which the outcome was known, were cured or improved.
High‐density genome‐wide association mapping implicates an F‐box encoding gene in Medicago truncatula resistance to Aphanomyces euteiches
Authors: Bonhomme Maxime , André Olivier , Badis Yacine , Ronfort Joëlle , Burgarella Concetta , Chantret Nathalie , Prosperi Jean‐Marie , Briskine Roman , Mudge Joann , Debéllé Frédéric , Navier Hélène , Miteul Henri , Hajri Ahmed , Baranger Alain , Tiffin Peter , Dumas Bernard , Pilet‐Nayel Marie‐Laure , Young Nevin D. , Jacquet Christophe
Published: November 2013

The use of quantitative disease resistance (QDR) is a promising strategy for promoting durable resistance to plant pathogens, but genes involved in QDR are largely unknown. To identify genetic components and accelerate improvement of QDR in legumes to the root pathogen Aphanomyces euteiches, we took advantage of both the recently generated massive genomic data for Medicago truncatula and natural variation of this model legume.

A high‐density (≈5.1 million single nucleotide polymorphisms (SNPs)) genome‐wide association study (GWAS) was performed with both in vitro and glasshouse phenotyping data collected for 179 lines.

GWAS identified several candidate genes and pinpointed two independent major loci on the top of chromosome 3 that were detected in both phenotyping methods. Candidate SNPs in the most significant locus ( = 23%) were in the promoter and coding regions of an F‐box protein coding gene. Subsequent qRT‐PCR and bioinformatic analyses performed on 20 lines demonstrated that resistance is associated with mutations directly affecting the interaction domain of the F‐box protein rather than gene expression.

These results refine the position of previously identified QTL to specific candidate genes, suggest potential molecular mechanisms, and identify new loci explaining QDR against A. euteiches.
A dual gene‐silencing vector system for monocot and dicot plants
Authors: Liou Ming‐Ru , Huang Ying‐Wen , Hu Chung‐Chi , Lin Na‐Sheng , Hsu Yau‐Heiu
Published: November 2013

Plant virus‐based gene‐silencing vectors have been extensively and successfully used to elucidate functional genomics in plants. However, only limited virus‐induced gene‐silencing (VIGS) vectors can be used in both monocot and dicot plants. Here, we established a dual gene‐silencing vector system based on Bamboo mosaic virus (BaMV) and its satellite RNA (satBaMV). Both BaMV and satBaMV vectors could effectively silence endogenous genes in Nicotiana benthamiana and Brachypodium distachyon. The satBaMV vector could also silence the green fluorescent protein (GFP) transgene in GFP transgenic N. benthamiana. GFP transgenic plants co‐agro‐inoculated with BaMV and satBaMV vectors carrying sulphur and GFP genes, respectively, could simultaneously silence both genes. Moreover, the silenced plants could still survive with the silencing of genes essential for plant development such as heat‐shock protein 90 (Hsp90) and Hsp70. In addition, the satBaMV‐ but not BaMV‐based vector could enhance gene‐silencing efficiency in newly emerging leaves of N. benthamiana deficient in RNA‐dependant RNA polymerase 6. The dual gene‐silencing vector system of BaMV and satBaMV provides a novel tool for comparative functional studies in monocot and dicot plants.
Long‐Term Treatment with Oral Propranolol Reduces Relapses of Infantile Hemangiomas
Authors: Giachetti Ana , Garcia‐Monaco Ricardo , Sojo Magdalena , Scacchi María F. , Cernadas Carolina , Guerchicoff Lemcke Marianna , Dovasio Fernanda
Published: November 2013

Oral propranolol (OP) has been shown to be effective in the treatment of complicated infantile hemangiomas (IHs), but optimal treatment duration to avoid relapses after stopping OP treatment has not been established. The objective of this study was to compare the frequency of relapses in long‐term OP treatment with that of short‐term OP treatment. This was a retrospective cohort study of 30 patients with complicated IHs who received treatment with OP. Patients were divided into two groups: OP treatment of 8 months or less and OP treatment of longer than 8 months. OP was started at 1 mg/kg/day in three doses every 8 hours for 1 week and increased to 1.5 to 4 mg/kg/day afterward. Ultrasound was used to objectively measure the response to treatment. Clinical and ultrasound assessment showed a decrease in IH size and resolution of complications in all patients (n = 30). In the short‐term group (n = 10), nine patients (90%) relapsed after stopping treatment. In the long‐term group (n = 20), the duration of treatment was 12 months in all patients, and only 1 patient out of the 20 treated (5%) showed relapse 2 months after finishing the full treatment (odds ratio = 18, 95% confidence interval 2.6, 123, p < 0.001. Twelve months of treatment of IH with OP is associated with a significantly lower rate of relapse than with shorter treatment.
Impact of palifermin on incidence of oral mucositis and healthcare utilization in children undergoing autologous hematopoietic stem cell transplantation for malignant diseases
Authors: Vitale Kelly M. , Violago Leah , Cofnas Paige , Bishop Jacquelyn , Jin Zhezhen , Bhatia Monica , Kung Andrew L. , George Diane , Garvin James , Satwani Prakash
Published: November 2013

Palifermin has been demonstrated to decrease the incidence of severe oral mucositis in adults following TBI containing conditioning regimens prior to AHSCT. The impact of palifermin on the incidence of oral mucositis in children undergoing AHSCT has never been studied. We compared the effect of palifermin on the incidence of oral mucositis and supportive care in 58 children undergoing myeloablative AHSCT; 25 children received palifermin and 33 children did not receive palifermin (control arm). Oral mucositis was graded as per WHO criteria. The demographic characteristics were comparable between the two arms. Results comparing the palifermin vs. control arm showed that the incidence of grade III–IV oral mucositis was 20% vs. 42.4% (p = 0.072). The number of days patients received patient‐controlled analgesia and total parenteral nutrition in the palifermin vs. control arm were 8.80 ± 8.39 vs. 8.30 ± 8.54 (p = 0.826) and 13.52 ± 11.32 vs. 11.55 ± 9.63 (p = 0.484), respectively. The average length of hospitalization in the palifermin vs. control arm was 31.44 ± 7.42 vs. 28.61 ± 10.38 (p = 0.252), respectively. In this study, we were unable to demonstrate a statistical difference in the incidence of oral mucositis and other supportive care needs or a decrease in hospital stay between the two arms.
Philosophy and Phylogenetics
Authors: Velasco Joel D.
Published: November 2013

Phylogenetics is the study and reconstruction of evolutionary history and is filled with numerous foundational issues of interest to philosophers. This paper briefly introduces some central concepts in the field, describes some of the main methods for inferring phylogenies, and provides some arguments for the superiority of model‐based methods such as Likelihood and Bayesian methods over nonparametric methods such as parsimony. It also raises some underdeveloped issues in the field of interest to philosophers.
Nutritional abrogation of photoimmunosuppression: in vivo investigations
Authors: Pilkington Suzanne M. , Gibbs Neil K. , Friedmann Peter S. , Rhodes Lesley E.
Published: November 2013

Skin cancer is a major public health concern, and the primary aetiological factor in the majority of skin cancers is ultraviolet radiation (UVR) exposure. UVR not only induces potentially mutagenic DNA damage but also suppresses cell‐mediated immunity (CMI), allowing cancerous cells to escape destruction and progress to tumours. A considerable proportion of an individual's annual sun exposure is obtained outside the vacation period when topical and physical measures for photoprotection are irregularly used. Certain nutrients could provide an adjunctive protective role, and evidence is accruing from experimental studies to support their use in abrogation of photoimmunosuppression. Moreover, developments in clinical research methods to evaluate impact of solar‐simulated radiation on cutaneous CMI allow the immune protective potential of nutritional agents to be examined in humans in vivo. This article summarises the mediation of CMI and its suppression by UVR, evaluates the methodology for quantitative assessment in vivo, reviews the human studies reported on nutritional abrogation of photoimmunosuppression including recent randomized controlled trials and discusses the mechanisms of photoprotection by the nutrients. This includes, in addition to antioxidants, novel studies of omega‐3 polyunsaturated fatty acids and nicotinamide.
Genotypic variation and population structure of Sclerotinia trifoliorum infecting chickpea in California
Authors: Njambere E. N. , Peever T. L. , Vandemark G. , Chen W.
Published: November 2013

Sclerotinia trifoliorum, an important pathogen of cool season legumes, displays both homothallism and heterothallism in its life cycle, unique among members of the genus Sclerotinia. Very little is known about its genetic diversity and population structure. A sample of 129 isolates of S. trifoliorum from diseased chickpea in California was investigated for genetic diversity, population differentiation and reproductive mode. Genetic diversity was estimated using mycelial compatibility (MCG) phenotypes, rDNA intron variation, and allelic diversity at seven microsatellite loci. Genetic analysis revealed high levels of genotypic diversity demonstrated by high genotypic richness (0·88). Similarly, high levels of gene diversity (mean expected heterozygosity HE = 0·68) were observed at the microsatellite loci. Geographic populations of S. trifoliorum were highly admixed as evident from low FST values (0–0·11), suggesting high contemporary or historical gene flow. Hierarchical analysis of molecular variance showed that more than 92% of the genetic variation occurred among isolates within populations. Bayesian clustering analysis identified four cryptic genetic populations that were not correlated to geographic location, and index of multilocus association was non‐significant in each of the four genetic populations. However, the presence of identical haplotypes within and among populations indicates clonal reproduction. The high levels of haplotype diversity and population heterogeneity, a lack of correspondence between MCG and microsatellite haplotype, and low levels of population differentiation suggest that populations of S. trifoliorum in chickpea have been undergoing extensive outcrossing and migration events probably shaped by human‐mediated dissemination, the underlying diverse cropping systems, and chickpea disease management practices.
The Sputum Colour Chart as a predictor of lung inflammation, proteolysis and damage in non‐cystic fibrosis bronchiectasis: A case–control analysis
Authors: Goeminne Pieter C. , Vandooren Jennifer , Moelants Eva A. , Decraene Ann , Rabaey Evelyn , Pauwels Ans , Seys Sven , Opdenakker Ghislain , Proost Paul , Dupont Lieven J.
Published: November 2013

Background and objective

Non‐cystic fibrosis bronchiectasis (NCFB) is characterized by a vicious cycle of airway infection, inflammation and structural damage with inappropriate mucus clearance. Our aim was to relate the value of proteolytic enzymes, proteolytic enzyme activity and inflammatory markers to disease severity and symptoms in patients with NCFB.

Methods

Sputum induction in NCFB patients and healthy controls was performed. Sputum was analysed for total and differential cell count, markers of inflammation (CXCL8 (also known as interleukin‐8) and tumour necrosis factor‐α (TNF‐α)) and proteolytic enzymes (neutrophil elastase (NE), gelatin zymography and total gelatinolytic activity (TGA)). Each patient was evaluated by spirometry, Leicester Cough Questionnaire (LCQ) and Sputum Colour Chart (SCC). Patient files were analysed to determine Pseudomonas aeruginosa colonization status. The computed tomography (CT) closest to the date sputum induction was scored by a radiologist.

Results

NCFB patients showed significantly higher neutrophils, CXCL8, TNF‐α, NE and TGA than healthy controls. TGA subanalysis showed that the majority of the activity was NE (82 ± 6.4%). Residual activity was mainly zinc ion‐dependent matrix metalloproteinase (MMP) activity (18 ± 6.4%). Subanalysis showed that patients with chronic Pseudomonas aeruginosa colonization had more activated MMP‐9. Correlations were seen between proteolytic enzymes and inflammation and disease severity (spirometry and CT score), but not with the LCQ. SCC was associated with increased markers of inflammation, proteolytic enzymes and worse CT score.

Conclusions

We show that sputum purulence assessment in daily clinical practice using the SCC is a quick and easy tool that reflects severity of inflammation, destruction and proteolytic enzymatic activity/presence.
Farmers' Contribution to Agricultural Social Capital: Evidence from Southern Spain
Authors: Gómez‐Limón José A. , Vera‐Toscano Esperanza , Garrido‐Fernández Fernando E.
Published: November 2013

Social capital is the whole set of shared norms, values, attitudes, and beliefs that promote cooperation among individuals within the community and that has proved to be a key factor in explaining development processes. This article aims to provide an analytically reliable notion of social capital within the farming sector and a methodological tool for empirically measuring how social capital is accumulated at the farmer level. The theoretical framework proposed is based on the multidimensionality of the complex concept of social capital. Thus, to develop a comprehensive index for social capital, we identify three dimensions of the concept, structural, relational, and cognitive social capital, each one also comprising several subdimensions. This integrative approach permits creation of a composite indicator of the agricultural social capital accumulated at the farmer level, further identifying socioeconomic factors that influence its accumulation at that level. We empirically apply this methodological approach to farmers in Andalusia in southern Spain as a case study. This research provides an interesting starting point for informing policymakers about social capital and helping them implement the necessary programs to facilitate sustainable development in the agricultural sector.
Full‐length sequence of KIR3DL1*01501 allele found in Sub‐Saharan Africa by long‐range sequencing
Authors: Yindom L.‐M. , de Silva T. I. , Rowland‐Jones S. L.
Published: November 2013

Full‐length KIR3DL1*01501 differing from KIR3DL1*0150201 with 10 SNPs and 2 nucleotide deletion in intron 7.
Expansion of the dengue transmission area in Brazil: the role of climate and cities
Authors: Barcellos Christovam , Lowe Rachel
Published: November 2013

Objectives

To examine the spatial and temporal patterns of the recent expansion of dengue transmission area in Brazil (2001–2012) with the aim to identify pathways and constraints to dengue diffusion.

Methods

Synthetic indicators were calculated to characterise timing (year of first dengue outbreak), permanence (number of years with dengue outbreaks) and intensity (outbreak occurrence). The indicators were used to map dengue diffusion and compare cities within different climatic zones, with varying population densities.

Results

Currently, a large portion of the country comprises a dengue transmission area, but cities situated in the mesothermal zone, in the south, and remote areas, in the north, are relatively exempt. Diffusion waves are spread from metropolitan areas towards medium and small cities generating outbreaks in their influence region. However, long‐term permanence of transmission depends on the existence of a favourable climate, abundant population and connectivity.

Conclusions

Large and warm cities sustain and spread dengue viruses, for which specific dengue control measures must be developed. The concentration of outbreaks along climate transition fringes indicates a boundary between two transmission regimes and raises awareness to the effects of ongoing climatic and socio‐economic changes.
Flows Through Reconstructed Porous Media Using Immersed Boundary Methods
Authors: Nagendra Krishnamurthy , Tafti Danesh K.
Published: November 2013

Understanding flow through real porous media is of considerable importance given their significance in a wide range of applications. Direct numerical simulations of such flows are very useful in their fundamental understanding. Past works have focused mainly on ordered and disordered arrays of regular shaped structures such as cylinders or spheres to emulate porous media. More recently, extension of these studies to more realistic pore spaces are available in the literature highlighting the enormous potential of such studies in helping the fundamental understanding of pore-level flow physics. In an effort to advance the simulation of realistic porous media flows further, an immersed boundary method (IBM) framework capable of simulating flows through arbitrary surface contours is used in conjunction with a stochastic reconstruction procedure based on simulated annealing. The developed framework is tested in a two-dimensional channel with two types of porous sections—one created using a random assembly of square blocks and another using the stochastic reconstruction procedure. Numerous simulations are performed to demonstrate the capability of the developed framework. The computed pressure drops across the porous section are compared with predictions from the Darcy–Forchheimer equation for media composed of different structure sizes. Finally, the developed methodology is applied to study CO2 diffusion in porous spherical particles of varying porosities.
Elastohydrodynamic Lubrication Model With Limiting Shear Stress Behavior Considering Realistic Shear-Thinning and Piezo-Viscous Response
Authors: Kumar Punit , Anuradha Parinam
Published: November 2013

This paper addresses a largely ignored aspect pertaining to the elastohydrodynamic lubrication (EHL) traction behavior of fragile lubricants which undergo transition to glassy state at typical EHL contact zone pressures. For such lubricants, a conventional EHL model predicts extremely high and unrealistic values of traction coefficient, especially under near pure rolling conditions where thermal effect is negligible. Therefore, an EHL model incorporating the effect of limiting shear stress and the associated wall slip phenomenon is presented herein. Unlike the other such investigations involving limiting shear stress behavior, the present model employs Carreau-type power-law based models to describe the rheology of lubricants below the limiting shear stress along with realistic pressure-viscosity relationships (WLF and Doolittle-Tait). The use of Carreau-type shear-thinning model in this analysis allows the simultaneous prediction of minimum film thickness and traction coefficient for lubricants which shear-thin in the inlet zone and exhibit limiting shear stress behavior in the contact zone, a feature absent in the existing EHL models utilizing ideal visco-plastic or some other unrealistic rheological model. Using published experimental data pertaining to the shear-thinning and pressure-viscosity response of two fragile lubricants (L100 and LVI260), it has been demonstrated that the present model can explain the appearance of plateau in the experimental traction curve. Also, the influence of shear-thinning parameters and the pressure-viscosity coefficient on the predicted limiting shear stress zone has been studied.
Comparative performance of modern digital mammography systems in a large breast screening program
Authors: Yaffe Martin J. , Bloomquist Aili K. , Hunter David M. , Mawdsley Gordon E. , Chiarelli Anna M. , Muradali Derek , Mainprize James G.
Published: November 2013

Purpose:

To compare physical measures pertaining to image quality among digital mammography systems utilized in a large breast screening program. To examine qualitatively differences in these measures and differences in clinical cancer detection rates between CR and DR among sites within that program.

Methods:

As part of the routine quality assurance program for screening, field measurements are made of several variables considered to correlate with the diagnostic quality of medical images including: modulation transfer function, noise equivalent quanta, d′ (an index of lesion detectability) and air kerma to allow estimation of mean glandular dose. In addition, images of the mammography accreditation phantom are evaluated.

Results:

It was found that overall there were marked differences between the performance measures of DR and CR mammography systems. In particular, the modulation transfer functions obtained with the DR systems were found to be higher, even for larger detector element sizes. Similarly, the noise equivalent quanta, d′, and the phantom scores were higher, while the failure rates associated with low signal‐to‐noise ratio and high dose were lower with DR. These results were consistent with previous findings in the authors’ program that the breast cancer detection rates at sites employing CR technology were, on average, 30.6% lower than those that used DR mammography.

Conclusions:

While the clinical study was not large enough to allow a statistically powered system‐by‐system assessment of cancer detection accuracy, the physical measures expressing spatial resolution, and signal‐to‐noise ratio are consistent with the published finding that sites employing CR systems had lower cancer detection rates than those using DR systems for screening mammography.
Nanoscale Fe
2
O
3
-Based Catalysts for Selective Hydrogenation of Nitroarenes to Anilines
Authors: Jagadeesh Rajenahally V. , Surkus Annette-Enrica , Junge Henrik , Pohl Marga-Martina , Radnik Jörg , Rabeah Jabor , Huan Heming , Schünemann Volker , Brückner Angelika , Beller Matthias
Published: November 2013

Lighter Hydrogenation Catalysts

Enzymes have evolved to use abundant metals such as iron, cobalt, and nickel for redox catalysis. However, synthetic catalysis has generally relied on the rarer, heavier relatives of these elements: ruthenium, rhodium, iridium, palladium, and platinum (see the Perspective by

Bullock

).

Friedfeld
et al.

(p.
1076
) used high-throughput screening to show that the right cobalt precursor can be activated for asymmetric hydrogenation catalysis by using the traditional ligands developed for the precious metals.

Zuo
et al.

(p.
1080
) focused on iron, demonstrating a highly effective asymmetric transfer hydrogenation catalyst that uses a ligand rationally designed after careful mechanistic study.

Jagadeesh
et al.

(p.
1073
) prepared supported iron catalysts that selectively reduce nitro substituents on aromatic rings to amines, thereby facilitating the preparation of a wide range of aniline derivatives.
Devices for Low-Resource Health Care
Authors: Richards-Kortum Rebecca , Oden Maria
Published: November 2013

Devices designed for low-resource settings can improve access to life-saving health care around the world.
Cobalt Precursors for High-Throughput Discovery of Base Metal Asymmetric Alkene Hydrogenation Catalysts
Authors: Friedfeld Max R. , Shevlin Michael , Hoyt Jordan M. , Krska Shane W. , Tudge Matthew T. , Chirik Paul J.
Published: November 2013

Lighter Hydrogenation Catalysts

Enzymes have evolved to use abundant metals such as iron, cobalt, and nickel for redox catalysis. However, synthetic catalysis has generally relied on the rarer, heavier relatives of these elements: ruthenium, rhodium, iridium, palladium, and platinum (see the Perspective by

Bullock

).

Friedfeld
et al.

(p.
1076
) used high-throughput screening to show that the right cobalt precursor can be activated for asymmetric hydrogenation catalysis by using the traditional ligands developed for the precious metals.

Zuo
et al.

(p.
1080
) focused on iron, demonstrating a highly effective asymmetric transfer hydrogenation catalyst that uses a ligand rationally designed after careful mechanistic study.

Jagadeesh
et al.

(p.
1073
) prepared supported iron catalysts that selectively reduce nitro substituents on aromatic rings to amines, thereby facilitating the preparation of a wide range of aniline derivatives.
Amine(imine)diphosphine Iron Catalysts for Asymmetric Transfer Hydrogenation of Ketones and Imines
Authors: Zuo Weiwei , Lough Alan J. , Li Young Feng , Morris Robert H.
Published: November 2013

Lighter Hydrogenation Catalysts

Enzymes have evolved to use abundant metals such as iron, cobalt, and nickel for redox catalysis. However, synthetic catalysis has generally relied on the rarer, heavier relatives of these elements: ruthenium, rhodium, iridium, palladium, and platinum (see the Perspective by

Bullock

).

Friedfeld
et al.

(p.
1076
) used high-throughput screening to show that the right cobalt precursor can be activated for asymmetric hydrogenation catalysis by using the traditional ligands developed for the precious metals.

Zuo
et al.

(p.
1080
) focused on iron, demonstrating a highly effective asymmetric transfer hydrogenation catalyst that uses a ligand rationally designed after careful mechanistic study.

Jagadeesh
et al.

(p.
1073
) prepared supported iron catalysts that selectively reduce nitro substituents on aromatic rings to amines, thereby facilitating the preparation of a wide range of aniline derivatives.
Protein Expression Under Pressure
Authors: Vogel Christine
Published: November 2013

Cellular protein concentrations are generally under stronger evolutionary pressure than mRNA concentrations.

[Also see Report by

Khan
et al.

]
Chinese Mission Ushers in New Era of Lunar Exploration
Authors: Qiu Jane , Stone Richard
Published: November 2013

Chang'e-3, the first spacecraft expected to make a soft landing on the moon since 1976, has a robust science payload that will study the lunar crust underfoot and Earth and stars overhead.
Absence of an Important Vaccine and Diagnostic Target in Carriage- and Disease-Related Nontypeable Haemophilus influenzae
Authors: Smith-Vaughan Heidi C. , Chang Anne B. , Sarovich Derek S. , Marsh Robyn L. , Grimwood Keith , Leach Amanda J. , Morris Peter S. , Price Erin P.
Published: November 2013

NontypeableHaemophilus influenzae(NTHi)-associated disease is a major health problem globally. Whole-genome sequence analysis identified the absence ofhpdgenes encodingHaemophilusprotein D in 3 of 16 phylogenetically distinct NTHi isolates. This novel finding is of potential clinical significance, as protein D andhpdrepresent important NTHi vaccine antigen and diagnostic targets, respectively.
Characterization of the Complete Genome Sequence of a Beak and Feather Disease Virus from a Moluccan Red Lory (
Eos bornea
)
Authors: Sarker Subir , Ghorashi Seyed A. , Forwood Jade K. , Metz Stewart , Raidal Shane R.
Published: November 2013

The complete genome sequence of a beak and feather disease virus (BFDV) encoding two major open reading frames (ORFs) was characterized in a wild Moluccan red lory (
Eos bornea
). This is the first report of a BFDV genome from Indonesia and the first reported BFDV infection for this host species.
Changuinola Virus Serogroup, New Genomes within the Genus
Orbivirus
(Family
Reoviridae
) Isolated in the Brazilian Amazon Region
Authors: Silva Sandro P. , Dilcher Meik , Weidmann Manfred , Carvalho Valéria L. , Casseb Alexandre R. , Silva Eliana V. P. , Nunes Keley N. B. , Chiang Jannifer O. , Martins Lívia C. , Vasconcelos Pedro F. C. , Nunes Márcio R. T.
Published: November 2013

We report here the first complete genome sequence of a
Changuinola virus
(CGLV) serotype
Irituia virus
(BE AN 28873) isolated from a wild rodent (
Oryzomys goeldi
) in the municipality of Ipixuna, State of Pará, northern Brazil. All genome segments showed similarity with those belonging to members of the genus
Orbivirus
, family
Reoviridae
.
Draft Genome Sequence of Marine Cyanobacterium
Synechococcus
sp. Strain NKBG15041c
Authors: Yoshino Tomoko , Honda Toru , Tanaka Masayoshi , Tanaka Tsuyoshi
Published: November 2013

Synechococcus
sp. strain NKBG15041c was isolated as a fast-growing marine cyanobacterium. Genetic transformation techniques using this strain have been well established for metabolic engineering. Here we report the draft genome sequence for this strain, consisting of 44 contigs containing a total of 3,180,043 bp and 3,224 putative protein-coding genes.
Genome Sequence of the Extreme Obligate Alkaliphile Bacillus marmarensis Strain DSM 21297
Authors: Wernick David G. , Choi Kwon-Young , Tat Christine A. , Lafontaine Rivera Jimmy G. , Liao James C.
Published: November 2013

Bacillus marmarensis
strain DSM 21297 is an extreme obligate alkaliphile able to grow in medium up to pH 12.5. A whole-shotgun strategy and
de novo
assembly led to the generation of a 4-Mbp genome of this strain. The genome features alkaliphilic adaptations and pathways for
n
-butanol and poly(3-hydroxybutyrate) synthesis.
Draft Genome Sequence of Serratia fonticola UTAD54, a Carbapenem-Resistant Strain Isolated from Drinking Water
Authors: Henriques Isabel , Jucá Ramos Rommel Thiago , Baraúna Rafael Azevedo , de Sá Pablo Henrique , Marinho Almeida Diogo , Carneiro Adriana Ribeiro , Barbosa Silvanira , Pereira Anabela , Alves Artur , Saavedra Maria José , Egas Conceição , Silva Artur , Correia António
Published: November 2013

Serratia fonticola
UTAD54 is an environmental isolate that is resistant to carbapenems due to the presence of a class A carbapenemase and a metallo-β-lactamase that are unique to this strain. Its draft genome sequence was obtained to clarify the molecular basis of its carbapenem resistance and identify the genomic context of its carbapenem resistance determinants.
Genome Sequence of Rickettsia gravesii, Isolated from Western Australian Ticks
Authors: Sentausa Erwin , Abdad Mohammad Yazid , Robert Catherine , Stenos John , Raoult Didier , Fournier Pierre-Edouard
Published: November 2013

Rickettsia gravesii
is a new
Rickettsia
species closely related to the human pathogen
Rickettsia massiliae
. Here, we describe the genome sequence of
R. gravesii
strain BWI-1, isolated from
Amblyomma triguttatum triguttatum
ticks collected from humans on Barrow Island, Western Australia.
GeneXpert MTB/RIF Version G4 for Identification of Rifampin-Resistant Tuberculosis in a Programmatic Setting
Authors: Osman Muhammad , Simpson John A. , Caldwell Judy , Bosman Marlein , Nicol Mark P.
Published: November 2013

A recent Cochrane review estimated GeneXpert MTB/RIF specificity for rifampin resistance as 98% (95% confidence interval [CI], 97 to 99), based on results from earlier test versions. The measured positive predictive value of the new generation test from programmatic implementation in Cape Town, South Africa, was 99.5% (95% CI, 98.5 to 100), confirming excellent specificity.
Ethambutol Resistance as Determined by Broth Dilution Method Correlates Better than Sequencing Results with
embB
Mutations in Multidrug-Resistant Mycobacterium tuberculosis Isolates
Authors: Zhang Zhijian , Wang Yufeng , Pang Yu , Kam Kai Man
Published: November 2013

We evaluated the correlation of phenotypic ethambutol (EMB) susceptibility as determined by two drug susceptibility methods with
embB
mutations in multidrug-resistant (MDR)
Mycobacterium tuberculosis
strains. The concordance rate for EMB resistance between broth dilution method and sequencing results (83.6%) was significantly higher than between the proportion method and sequencing results (61.7%) (
P
= 0.004). Of the
embB
mutants, 75.4% (46/61) possessed a mutation at
embB306
. Our results demonstrated that ethambutol resistance determined by broth dilution method reveals better correlation with
embB
mutations than the proportion method in MDR isolates.
Cellular Vimentin Regulates Construction of Dengue Virus Replication Complexes through Interaction with NS4A Protein
Authors: Teo Catherine Su Hui , Chu Justin Jang Hann
Published: November 2013

Dengue virus (DENV) interacts with host cellular factors to construct a more favorable environment for replication, and the interplay between DENV and the host cellular cytoskeleton may represent one of the potential antiviral targeting sites. However, the involvement of cellular vimentin intermediate filaments in DENV replication has been explored less. Here, we revealed the direct interaction between host cellular vimentin and DENV nonstructural protein 4A (NS4A), a known component of the viral replication complex (RC), during DENV infection using tandem affinity purification, coimmunoprecipitation, and scanning electron microscopy. Furthermore, the dynamics of vimentin-NS4A interaction were demonstrated by using confocal three-dimensional (3D) reconstruction and proximity ligation assay. Most importantly, we report for the first time the discovery of the specific region of NS4A that interacts with vimentin lies within the first 50 amino acid residues at the cytosolic N-terminal domain of NS4A (N50 region). Besides identifying vimentin-NS4A interaction, vimentin reorganization and phosphorylation by calcium calmodulin-dependent protein kinase II occurs during DENV infection, signifying that vimentin reorganization is important in maintaining and supporting the DENV RCs. Interestingly, we found that gene silencing of vimentin by small interfering RNA induced a significant alteration in the distribution of RCs in DENV-infected cells. This finding further supports the crucial role of intact vimentin scaffold in localizing and concentrating DENV RCs at the perinuclear site, thus facilitating efficient viral RNA replication. Collectively, our findings implicate the biological and functional significance of vimentin during DENV replication, as we propose that the association of DENV RCs with vimentin is mediated by DENV NS4A.
Genetic Resistance to Scrapie Infection in Experimentally Challenged Goats
Authors: Lacroux Caroline , Perrin-Chauvineau Cécile , Corbière Fabien , Aron Naima , Aguilar-Calvo Patricia , Torres Juan Maria , Costes Pierrette , Brémaud Isabelle , Lugan Séverine , Schelcher François , Barillet Francis , Andréoletti Olivier
Published: November 2013

In goats, several field studies have identified coding mutations of the gene encoding the prion protein (I/M
142
, N/D
146
, S/D
146
, R/Q
211
, and Q/K
222
) that are associated with a lower risk of developing classical scrapie. However, the data related to the levels of resistance to transmissible spongiform encephalopathies (TSEs) of these different
PRNP
gene mutations are still considered insufficient for developing large-scale genetic selection against scrapie in this species. In this study, we inoculated wild-type (WT)
PRNP
(I
142
R
154
R
211
Q
222
) goats and homozygous and/or heterozygous I/M
142
, R/H
154
, R/Q
211
, and Q/K
222
goats with a goat natural scrapie isolate by either the oral or the intracerebral (i.c.) route. Our results indicate that the I/M
142
PRNP
polymorphism does not provide substantial resistance to scrapie infection following intracerebral or oral inoculation. They also demonstrate that H
154
, Q
211
, and K
222
PRNP
allele carriers are all resistant to scrapie infection following oral exposure. However, in comparison to WT animals, the H
154
and Q
211
allele carriers displayed only moderate increases in the incubation period following i.c. challenge. After i.c. challenge, heterozygous K
222
and a small proportion of homozygous K
222
goats also developed the disease, but with incubation periods that were 4 to 5 times longer than those in WT animals. These results support the contention that the K
222
goat prion protein variant provides a strong but not absolutely protective effect against classical scrapie.
Identification and Characterization of Antibody-Binding Epitopes on the Norovirus GII.3 Capsid
Authors: Mahar Jackie E. , Donker Nicole C. , Bok Karin , Talbo Gert H. , Green Kim Y. , Kirkwood Carl D.
Published: November 2013

Genotype II.3 (GII.3) noroviruses are a major cause of sporadic gastroenteritis, particularly in children. The greater incidence of GII.3 noroviruses in the pediatric population compared to the adult demographic suggests development of herd immunity to this genotype, possibly as a consequence of limited evolution of immune epitopes. This study aimed to identify and characterize immune epitopes on the GII.3 capsid protein and to determine the level of immune cross-reactivity within the genotype. A panel of seven GII.3 virus-like particles (VLPs), representing norovirus strains isolated during 1975 to 2008, was tested by enzyme-linked immunosorbent assay (ELISA) for reactivity with human sera and a rabbit anti-GII.3 strain-specific polyclonal serum generated against the 2008 GII.3 VLP. Immunoprecipitation of protease-digested GII.3 VLPs and sequencing of bound peptides via mass spectrometry were used to locate epitopes on the capsid. Two epitopes were investigated further using Mimotopes technology. Serum binding studies demonstrated complete intragenotype GII.3 cross-reactivity using both human and rabbit serum. Six immunoreactive regions containing epitopes were located on the GII.3 capsid protein, two within each capsid domain. Epitopes in the S and P1 domains were highly conserved within GII.3 noroviruses. P2 domain epitopes were variable and contained evolutionarily important residues and histo-blood group antigen (HBGA) binding residues. In conclusion, anti-GII.3 antibody-binding epitopes are highly cross-reactive and mostly conserved within GII.3 strains. This may account for the limited GII.3 prevalence in adults and suggests that a GII.3 strain may be a valuable inclusion in a multivalent pediatric targeted VLP vaccine. Exploration of norovirus immune epitopes is vital for effective vaccine design.

IMPORTANCE
This study represents an important contribution to the understanding of norovirus immunology in a pediatric genotype. The high cross-reactivity and conservation of GII.3 epitopes suggest development of herd immunity against GII.3 and indicate that a GII.3 strain would be a valuable inclusion in a pediatric targeted multivalent vaccine. Immunological understanding of pediatric norovirus strains is important since norovirus vaccines will likely target high-risk groups such as the pediatric population.
Therapeutic Depletion of Natural Killer Cells Controls Persistent Infection
Authors: Waggoner Stephen N. , Daniels Keith A. , Welsh Raymond M.
Published: November 2013

Persistent viral infections are associated with host and viral factors that impair effective antiviral immunity. Natural killer (NK) cells contribute to establishment of persistent lymphocytic choriomeningitis virus (LCMV) infection in mice through suppression of virus-specific T cell responses during the first few days of infection, but NK cell depletion during those early time points can enable severe T cell-mediated immune pathology and death of the host. Here we show that long after their peak in cytolytic activation, NK cells continue to support viral persistence at later times of infection. Delayed depletion of NK cells, 2 to 3 weeks after infection, enhanced virus-specific T cell responses and viral control. This enhancing effect of delayed NK cell depletion on antiviral immunity, in contrast to early NK cell depletion, was not associated with increased morbidity and mortality, and mice quickly regained weight after treatment. The efficacy of the depletion depended in part upon the size of the original virus inoculum, the viral load at the time of depletion, and the presence of CD4 T cells. Each of these factors is an important contributor to the degree of CD8 T cell dysfunction during viral persistence. Thus, NK cells may continuously contribute to exhaustion of virus-specific T cells during chronic infection, possibly by depleting CD4 T cells. Targeting of NK cells could thus be considered in combination with blockade of other immunosuppressive pathways, such as the interleukin-10 (IL-10) and programmed death 1 (PD-1) pathways, as a therapy to cure chronic human infections, including those with HIV or hepatitis C virus.

IMPORTANCEPersistent virus infections are a major threat to global human health. The capacity of viruses, including HIV and hepatitis C virus, to overwhelm or subvert host immune responses contributes to a prolonged state of dampened antiviral immune functionality, which in turn facilitates viral persistence. Recent efforts have focused on therapeutics that can restore the effector functions of these functionally exhausted virus-specific T cells in order to expedite viral clearance. Here we establish that natural killer (NK) cells actively contribute to immune dysfunction and viral persistence at later stages of infection. This previously undescribed mechanism of immune suppression during chronic infection provides a vital clue for the design of novel therapeutic strategies targeting NK cell immunosuppressive activity in order to restore immune function and enhance viral control in chronically infected individuals.
A Bromodomain-Containing Host Protein Mediates the Nuclear Importation of a Satellite RNA of Cucumber Mosaic Virus
Authors: Chaturvedi Sonali , Kalantidis Kriton , Rao A. L. N.
Published: November 2013

Replication of the satellite RNA (satRNA) of
Cucumber Mosaic Virus
is dependent on replicase proteins of helper virus (HV). However, we recently demonstrated that like with
Potato spindle tuber viroid
(PSTVd), a satRNA associated with
Cucumber Mosaic Virus
strain Q (Q-satRNA) has the propensity to localize in the nucleus and generate multimers that subsequently serve as templates for HV-dependent replication. But the mechanism regulating the nuclear importation of Q-satRNA is unknown. Here we show that the nuclear importation of Q-satRNA is mediated by a bromodomain-containing host protein (BRP1), which is also apparently involved in the nuclear localization of PSTVd. A comparative analysis of nuclear and cytoplasmic fractions from
Nicotiana benthamiana
plants coinfected with Q-satRNA and its HV confirmed the association of Q-satRNA but not HV with the nuclear compartment. A combination of the MS2-capsid protein-based RNA tagging assay and confocal microscopy demonstrated that the nuclear localization of Q-satRNA was completely blocked in transgenic lines of
Nicotiana benthamiana
(ph5.2nb) that are defective in BRP1 expression. This defect, however, was restored when the ph5.2nb lines of
N. benthamiana
were
trans
-complemented by ectopically expressed BRP1. The binding specificity of BRP1 with Q-satRNA was confirmed
in vivo
and
in vitro
by coimmunoprecipitation and electrophoretic mobility shift assays, respectively. Finally, infectivity assays involving coexpression of Q-satRNA and its HV in wild-type and ph5.2nb lines of
N. benthamiana
accentuated a biological role for BRP1 in the Q-satRNA infection cycle. The significance of these results in relation to a possible evolutionary relationship to viroids is discussed.