bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative transcriptomics with a motility‐deficient mutant leads to identification of a novel polysaccharide secretion system in Nostoc punctiforme
Authors: Risser Douglas D. , Meeks John C.
Published: December 2012

Many filamentous cyanobacteria are capable of gliding motility by an undefined mechanism. Within the heterocyst‐forming clades, some strains, such as the Nostoc spp. and Fisherella spp., are motile only as specialized filaments termed hormogonia. Here we report on the phenotype of inactivation of a methyl‐accepting chemotaxis‐like protein in Nostoc punctiforme, designated HmpD. The gene hmpD was found to be essential for hormogonium development, motility and polysaccharide secretion. Comparative global transcriptional profiling of the ΔhmpD strain demonstrated that HmpD has a profound effect on the transcriptional programme of hormogonium development, influencing approximately half of the genes differentially transcribed during differentiation. Utilizing this transcriptomic data, we identified a gene locus, designated here as hps, that appears to encode for a novel polysaccharide secretion system. Transcripts for the genes in the hps locus are upregulated in two steps, with the second step dependent on HmpD. Deletion of hpsA, hpsBCD or hpsEFG resulted in the complete loss of motility and polysaccharide secretion, similar to deletion of hmpD. Genes in the hps locus are highly conserved in the filamentous cyanobacteria, but generally absent in unicellular strains, implying a common mechanism of motility unique to the filamentous cyanobacteria.
Glucose and lactose as cryoprotectants for fungal strains immobilised in sodium alginate: an emphasis on the conservation of the zygomycetes Rhizopus and Mucor
Authors: Rocha Marcos F. G. , Lima Daniel T. , Brilhante Raimunda S. N. , Cordeiro Rossana A. , Monteiro André J. , Teixeira Carlos E. C. , Ribeiro Joyce F. , Castelo‐Branco Débora S. C. M. , Sidrim José J. C.
Published: December 2012

This research aimed at investigating the cryoprotectant action of glucose and lactose on strains of Malassezia spp. and zygomycetes immobilised in sodium alginate. Twelve strains of Malassezia spp. (nine M. furfur, two M. globosa and one M. sympodialis) and 12 zygomycetes (five Rhizopus oryzae and seven Mucor hiemales) were immobilised in sodium alginate, within plastic beads, maintained in appropriate media containing glucose and lactose at concentrations of 9% and 23% and preserved at temperatures of −20 and −80 °C. Strain viability was evaluated from 15 to 270 days of storage, through the observation of macro–micromorphologic characteristics. The Malassezia spp. strains were only viable until 90 days of storage, whereas for zygomycetes, viable strains were observed until after 270 days of storage at −80 °C, in the media containing 23% glucose or lactose. The use of 23% glucose or lactose at −80 °C in a sodium alginate cell immobilisation system is efficient for cryopreserving zygomycetes. This research creates perspectives for the use of glucose and lactose in sodium alginate cell immobilisation systems for the preservation of fungi with low viability.
Melioidosis and the kidney
Authors: Jabbar Zulfikar , Currie Bart J
Published: December 2012

Melioidosis, caused by the saprophytic soil and freshwater Gram‐negative aerobic bacillus Burkholderia pseudomallei, is classically characterized by pneumonia, sometimes with multiple organ abscesses, usually in patients with defined risk factors and with a mortality rate of up to 40%. It is a major cause of community‐acquired sepsis in Southeast Asia and tropical northern Australia with an expanding global geographical distribution. It is increasingly recognized as an opportunistic infectious disease of importance to physicians, who may need to suspect it in at‐risk patients that may come from or visit endemic areas, and could be fatal if treated late or inappropriately. Mortality could be prevented by early institution of specific antimicrobial therapy. Epidemiology, clinical features, overall management, and aspects of melioidosis particularly relevant to kidney disease and immunosuppression are discussed in this review.
Differential selection pressures exerted by host resistance quantitative trait loci on a pathogen population: a case study in an apple × Venturia inaequalis pathosystem
Authors: Van Amandine Lê , Caffier Valérie , Lasserre‐Zuber Pauline , Chauveau Aurélie , Brunel Dominique , Le Cam Bruno , Durel Charles‐Eric
Published: December 2012

Understanding how pathogens evolve according to pressures exerted by their plant hosts is essential for the derivation of strategies aimed at the durable management of resistant cultivars. The spectrum of action of the resistance factors in the partially resistant cultivars is thought to be an important determinant of resistance durability. However, it has not yet been demonstrated whether the pressures exerted by quantitative resistance are different according to their spectrum of action.

To investigate selection pressures exerted by apple genotypes harbouring various resistance quantitative trait loci (QTLs) on a mixed inoculum of the scab disease agent, Venturia inaequalis, we monitored V. inaequalis isolate proportions on diseased apple leaves of an F1 progeny using quantitative pyrosequencing technology and QTL mapping.

Broad‐spectrum resistances did not exert any differential selection pressures on the mixed inoculum, whereas narrow‐spectrum resistances decreased the frequencies of some isolates in the mixture relative to the susceptible host genotypes.

Our results suggest that the management of resistant cultivars should be different according to the spectrum of action of their resistance factors. The pyramiding of broad‐spectrum factors or the use of a mixture of apple genotypes that carry narrow‐spectrum resistance factors are two possible strategies for the minimization of resistance erosion.
Diagnosis of hidden bronchial obstruction using computer‐assessed tracheal forced expiratory noise time
Authors: Pochekutova Irina A. , Korenbaum Vladimir I.
Published: December 2012

Background and objective

Increased forced expiratory time was first recognized as a marker of obstruction half a century ago. However, the reported diagnostic capabilities of both auscultated forced expiratory time (FETas) and spirometric forced expiratory time are contradictory. Computer analysis of respiratory noises provides a precise estimation of acoustic forced expiratory noise time (FETa) being the object‐measured analogue of FETas. The aim of this study was to analyse FETa diagnostic capabilities in patients with asthma based on the hypothesis that FETa could reveal hidden bronchial obstruction.

Methods

A group of asthma patients involved 149 males aged 16–25 years. In this group, 71 subjects had spirometry features of bronchial obstruction, meanwhile, the remaining 78 had normal spirometry. A control group involved 77 healthy subjects. Spirometry and forced expiratory tracheal noise recording were sequentially measured for each participant. FETa values were estimated by means of a developed computer procedure, including bandpass filtration (200–2000 Hz), waveform envelope calculation with accumulation period of 0.01 s, automated measurement of FETa at 0.5% level from the peak amplitude.

Results

Specificity, sensitivity and area under Receiver Operating Characteristic curve of FETa and its ratios to squared chest circumference, height, weight were indistinguishable with baseline spirometry index FEV1/forced vital capacity. Meanwhile, acoustic features of obstruction were revealed in 41%–49% of subgroup of patients with asthma but normal spirometry.

Conclusions

FETa of tracheal noise and its ratio to anthropometric parameters seem to be sensitive and specific tests of hidden bronchial obstruction in young male asthma patients.
Implications of trace element composition of syntaxial quartz cements for the geochemical conditions during quartz precipitation in sandstones
Authors: Götte Thomas , Ramseyer Karl , Pettke Thomas , Koch‐Müller Monika
Published: December 2012

A petrographic investigation revealed polyphase quartz cementation in the Finefrau Sandstone (Upper Carboniferous, Western Germany) and the Solling Sandstone (Lower Triassic, Central Germany). Three different cements could be distinguished in each sandstone based on their cathodoluminescence and trace element composition. The first quartz generation is suggested to have been formed during eogenesis due to dissolution and replacement of feldspar. The mesogenetic paragenesis comprises two generations of quartz and illite, which are accompanied by albite in the Solling Sandstone. Sharp luminescence zoning in quartz overgrowths points to distinct episodes of cementation in both sandstones. Significant amounts of Al, Li and H and traces of Ge and B have been detected in the quartz overgrowths. The Al‐content of the quartz cements in the Finefrau Sandstones exceeds that in the quartz cements in the Solling Sandstone by a factor of five. It is suggested that this compositional variation reflects the conditions in the pore‐water, such as temperature and pH. The Al‐concentration is generally correlated to the Li‐content with the exception of the latest quartz generation in the Finefrau Sandstones which is also most enriched in trace elements. The ratio of Li/Al varies between 0·11 and 0·25 in the two sandstones. The Li/H‐ratio, which ranges from 0·12 to 0·3, is controlled by the activity ratio of Li and H in the pore fluid. Clay minerals are the most important source for Li and high salinities favour the mobilization of Li during diagenesis. Thus, a relatively low salinity and low pH are responsible for the low Li/H‐ratio in the Finefrau Sandstone, while high salinity and neutral to alkaline pH results in a high Li/H‐ratio for the Solling Sandstone. The Ge‐contents are generally near the average of detrital quartz and indicate that pressure dissolution is a major source for quartz cementation. Different chemical compositions of distinct quartz generations indicate changes in the physico‐chemical conditions and point to mobilization of silica from different sources (for example, pressure solution and clay mineral transformations).
Issue Voting and Immigration: Do Restrictionist Policies Cost Congressional Republicans Votes?
Authors: Hawley George
Published: December 2012

Objective

I test the hypothesis that Latino voters were less likely to support Republican incumbents with strong anti‐immigration records in the 2006 congressional elections in comparison to Republicans with less restrictive records. I also test whether non‐Hispanic white voters were similarly sensitive to incumbent immigration records when determining vote choice.

Method

To examine these questions, I created hierarchical models in which incumbent immigration records, individual views on immigration, and an interaction between the two were used to predict vote choice in the 2006 midterm elections. Individual‐level data were provided by the 2006 Cooperative Congressional Election Study and incumbent immigration records were provided by NumbersUSA.

Results

This analysis found little or no evidence suggesting that Latino voters are less likely to support Republican incumbents with anti‐immigration records. There was evidence suggesting that vote choice among non‐Hispanic whites was influenced by incumbent records on immigration, but the effect varied according to the respondent's own views on immigration.

Conclusion

This study found no evidence that incumbent Republicans could increase their share of the Latino vote by embracing less restrictive immigration policies. In fact, doing so may cost them votes among non‐Hispanic whites.
The maize lipoxygenase, ZmLOX10, mediates green leaf volatile, jasmonate and herbivore‐induced plant volatile production for defense against insect attack
Authors: Christensen Shawn A. , Nemchenko Andriy , Borrego Eli , Murray Ian , Sobhy Islam S. , Bosak Liz , DeBlasio Stacy , Erb Matthias , Robert Christelle A.M. , Vaughn Kathy A. , Herrfurth Cornelia , Tumlinson Jim , Feussner Ivo , Jackson David , Turlings Ted C.J. , Engelberth Jurgen , Nansen Christian , Meeley Robert , Kolomiets Michael V.
Published: December 2012

Fatty acid derivatives are of central importance for plant immunity against insect herbivores; however, major regulatory genes and the signals that modulate these defense metabolites are vastly understudied, especially in important agro‐economic monocot species. Here we show that products and signals derived from a single Zea mays (maize) lipoxygenase (LOX), ZmLOX10, are critical for both direct and indirect defenses to herbivory. We provide genetic evidence that two 13‐LOXs, ZmLOX10 and ZmLOX8, specialize in providing substrate for the green leaf volatile (GLV) and jasmonate (JA) biosynthesis pathways, respectively. Supporting the specialization of these LOX isoforms, LOX8 and LOX10 are localized to two distinct cellular compartments, indicating that the JA and GLV biosynthesis pathways are physically separated in maize. Reduced expression of JA biosynthesis genes and diminished levels of JA in lox10 mutants indicate that LOX10‐derived signaling is required for LOX8‐mediated JA. The possible role of GLVs in JA signaling is supported by their ability to partially restore wound‐induced JA levels in lox10 mutants. The impaired ability of lox10 mutants to produce GLVs and JA led to dramatic reductions in herbivore‐induced plant volatiles (HIPVs) and attractiveness to parasitoid wasps. Because LOX10 is under circadian rhythm regulation, this study provides a mechanistic link to the diurnal regulation of GLVs and HIPVs. GLV‐, JA‐ and HIPV‐deficient lox10 mutants display compromised resistance to insect feeding, both under laboratory and field conditions, which is strong evidence that LOX10‐dependent metabolites confer immunity against insect attack. Hence, this comprehensive gene to agro‐ecosystem study reveals the broad implications of a single LOX isoform in herbivore defense.
Zhu Rongji Might Be Right: Understanding the Mechanism of Fast Economic Development in China
Authors: Zhang Jun
Published: December 2012

Understanding the facilitating role of regional governments and the source of regional competition is the key to demystifying the success of China’s fast economic development since the 1990s. This paper, as the product of the lecture the author delivered at The World Economy China Annual Lecture on 3 November 2011 at University of Nottingham, provides a framework that better illustrates the mechanism that motivates China’s economic growth over the past 20 years. It shows that the current growth mechanism in China is largely the result of institutional reforms and fiscal recentralisation that occurred in 1994 under the leadership of Premier Zhu Rongji. Being allowed to have their own source of tax revenue under the new fiscal reform, Chinese regional governments are motivated to pursue the goal of economic growth through fast capital formation and industrialisation. The newly designed intergovernmental fiscal relationship, as the most important reform programme in China, has also helped create a growth incentive that is compatible between central and local governments, and resulted in a Tibout‐type regional competition in the sense that inefficient use of resources, including public land, would be substantially eliminated by the strategic behaviour of regional governments being more attractive to external direct investment. Such regional competition makes the regional governments preserve and use the markets rather than replace them, and has generated consistent and powerful development momentum for the post‐1994 economy of China.
Restructuring of the Honda Auto Parts Union in Guongdong, China: A 2‐year Assessment of the 2010 Strike
Authors: Lau Rena
Published: December 2012

Since the 1990s, Chinese workers at state‐owned enterprises had put up many fights against privatization but with lackluster results. The migrant workers, on the other hand, have mostly been a silent majority, putting up with appalling working conditions. Though resistances among some of them have often arisen, most of these are spontaneous and not organized. However, the CHAM workers had been successful not only in winning an increase in their wages but also pushing the government and the company to agree to a revamp of the workplace union after a 19‐day strike in 2010. The CHAM case attracted international concern on the potential rise of the Chinese workers’ power and this also pushed the ACFTU to make further reform. Yet, the question remains—does the re‐elected Honda trade union really represent the workers? In this article, we will reveal the truth about the ACFTU's engineered reform of the Honda trade union through workers interviews and data analysis.
The Communist International and the Dilemma of the American “Negro Problem”: Limitations of the Black Belt Self‐Determination Thesis
Authors: Tomek Beverly
Published: December 2012

In hopes of solving the American “Negro Problem” in a way that would bring African Americans into the communist fold, the Communist International developed an agenda that included a “Black Belt Self‐Determination Thesis.” According to this thesis, American blacks were an oppressed nation within a nation and should thus have the right of self‐determination in the part of the United States known as the Black Belt. This thesis failed to gain traction beyond a small group of intellectuals within the Communist Party. Realizing the impractical nature of the thesis, leaders of the American Communist Party (CPUSA) devised more practical means of helping Black Americans fight racism and injustice in the U.S. Even though the thesis ultimately failed to bring masses of Black Americans into the Party, it did help foster the development and growth of African‐American history and studies that examine the role of race in U.S. history.
Uncertainty Management in the Design of Multiscale Systems
Authors: Sinha Ayan , Bera Nilanjan , Allen Janet K. , Panchal Jitesh H. , Mistree Farrokh
Published: December 2012

In this paper, the opportunities for managing uncertainty in simulation-based design of multiscale systems are explored using constructs from information management and robust design. A comprehensive multiscale design problem, the concurrent design of material and product is used to demonstrate our approach. The desired accuracy of the simulated performance is determined by the trade-off between computational cost for model refinement and the benefits of mitigated uncertainty from the refined models. Our approach consists of integrating: (i) a robust design method for multiscale systems and (ii) an improvement potential based approach for quantifying the cost-benefit trade-off for reducing uncertainty in simulation models. Specifically, our approach focuses on allocating resources for reducing model parameter uncertainty arising due to insufficient data from simulation models. Using this approach, system level designers can efficiently allocate resources for sequential simulation model refinement in multiscale systems.
Pressure Increase in Elliptical Impact Elastohydrodynamic Lubrication Contacts With Longitudinal Asperities
Authors: Kaneta M. , Guo F. , Wang J. , Krupka I. , Hartl M.
Published: December 2012

The phenomena that occur when an elliptical steel body impacts a stationary steel plate with surface asperities are discussed through isothermal Newtonian numerical analysis using sinusoidal roughness. The ridges of the surface asperities produce large local pressures, especially at a large ellipticity ratio, when the surfaces are approaching each other under the applied load. The values of the local pressures are larger when the ridges are along the major axis than when the ridges are along the minor axis. Furthermore, as the loading speed increases, the pressure increases. As a result, the microgrooves are produced in the ridges and the horseshoe-shaped constrictions are formed at the ridges located around the contact edge.
The Optimum Design of a Cavitator for High-Speed Axisymmetric Bodies in Partially Cavitating Flows
Authors: Rashidi I. , Passandideh-Fard Mo. , Pasandideh-Fard Ma.
Published: December 2012

In this paper, the partially cavitating flow over an axisymmetric projectile is studied in order to obtain the optimum cavitator such that, at a given cavitation number, the total drag coefficient of the projectile is minimum. For this purpose, the boundary element method and numerical simulations are used. A large number of cavitator profiles are produced using a parabolic expression with three geometric parameters. The potential flow around these cavitators is then solved using the boundary element method. In order to examine the optimization results, several cavitators with a total drag coefficient close to that of the optimum cavitators are also numerically simulated. Eventually, the optimum cavitator is selected using both the boundary element method and numerical simulations. The effects of the body radius and the length of the conical section of the projectile on the shape of the optimized cavitator are also investigated. The results show that for all cavitation numbers, the cavitator that creates a cavity covering the entire conical section of the projectile with a minimum total drag coefficient is optimal. It can be seen that increasing the cavitation number causes the optimum cavitator to approach the disk cavitator. The results also show that at a fixed cavitation number, the increase in both the radius and length of the conical section causes the cavitator shape to approach that of the disk cavitator.
Boson Sampling on a Photonic Chip
Authors: Spring Justin B. , Metcalf Benjamin J. , Humphreys Peter C. , Kolthammer W. Steven , Jin Xian-Min , Barbieri Marco , Datta Animesh , Thomas-Peter Nicholas , Langford Nathan K. , Kundys Dmytro , Gates James C. , Smith Brian J. , Smith Peter G. R. , Walmsley Ian A.
Published: December 2012

Computing Power of Quantum Mechanics

There is much interest in developing quantum computers in order to perform certain tasks much faster than, or that are intractable for, a classical computer. A general quantum computer, however, requires the fabrication and operation a number of quantum logic devices (see the Perspective by

Franson

).

Broome
et al.

(p.
794
, published online 20 December) and

Spring
et al.

(p.
798
, published online 20 December) describe experiments in which single photons and quantum interference were used to perform a calculation (the permanent of a matrix) that is very difficult on a classical computer. Similar to random walks, quantum walks on a graph describe the movement of a walker on a set of predetermined paths; instead of flipping a coin to decide which way to go at each point, a quantum walker can take several paths at once.

Childs
et al.

(p.
791
) propose an architecture for a quantum computer, based on quantum walks of multiple interacting walkers. The system is capable of performing any quantum operation using a subset of its nodes, with the size of the subset scaling favorably with the complexity of the operation.
Blue Light Rescues Mice from Potentially Fatal Pseudomonas aeruginosa Burn Infection: Efficacy, Safety, and Mechanism of Action
Authors: Dai Tianhong , Gupta Asheesh , Huang Ying-Ying , Yin Rui , Murray Clinton K. , Vrahas Mark S. , Sherwood Margaret E. , Tegos George P. , Hamblin Michael R.
Published: December 2012

Blue light has attracted increasing attention due to its intrinsic antimicrobial effect without the addition of exogenous photosensitizers. However, the use of blue light for wound infections has not been established yet. In this study, we demonstrated the efficacy of blue light at 415 nm for the treatment of acute, potentially lethal
Pseudomonas aeruginosa
burn infections in mice. Our
in vitro
studies demonstrated that the inactivation rate of
P. aeruginosa
cells by blue light was approximately 35-fold higher than that of keratinocytes (
P
= 0.0014). Transmission electron microscopy revealed blue light-mediated intracellular damage to
P. aeruginosa
cells. Fluorescence spectroscopy suggested that coproporphyrin III and/or uroporphyrin III are possibly the intracellular photosensitive chromophores associated with the blue light inactivation of
P. aeruginosa
.
In vivo
studies using an
in vivo
bioluminescence imaging technique and an area-under-the-bioluminescence-time-curve (AUBC) analysis showed that a single exposure of blue light at 55.8 J/cm
2
, applied 30 min after bacterial inoculation to the infected mouse burns, reduced the AUBC by approximately 100-fold in comparison with untreated and infected mouse burns (
P
< 0.0001). Histological analyses and terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling (TUNEL) assays indicated no significant damage in the mouse skin exposed to blue light at the effective antimicrobial dose. Survival analyses revealed that blue light increased the survival rate of the infected mice from 18.2% to 100% (
P
< 0.0001). In conclusion, blue light therapy might offer an effective and safe alternative to conventional antimicrobial therapy for
P. aeruginosa
burn infections.
Growth Inhibition of Pathogenic Bacteria by Sulfonylurea Herbicides
Authors: Kreisberg Jason F. , Ong Nicholas T. , Krishna Aishwarya , Joseph Thomas L. , Wang Jing , Ong Catherine , Ooi Hui Ann , Sung Julie C. , Siew Chern Chiang , Chang Grace C. , Biot Fabrice , Cuccui Jon , Wren Brendan W. , Chan Joey , Sivalingam Suppiah P. , Zhang Lian-Hui , Verma Chandra , Tan Patrick
Published: December 2012

Emerging resistance to current antibiotics raises the need for new microbial drug targets. We show that targeting branched-chain amino acid (BCAA) biosynthesis using sulfonylurea herbicides, which inhibit the BCAA biosynthetic enzyme acetohydroxyacid synthase (AHAS), can exert bacteriostatic effects on several pathogenic bacteria, including
Burkholderia pseudomallei
,
Pseudomonas aeruginosa
, and
Acinetobacter baumannii
. Our results suggest that targeting biosynthetic enzymes like AHAS, which are lacking in humans, could represent a promising antimicrobial drug strategy.
Detection of Borrelia burgdorferi Sensu Stricto
ospC
Alleles Associated with Human Lyme Borreliosis Worldwide in Non-Human-Biting Tick Ixodes affinis and Rodent Hosts in Southeastern United States
Authors: Rudenko Nataliia , Golovchenko Maryna , Hönig Václav , Mallátová Nadja , Krbková Lenka , Mikulášek Peter , Fedorova Natalia , Belfiore Natalia M. , Grubhoffer Libor , Lane Robert S. , Oliver James H.
Published: December 2012

Comparative analysis of
ospC
genes from 127
Borrelia burgdorferi
sensu stricto strains collected in European and North American regions where Lyme disease is endemic and where it is not endemic revealed a close relatedness of geographically distinct populations.
ospC
alleles A, B, and L were detected on both continents in vectors and hosts, including humans. Six
ospC
alleles, A, B, L, Q, R, and V, were prevalent in Europe; 4 of them were detected in samples of human origin. Ten
ospC
alleles, A, B, D, E3, F, G, H, H3, I3, and M, were identified in the far-western United States. Four
ospC
alleles, B, G, H, and L, were abundant in the southeastern United States. Here we present the first expanded analysis of
ospC
alleles of
B. burgdorferi
strains from the southeastern United States with respect to their relatedness to strains from other North American and European localities. We demonstrate that
ospC
genotypes commonly associated with human Lyme disease in European and North American regions where the disease is endemic were detected in
B. burgdorferi
strains isolated from the non-human-biting tick
Ixodes affinis
and rodent hosts in the southeastern United States. We discovered that some
ospC
alleles previously known only from Europe are widely distributed in the southeastern United States, a finding that confirms the hypothesis of transoceanic migration of
Borrelia
species.
Anaplasma phagocytophilum in Questing Ixodes ricinus Ticks: Comparison of Prevalences and Partial 16S rRNA Gene Variants in Urban, Pasture, and Natural Habitats
Authors: Overzier Evelyn , Pfister Kurt , Thiel Claudia , Herb Ingrid , Mahling Monia , Silaghi Cornelia
Published: December 2012

Urban, natural, and pasture areas were investigated for prevalences and 16S rRNA gene variants of
Anaplasma phagocytophilum
in questing
Ixodes ricinus
ticks. The prevalences differed significantly between habitat types, and year-to-year variations in prevalence and habitat-dependent occurrence of 16S rRNA gene variants were detected.
Depletion of Unwanted Nucleic Acid Templates by Selective Cleavage: LNAzymes, Catalytically Active Oligonucleotides Containing Locked Nucleic Acids, Open a New Window for Detecting Rare Microbial Community Members
Authors: Dolinšek Jan , Dorninger Christiane , Lagkouvardos Ilias , Wagner Michael , Daims Holger
Published: December 2012

Many studies of molecular microbial ecology rely on the characterization of microbial communities by PCR amplification, cloning, sequencing, and phylogenetic analysis of genes encoding rRNAs or functional marker enzymes. However, if the established clone libraries are dominated by one or a few sequence types, the cloned diversity is difficult to analyze by random clone sequencing. Here we present a novel approach to deplete unwanted sequence types from complex nucleic acid mixtures prior to cloning and downstream analyses. It employs catalytically active oligonucleotides containing locked nucleic acids (LNAzymes) for the specific cleavage of selected RNA targets. When combined within vitrotranscription and reverse transcriptase PCR, this LNAzyme-based technique can be used with DNA or RNA extracts from microbial communities. The simultaneous application of more than one specific LNAzyme allows the concurrent depletion of different sequence types from the same nucleic acid preparation. This new method was evaluated with defined mixtures of cloned 16S rRNA genes and then used to identify accompanying bacteria in an enrichment culture dominated by the nitrite oxidizer “CandidatusNitrospira defluvii.”In silicoanalysis revealed that the majority of publicly deposited rRNA-targeted oligonucleotide probes may be used as specific LNAzymes with no or only minor sequence modifications. This efficient and cost-effective approach will greatly facilitate tasks such as the identification of microbial symbionts in nucleic acid preparations dominated by plastid or mitochondrial rRNA genes from eukaryotic hosts, the detection of contaminants in microbial cultures, and the analysis of rare organisms in microbial communities of highly uneven composition.
Patterns of Nucleotide Diversity of the
ldpA
Circadian Gene in Closely Related Species of Cyanobacteria from Extreme Cold Deserts
Authors: Ng Ka Wai , Pointing Stephen B. , Dvornyk Volodymyr
Published: December 2012

In the circadian system of cyanobacteria, the
ldpA
gene is a component of the input to the clock. We comparatively analyzed nucleotide polymorphism of this gene in populations of two closely related species of cyanobacteria (denoted as
Synechococcus
species S1 and S2, respectively) from extreme cold deserts in Antarctica, the Canadian Arctic, and Tibet. Although both species manifested similarly high haplotype diversities (0.990 and 0.809, respectively), the nucleotide diversity differed significantly (0.0091 in S1 and 0.0037 in S2). The populations of species S2 were more differentiated (

F
ST

= 0.2242) compared to those of species S1 (

F
ST

between 0.0296 and 0.1188). An analysis of positive selection with several tests yielded highly significant values (
P
< 0.01) for both species. On the other hand, these results may be somewhat compromised by fluctuating population sizes of the species. The apparent selection pressure coupled with the pronounced demographic factors, such as population expansion, small effective population size, and genetic drift, may thus result in the observed significant interpopulation differentiation and subsequent speciation of cyanobacteria.
Members of the Penicillium chrysogenum Velvet Complex Play Functionally Opposing Roles in the Regulation of Penicillin Biosynthesis and Conidiation
Authors: Kopke Katarina , Hoff Birgit , Bloemendal Sandra , Katschorowski Alexandra , Kamerewerd Jens , Kück Ulrich
Published: December 2012

A velvet multisubunit complex was recently detected in the filamentous fungusPenicillium chrysogenum, the major industrial producer of the β-lactam antibiotic penicillin. Core components of this complex areP. chrysogenumVelA (PcVelA) and PcLaeA, which regulate secondary metabolite production, hyphal morphology, conidiation, and pellet formation. Here we describe the characterization of PcVelB, PcVelC, and PcVosA as novel subunits of this velvet complex. Using yeast two-hybrid analysis and bimolecular fluorescence complementation (BiFC), we demonstrate that all velvet proteins are part of an interaction network. Functional analyses using single- and double-knockout strains clearly indicate that velvet subunits have opposing roles in the regulation of penicillin biosynthesis and light-dependent conidiation. PcVelC, together with PcVelA and PcLaeA, activates penicillin biosynthesis, while PcVelB represses this process. In contrast, PcVelB and PcVosA promote conidiation, while PcVelC has an inhibitory effect. Our genetic analyses further show that light-dependent spore formation depends not only on PcVelA but also on PcVelB and PcVosA. The results provided here contribute to our fundamental understanding of the function of velvet subunits as part of a regulatory network mediating signals responsible for morphology and secondary metabolism and will be instrumental in generating mutants with newly derived properties that are relevant to strain improvement programs.
Divergence of Erv1-Associated Mitochondrial Import and Export Pathways in Trypanosomes and Anaerobic Protists
Authors: Basu Somsuvro , Leonard Joanne C. , Desai Nishal , Mavridou Despoina A. I. , Tang Kong Ho , Goddard Alan D. , Ginger Michael L. , Lukeš Julius , Allen James W. A.
Published: December 2012

In yeast (
Saccharomyces cerevisiae
) and animals, the sulfhydryl oxidase Erv1 functions with Mia40 in the import and oxidative folding of numerous cysteine-rich proteins in the mitochondrial intermembrane space (IMS). Erv1 is also required for Fe-S cluster assembly in the cytosol, which uses at least one mitochondrially derived precursor. Here, we characterize an essential Erv1 orthologue from the protist
Trypanosoma brucei
(TbERV1), which naturally lacks a Mia40 homolog. We report kinetic parameters for physiologically relevant oxidants cytochrome
c
and O
2
, unexpectedly find O
2
and cytochrome
c
are reduced simultaneously, and demonstrate that efficient reduction of O
2
by TbERV1 is not dependent upon a simple O
2
channel defined by conserved histidine and tyrosine residues. Massive mitochondrial swelling following Tb
ERV1
RNA interference (RNAi) provides evidence that trypanosome Erv1 functions in IMS protein import despite the natural absence of the key player in the yeast and animal import pathways, Mia40. This suggests significant evolutionary divergence from a recently established paradigm in mitochondrial cell biology. Phylogenomic profiling of genes also points to a conserved role for TbERV1 in cytosolic Fe-S cluster assembly. Conversely, loss of genes implicated in precursor delivery for cytosolic Fe-S assembly in
Entamoeba
,
Trichomonas
, and
Giardia
suggests fundamental differences in intracellular trafficking pathways for activated iron or sulfur species in anaerobic versus aerobic eukaryotes.
Mycobacterial Trehalose Dimycolate Reprograms Macrophage Global Gene Expression and Activates Matrix Metalloproteinases
Authors: Sakamoto Kaori , Kim Mi Jeong , Rhoades Elizabeth R. , Allavena Rachel E. , Ehrt Sabine , Wainwright Helen C. , Russell David G. , Rohde Kyle H.
Published: December 2012

Trehalose 6,6′-dimycolate (TDM) is a cell wall glycolipid and an important virulence factor of mycobacteria. In order to study the role of TDM in the innate immune response toMycobacterium tuberculosis, microarray analysis was used to examine gene regulation in murine bone marrow-derived macrophages in response to 90-μm-diameter polystyrene microspheres coated with TDM. A large number of genes, particularly those involved in the immune response and macrophage function, were up- or downregulated in response to these TDM-coated beads compared to control beads. Genes involved in the immune response were specifically upregulated in a myeloid differentiation primary response gene 88 (MyD88)-dependent manner. The complexity of the transcriptional response also increased greatly between 2 and 24 h. Matrix metalloproteinases (MMPs) were significantly upregulated at both time points, and this was confirmed by quantitative real-time reverse transcription-PCR (RT-PCR). Using anin vivoMatrigel granuloma model, the presence and activity of MMP-9 were examined by immunohistochemistry andin situzymography (ISZ), respectively. We found that TDM-coated beads induced MMP-9 expression and activity in Matrigel granulomas. Macrophages were primarily responsible for MMP-9 expression, as granulomas from neutrophil-depleted mice showed staining patterns similar to that for wild-type mice. The relevance of these observations to human disease is supported by the similar induction of MMP-9 in human caseous tuberculosis (TB) granulomas. Given that MMPs likely play an important role in both the construction and breakdown of tuberculous granulomas, our results suggest that TDM may drive MMP expression during TB pathogenesis.
Survival after cardiopulmonary arrest with extreme hyperkalaemia and hypothermia in a patient with metformin-associated lactic acidosis
Authors: Tay Stan , Lee I-Lynn
Published: December 2012

Potassium levels are regularly used as a prognostic factor to cease resuscitation in significant hypothermia. In this case report, we highlight how survival is still possible with extreme hyperkalaemia in severe hypothermia. We present a case of a 65-year-old Caucasian man who presented with metformin associated lactic acidosis. On presentation he had potassium of 9.1 mmol/l and a temperature of 31.5°C. Cardiopulmonary resuscitation was commenced when he went into asystolic arrest. This presentation would commonly make attempts at resuscitation futile with a 100% death rate. However, with appropriate management this patient's condition improved and survival was possible. We provide evidence that survival is possible in profound hyperkalaemia and hypothermia. Effective cardiopulmonary resuscitation with early haemofiltration can be successful.
Laparosopic management of reduction-en-masse
Authors: Sahoo Manash Ranjan , Kumar Anil
Published: December 2012

Reduction-en-masse of groin hernia is a problem which is rarely encountered by surgeons and in fact in world literature only 200 cases have been recorded till date. Most of the time this complication is overlooked by surgeons. Hence, surgeons repair the hernia leaving the incarcerated bowel inside which might lead to disaster. We report an unusual case of intestinal obstruction due to reduction-en-masse of a groin hernia because of manual reduction by the patient himself 7 days before, which was missed both by the radiologist as well as by the surgeons. It was found out in diagnostic laparoscopy and managed laparoscopically as well, relieving intestinal obstruction. He was discharged with an advice for definitive repair after 3 weeks. To conclude, in patients of groin hernia presenting in any form of intestinal obstruction we have to keep reduction-en-masse in mind and laparoscopy plays an important role in diagnosis and management.
Evaluating the impact and use of Transparent Reporting of Evaluations with Non-randomised Designs (TREND) reporting guidelines
Authors: Fuller Thomas , Pearson Mark , Peters Jaime L , Anderson Rob
Published: December 2012

Introduction

Accurate and full reporting of evaluation of interventions in health research is needed for evidence synthesis and informed decision-making. Evidence suggests that biases and incomplete reporting affect the assessment of study validity and the ability to include this data in secondary research. The Transparent Reporting of Evaluations with Non-randomised Designs (TREND) reporting guideline was developed to improve the transparency and accuracy of the reporting of behavioural and public health evaluations with non-randomised designs. Evaluations of reporting guidelines have shown that they can be effective in improving reporting completeness. Although TREND occupies a niche within reporting guidelines, and despite it being 8 years since publication, no study yet has assessed its impact on reporting completeness or investigated what factors affect its use by authors and journal editors. This protocol describes two studies that aim to redress this.

Methods and analysis

Study 1 will use an observational design to examine the uptake and use of TREND by authors, and by journals in their instructions to authors. A comparison of reporting completeness and study quality of papers that do and do not use TREND to inform reporting will be made. Study 2 will use a cross-sectional survey to investigate what factors inhibit or facilitate authors’ and journal editors’ use of TREND. Semistructured interviews will also be conducted with a subset of authors and editors to explore findings from study 1 and the surveys in greater depth.

Ethics and dissemination

These studies will generate evidence of how implementation and dissemination of the TREND guideline has affected reporting completeness in studies with experimental, non-randomised designs within behavioural and public health research. The project has received ethics approval from the Research Ethics Committee of the Peninsula College of Medicine and Dentistry, Universities of Exeter and Plymouth.
SECOND-ORDER CORRECTIONS TO THE MAGNETIC MOMENT OF ELECTRON AT FINITE TEMPERATURE
Authors: MASOOD SAMINA S. , HASEEB MAHNAZ Q.
Published: December 2012

Magnetic moment of electron at finite temperature is directly related to the modified electron mass in the background heat bath. Magnetic moment of electron gets modified at finite temperature also, when it couples with the magnetic field, through its temperature-dependent physical mass. We show that the second-order corrections to the magnetic moment of electron is a complicated function of temperature. We calculate the self-mass induced thermal contributions to the magnetic moment of electron, up to the two-loop level, for temperatures valid around the era of primordial nucleosynthesis. A comparison of thermal behavior of the magnetic moment is also quantitatively studied in detail, around the temperatures below and above the nucleosynthesis temperature.
NONLINEAR INSTABILITY OF DISHED SHALLOW SHELLS UNDER UNIFORMLY DISTRIBUTED LOAD
Authors: LIU CHANG-JIANG , ZHENG ZHOU-LIAN , HUANG CONG-BING , QIU WEI , HE XIAO-TING , SUN JUN-YI
Published: December 2012

In this paper, the nonlinear instability of dished shallow shells under a uniformly distributed load is investigated. The dimensionless governing differential equations for the problem are derived and the equations solved by using the Free-Parameter Perturbation Method with the Spline Function Method. By analyzing the instability modes of dished shallow shells, we obtain the variation rules of the maximum deflection area of initial instability of the uniformly loaded dished shallow shell, and discuss the relationship between the initial instability area and the maximum deflection area of initial instability. These results provide some theoretical basis for engineering design and instability prediction and control of shallow shell structures.
MODELING THE EFFECT OF VAN DER WAALS ATTRACTION ON THE INSTABILITY OF ELECTROSTATIC CANTILEVER AND DOUBLY-SUPPORTED NANO-BEAMS USING MODIFIED ADOMIAN METHOD
Authors: SOROUSH RAHMAN , KOOCHI ALI , KAZEMI ASIEH SADAT , ABADYAN MOHAMADREZA
Published: December 2012

A nano-scale continuum model is applied to investigating the effect of van der Waals (vdW) attraction on pull-in instability of nano-beams in the presence of electrostatic forces. Two cases including the cantilever and doubly-supported beams are considered. The modified Adomian decomposition (MAD) method is employed to solve the nonlinear constitutive equation of nano-beams in the presence of vdW and electrostatic forces for the first time. The results show that the effect of vdW attraction on the instability of the doubly-supported nano-beam is weak when compared to that of the cantilever due to the higher elastic stiffness of the former. Basic design parameters such as the critical deflection and pull-in voltage of the nano-beam are computed. The minimum initial gap and the detachment length of an actuator that does not stick to the substrate due to intermolecular attractions are determined. As a special case, the instability of freestanding nano-electromechanical systems (NEMS) due to vdW attraction is investigated. The MAD solutions are compared with the numerical ones and a proposed lumped model, as well as models available from the literature.
IL-17 induces type V collagen overexpression and EMT via TGF-β-dependent pathways in obliterative bronchiolitis
Authors: Vittal Ragini , Fan Lin , Greenspan Daniel S. , Mickler Elizabeth A. , Gopalakrishnan Bagavathi , Gu Hongmei , Benson Heather L. , Zhang Chen , Burlingham William , Cummings Oscar W. , Wilkes David S.
Published: December 2012

Obliterative bronchiolitis (OB), a fibrotic airway lesion, is the leading cause of death after lung transplantation. Type V collagen [col(V)] overexpression and IL-17-mediated anti-col(V) immunity are key contributors to OB pathogenesis. Here, we report a previously undefined role of IL-17 in inducing col(V) overexpression, leading to epithelial mesenchymal transition (EMT) and subsequent OB. We observed IL-17-mediated induction of col(V) α1 chains [α1 (V)] in normal airway epithelial cells in vitro and detected α1 (V)-specific antibodies in bronchoalveolar lavage fluid of lung transplant patients. Overexpression of IL-17 and col(V) was detected in OB lesions in patient lung biopsies and in a murine OB model. IL-17 is shown to induce EMT, TGF-β mRNA expression, and SMAD3 activation, whereas downregulating SMAD7 expression in vitro. Pharmacological inhibition of TGF-βRI tyrosine kinase, p38 MAPK, or focal adhesion kinase prevented col(V) overexpression and EMT. In murine orthotopic lung transplants, neutralizing IL-17 significantly decreased TGF-β mRNA and protein expression and prevented epithelial repair/OB. Our findings highlight a feed-forward loop between IL-17 and TGF-β, leading to induction of col(V) and associated epithelial repair, thus providing one possible link between autoimmunity and OB after lung transplantation.
Approximations of Antieigenvalue and Antieigenvalue-Type Quantities
Authors: Seddighin Morteza
Published: December 2012

We will extend the definition of antieigenvalue of an operator to antieigenvalue-type quantities, in the first section of this paper, in such a way that the relations between antieigenvalue-type quantities and their corresponding Kantorovich-type inequalities are analogous to those of antieigenvalue and Kantorovich inequality. In the second section, we approximate several antieigenvalue-type quantities for arbitrary accretive operators. Each antieigenvalue-type quantity is approximated in terms of the same quantity for normal matrices. In particular, we show that for an arbitrary accretive operator, each antieigenvalue-type quantity is the limit of the same quantity for a sequence of finite-dimensional normal matrices.