bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of organic forms of phosphorus and variable concentrations of sulfide on the metabolic generation of soluble-reactive phosphate by sulfur chemolithoautotrophs: a laboratory study
Authors: Guhathakurta Himadri , Biswas Raka , Dey Prabuddha , Mahapatra Piyali Gajendra , Mondal Bipasha 
Published: September 2007

Abstract
In aquatic systems, recycling of phosphorus (P) is strongly influenced by microbial metabolic responses. This study was designed to look at the generation of P (as soluble-reactive phosphate (SRP)) from organic P-enriched sediments by benthic sulfur chemolithoautotrophs. The study revealed that microbial density was greater in organic P-enriched sediments when compared to sediments without added organic P and the presence of organic P significantly influenced mobilization of SRP from sediment. Generation of SRP by sediment microbes was cumulative, dependent on time. The results indicated dissolved sulfide (S2−) to be necessary for initiation of the metabolism-related mobilization of P: there was no statistically significant effect of variations in ambient concentrations of sulfide (S2−). The results elucidate possible outcomes of addition of organic P in aquatic ecosystems.
The use of stable isotope probing to identify key iron-reducing microorganisms involved in anaerobic benzene degradation
Authors: Kunapuli Umakanth , Lueders Tillmann , Meckenstock Rainer U 
Published: September 2007

Abstract
Here, we present a detailed functional and phylogenetic characterization of an iron-reducing enrichment culture maintained in our lab with benzene as sole carbon and energy source. We used DNA-stable isotope probing to identify microbes within the enrichment most active in the assimilation of 13C-label. When 12C6- and 13C6-benzene were added as comparative substrates, marked differences in the quantitative buoyant density distribution became apparent especially for uncultured microbes within the Gram-positive Peptococcaceae, closely related to environmental clones retrieved from contaminated aquifers world wide and only distantly related to cultured representatives of the genus Thermincola. Prominent among the other constituents of the enrichment were uncultured Deltaproteobacteria, as well as members of the Actinobacteria. Although their presence within the enrichment seems to be stable they did not assimilate 13C-label as significantly as the Clostridia within the time course of our experiment. We hypothesize that benzene degradation in our enrichment involves an unusual syntrophy, where members of the Clostridia primarily oxidize benzene. Electrons from the contaminant are both directly transferred to ferric iron by the primary oxidizers, but also partially shared with the Desulfobulbaceae as syntrophic partners. Alternatively, electrons may also be quantitatively transferred to the partners, which then reduce the ferric iron. Thus our results provide evidence for the importance of a novel clade of Gram-positive iron-reducers in anaerobic benzene degradation, and a role of syntrophic interactions in this process. These findings shed a totally new light on the factors controlling benzene degradation in anaerobic contaminated environments.
Increasing Concerns about Corn Earworm Susceptibility to Pyrethroids in the Midwestern USA
Authors: Hutchison W. D. , Weinzierl R. A. 
Published: September 2007

Because of growing concern about inconsistent corn earworm (CEW control, particularly in Midwest sweet corn, and the documented migratory behavior of CEW adults, a symposium was organized for the Annual Meeting of the North Central Branch of the Entomological Society of America in 2006. The purpose of the symposium was to provide a comprehensive overview of the status and impact of H. zea resistance to synthetic pyrethroids, with a focus on the midwestern, northeastern, and southern US. Accepted for publication 4 June 2007. Published 19 July 2007.
The Aerobiology and Population Genetic Structure of Gibberella zeae
Authors: Schmale David G. , Bergstrom Gary C. 
Published: September 2007

Gibberella zeae causes Fusarium head blight (FHB) of wheat and barley and Gibberella ear rot (GER) of corn. Ascospores of G. zeae rely on atmospheric motion systems for transport to susceptible host plants. A long term objective of our research is to determine where inoculum for FHB and GER comes from and how far it travels. We measured the distance that ascospores of G. zeae were forcibly discharged in still air, and determined that long-range transport is favored by day-time ascospore release. We used remote-piloted aircraft to collect viable spores of G. zeae in the lower atmosphere. Viable spores of G. zeae were abundant in the lower atmosphere during all times of the day and night under a broad range of environmental conditions. Viable spores of G. zeae were deposited over wheat and corn fields mainly at random and predominantly at night. We used amplified fragment length polymorphisms (AFLPs) to characterize the genetic structure of atmospheric populations of G. zeae over multiple years. Genotypic diversity was high in the atmospheric populations of G. zeae, and nearly all of the isolates in each of the populations represented unique AFLP haplotypes. Diverse atmospheric populations of G. zeae are indicative of wellmixed sources of aerial inoculum, potentially originating from local and more distant sources. Introduced strains of G. zeae with altered virulence or mycotoxin profiles, moving over long distances, have the potential to spread rapidly into previously unexposed wheat and corn production regions. Accepted for publication 14 February 2007. Published 26 July 2007.
Soil mechanics: breaking ground
Authors: Einav Itai 
Published: September 2007

In soil mechanics, student's models are classified as simple models that teach us unexplained elements of behaviour; an example is the Cam clay constitutive models of critical state soil mechanics (CSSM). ‘Engineer's models’ are models that elaborate the theory to fit more behavioural trends; this is usually done by adding fitting parameters to the student's models. Can currently unexplained behavioural trends of soil be explained without adding fitting parameters to CSSM models, by developing alternative student's models based on modern theories?
Here I apply an alternative theory to CSSM, called ‘breakage mechanics’, and develop a simple student's model for sand. Its unique and distinctive feature is the use of an energy balance equation that connects grain size reduction to consumption of energy, which enables us to predict how grain size distribution (gsd) evolves—an unprecedented capability in constitutive modelling. With only four parameters, the model is physically clarifying what CSSM cannot for sand: the dependency of yielding and critical state on the initial gsd and void ratio.
mgpB and mgpC sequence diversity in Mycoplasma genitalium is generated by segmental reciprocal recombination with repetitive chromosomal sequences
Authors: Iverson‐Cabral Stefanie L. , Astete Sabina G. , Cohen Craig R. , Totten Patricia A. 
Published: September 2007

Summary Mycoplasma genitalium is associated with sexually transmitted infections in men and women that, if untreated, can persist, suggesting that mechanism(s) exist to facilitate immune evasion. Approximately 4% of the limited M. genitalium genome contains repeat sequences termed MgPar regions that have homology to mgpB and mgpC, which encode antigenic proteins associated with attachment. We have previously shown that mgpB sequences vary within a single strain of M. genitalium in a pattern consistent with recombination between mgpB and MgPar sequences (Iverson‐Cabral et al.). In the current study, we show that mgpC heterogeneity similarly occurs within the type strain, G‐37T, cultured in vitro and among cervical specimens collected from a persistently infected woman. In all cases, alternative mgpC sequences are indicative of recombination with MgPar regions. Additionally, the isolation of single‐colony M. genitalium clonal variants containing alternative mgpB or mgpC sequences allowed us to demonstrate that mgpB and mgpC heterogeneity is associated with corresponding changes within donor MgPar regions, consistent with reciprocal recombination. Better‐defined systems of antigenic variation are typically mediated by unidirectional gene conversion, so the generation of genetic diversity observed in M. genitalium by the mutual exchange of sequences makes this organism unique among bacterial pathogens.
Identification of the genes directly controlled by the response regulator CiaR in Streptococcus pneumoniae: five out of 15 promoters drive expression of small non‐coding RNAs
Authors: Halfmann Alexander , Kovács Márta , Hakenbeck Regine , Brückner Reinhold 
Published: September 2007

SummaryThe two‐component regulatory system CiaRH of Streptococcus pneumoniae has been implicated in β‐lactam resistance, maintenance of cell integrity, competence and virulence, but the genes that are regulated directly by the system have not been defined. Using transcriptional mapping, in vitro CiaR binding, and in vivo analysis of CiaR‐mediated regulation, 15 promoters were identified to be directly controlled by the response regulator CiaR. A direct repeat, TTTAAG‐N5‐TTTAAG, was found to be essential for CiaR binding and regulation. It is present, either completely or with subtle changes, in all promoter regions. Fourteen promoters of the regulon are activated by CiaR, and one was found to be controlled negatively. The genes that are transcribed from these promoters included ciaRH, loci that are predicted to be involved in the modification of teichoic acids (lic), in sugar metabolism (mal, man), stress response (htrA), chromosome segregation (parB), protease maturation (ppmA) and unknown functions. Remarkably, the five strongest promoters of the CiaR regulon drive expression of small RNAs. These small RNAs, designated csRNAs for cia‐dependent small RNAs, are non‐coding, between 87 and 151 nt in size, and show a high degree of similarity to each other. The analysis of deletion mutants in the csRNA genes revealed that csRNA4 and csRNA5 affect stationary‐phase autolysis. The identification of five small non‐coding regulatory RNAs opens new perspectives to approach the physiological role of the CiaRH two‐component regulatory system.
Role of the Escherichia coli SbmA in the antimicrobial activity of proline‐rich peptides
Authors: Mattiuzzo Maura , Bandiera Antonella , Gennaro Renato , Benincasa Monica , Pacor Sabrina , Antcheva Nikolinka , Scocchi Marco 
Published: September 2007

SummaryIn contrast to many antimicrobial peptides, members of the proline‐rich group of antimicrobial peptides inactivate Gram‐negative bacteria by a non‐lytic mechanism. Several lines of evidence indicate that they are internalized into bacteria and their activity mediated by interaction with unknown cellular components. With the aim of identifying such interactors, we selected mutagenized Escherichia coli clones resistant to the proline‐rich Bac7(1–35) peptide and analysed genes responsible for conferring resistance, whose products may thus be involved in the peptide's mode of action. We isolated a number of genomic regions bearing such genes, and one in particular coding for SbmA, an inner membrane protein predicted to be part of an ABC transporter. An E. coli strain carrying a point mutation in sbmA, as well as other sbmA‐null mutants, in fact showed resistance to several proline‐rich peptides but not to representative membranolytic peptides. Use of fluorescently labelled Bac7(1–35) confirmed that resistance correlated with a decreased ability to internalize the peptide, suggesting that a bacterial protein, SbmA, is necessary for the transport of, and for susceptibility to, proline‐rich antimicrobial peptides of eukaryotic origin.
Genome‐wide analysis of T‐DNA integration into the chromosomes ofMagnaporthe oryzae
Authors: Choi Jaehyuk , Park Jongsun , Jeon Junhyun , Chi Myoung‐Hwan , Goh Jaeduk , Yoo Sung‐Yong , Park Jaejin , Jung Kyongyong , Kim Hyojeong , Park Sook‐Young , Rho Hee‐Sool , Kim Soonok , Kim Byeong Ryun , Han Seong‐Sook , Kang Seogchan , Lee Yong‐Hwan 
Published: September 2007

SummaryAgrobacteriumtumefaciens‐mediatedtransformation (ATMT) has become a prevalent tool for functional genomics of fungi, but our understanding of T‐DNA integration into the fungal genome remains limited relative to that in plants. Using a model plant‐pathogenic fungus,Magnaporthe oryzae, here we report the most comprehensive analysis of T‐DNA integration events in fungi and the development of an informatics infrastructure, termed aT‐DNAanalysisplatform (TAP). We identified a total of 1110T‐DNA‐taggedlocations (TTLs) and processed the resulting data via TAP. Analysis of the TTLs showed that T‐DNA integration was biased among chromosomes and preferred the promoter region of genes. In addition, irregular patterns of T‐DNA integration, such as chromosomal rearrangement and readthrough of plasmid vectors, were also observed, showing that T‐DNA integration patterns into the fungal genome are as diverse as those of their plant counterparts. However, overall the observed junction structures between T‐DNA borders and flanking genomic DNA sequences revealed that T‐DNA integration into the fungal genome was more canonical than those observed in plants. Our results support the potential of ATMT as a tool for functional genomics of fungi and show that the TAP is an effective informatics platform for handling data from large‐scale insertional mutagenesis.
The role of iron in Mycobacterium smegmatis biofilm formation: the exochelin siderophore is essential in limiting iron conditions for biofilm formation but not for planktonic growth
Authors: Ojha Anil , Hatfull Graham F. 
Published: September 2007

SummaryMany species of mycobacteria form structured biofilm communities at liquid–air interfaces and on solid surfaces. Full development of Mycobacterium smegmatis biofilms requires addition of supplemental iron above 1 μM ferrous sulphate, although addition of iron is not needed for planktonic growth. Microarray analysis of the M. smegmatis transcriptome shows that iron‐responsive genes – especially those involved in siderophore synthesis and iron uptake – are strongly induced during biofilm formation reflecting a response to iron deprivation, even when 2 μM iron is present. The acquisition of iron under these conditions is specifically dependent on the exochelin synthesis and uptake pathways, and the strong defect of an iron–exochelin uptake mutant suggests a regulatory role of iron in the transition to biofilm growth. In contrast, although the expression of mycobactin and iron ABC transport operons is highly upregulated during biofilm formation, mutants in these systems form normal biofilms in low‐iron (2 μM) conditions. A close correlation between iron availability and matrix‐associated fatty acids implies a possible metabolic role in the late stages of biofilm maturation, in addition to the early regulatory role. M. smegmatis surface motility is similarly dependent on iron availability, requiring both supplemental iron and the exochelin pathway to acquire it.
Aerobic TMAO respiration in Escherichia coli
Authors: Ansaldi Mireille , Théraulaz Laurence , Baraquet Claudine , Panis Gaël , Méjean Vincent 
Published: September 2007

SummaryIn the absence of oxygen, Escherichia coli can use alternative exogenous electron acceptors, including trimethylamine oxide (TMAO), to generate energy. In this study, we showed that in contrast to the other anaerobic respiratory systems, the TMAO reductase (Tor) system was expressed during both aerobiosis and anaerobiosis. By using a torA–lacZ fusion and quantitative reverse transcription polymerase chain reaction, we established that the torCAD operon encoding the Tor system was induced in the presence of TMAO mainly during exponential phase, and that optimal induction required a certain level of DNA supercoiling. We also showed that the presence of oxygen prevented neither the biogenesis of the Tor system nor the reduction of TMAO. The physiological role of TMAO reduction during aerobiosis has not been yet established, but our experiments suggest that alkaline TMA production could enhance the growth conditions by increasing the pH of the culture.
A biosynthetic gene cluster for a secreted cellobiose lipid with antifungal activity from Ustilago maydis
Authors: Teichmann Beate , Linne Uwe , Hewald Sandra , Marahiel Mohamed A. , Bölker Michael 
Published: September 2007

SummaryThe phytopathogenic basidiomycetous fungus Ustilago maydis secretes large amounts of the glycolipid biosurfactant ustilagic acid (UA). UA consists of 15,16‐dihydroxypalmitic or 2,15,16‐trihydroxypalmitic acid, which is O‐glycosidically linked to cellobiose at its terminal hydroxyl group. In addition, the cellobiose moiety is acetylated and acylated with a short‐chain hydroxy fatty acid. We have identified a 58 kb spanning gene cluster that contains 12 open reading frames coding for most, if not all, enzymes needed for UA biosynthesis. Using a combination of genetic and mass spectrometric analysis we were able to assign functional roles to three of the proteins encoded by the gene cluster. This allowed us to propose a biosynthesis route for UA. The Ahd1 protein belongs to the family of non‐haem diiron reductases and is required for α‐hydroxylation of palmitic acid. Two P450 monooxygenases, Cyp1 and Cyp2, catalyse terminal and subterminal hydroxylation of palmitic acid. We could demonstrate that infection of tomato leaves by the plant pathogenic fungus Botrytis cinerea is prevented by co‐inoculation with wild‐type U. maydis sporidia. U. maydis mutants defective in UA biosynthesis were unable to inhibit B. cinerea infection indicating that UA secretion is critical for antagonistic activity.
Increased SA in NPR1‐silenced plants antagonizes JA and JA‐dependent direct and indirect defenses in herbivore‐attacked Nicotiana attenuata in nature
Authors: Rayapuram Cbgowda , Baldwin Ian T. 
Published: September 2007

SummaryThe phytohormone jasmonic acid (JA) is known to mediate herbivore resistance, while salicylic acid (SA) and non‐expressor of PR‐1 (NPR1) mediate pathogen resistance in many plants. Herbivore attack on Nicotiana attenuata elicits increases in JA and JA‐mediated defenses, but also increases SA levels and Na‐NPR1 transcripts from the plant’s single genomic copy. SA treatment of wild‐type plants increases Na‐NPR1 and Na‐PR1 transcripts. Plants silenced in NPR1 accumulation by RNAi (ir‐npr1) are highly susceptible to herbivore and pathogen attack when planted in their native habitat in Utah. They are also impaired in their ability to attract Geocorus pallens predators, due to their decreased ability to release cis‐α‐bergamotene, a JA‐elicited volatile ‘alarm call’. In the glasshouse, Spodoptera exigua larvae grew better on ir‐npr1 plants, which had low levels of JA, JA–isoleucine/leucine, lipoxygenase‐3 (LOX3) transcripts and JA‐elicited direct defense metabolites (nicotine, caffeoyl putrescine and rutin), but high levels of SA and isochorismate synthase (ICS) transcripts, suggesting de novo biosynthesis of SA. A microarray analysis revealed downregulation of many JA‐elicited genes and upregulation of SA biosynthetic genes. JA treatment restored nicotine levels and resistance to S. exigua in ir‐npr1 plants. We conclude that, during herbivore attack, NPR1 negatively regulates SA production, allowing the unfettered elicitation of JA‐mediated defenses; when NPR1 is silenced, the elicited increases in SA production antagonize JA and JA‐related defenses, making the plants susceptible to herbivores.
Metabolic engineering of morphinan alkaloids by over‐expression and RNAi suppression of salutaridinol 7‐O‐acetyltransferase in opium poppy
Authors: Allen Robert S. , Miller James A. C. , Chitty Julie A. , Fist Anthony J. , Gerlach Wayne L. , Larkin Philip J. 
Published: September 2007

SummaryWe demonstrate that both over‐expression and suppression of the gene encoding the morphinan pathway enzyme salutaridinol 7‐O‐acetyltransferase (SalAT) in opium poppy affects the alkaloid products that accumulate. Over‐expression of the gene in most of the transgenic events resulted in an increase in capsule morphine, codeine and thebaine on a dry‐weight basis. The transgenic line with the highest alkaloid content had 41%, 37% and 42% greater total alkaloids than the control in three independent trials over 3 years. DNA‐encoded hairpin RNA‐mediated suppression of SalAT resulted in the novel accumulation of the alkaloid salutaridine at up to 23% of total alkaloid; this alkaloid is not detectable in the parental genotype. Salutaridine is not the substrate of SalAT but the substrate of the previous enzyme in the pathway, salutaridine reductase. RNA transcript analysis of 16 primary T0 transformants and their segregating T1 progeny revealed an average reduction in SalAT transcript to about 12% of the control. Reduction in SalAT transcript was evident in both leaves and latex. Reverse transcriptase PCR and high‐performance liquid chromatography analyses confirmed cosegregation of the expressed transgene with the salutaridine accumulating phenotype.
Role of IFN‐γ in an experimental murine model of West Nile virus‐induced seizures
Authors: Getts Daniel R. , Matsumoto Izuru , Müller Marcus , Getts Meghann Teague , Radford Jane , Shrestha Bimmi , Campbell Iain L. , King Nicholas J. C. 
Published: September 2007

AbstractSeizures are a major complication of viral encephalitis. However, the mechanisms of seizure‐associated neuronal dysfunction remain poorly understood. We report that intranasal inoculation with West Nile virus (WNV) (Sarafend) causes limbic seizures in C57BL/6 mice, but not in interferon (IFN)‐γ‐deficient (IFN‐γ−/−) mice. Both strains showed similar levels of virus in the brain, as well as similar concentrations of the cytokines, tumor necrosis factor and interleukin‐6, both of which can alter neuronal excitability. Experiments in chimeric IFN‐γ−/−mice reconstituted with IFN‐γ‐producing leukocytes showed that IFN‐γ is not required during central nervous system infection for limbic seizure development, suggesting a role for IFN‐γ in the developing brain. This was supported responses to pentylenetetrazole, kainic acid (KA), andN‐methyl‐d‐aspartate (NMDA). Both strains of mice exhibited similar behavior after pentylenetetrazole challenge. However, while NMDA and KA treatment resulted in characteristic seizures in C57BL/6 mice, these responses were diminished (NMDA treatment) or absent (KA treatment) in IFN‐γ−/−mice. Furthermore, NMDA‐receptor blockade with MK‐801 in WNV‐infected C57BL/6 mice abrogated seizures and prolonged survival. Our data show that IFN‐γ plays an important role in the development of the excitatory seizure pathways in the brain and that these cascades become pathogenic in encephalitic WNV infection.