bluuebunny/crossref_metadata_2025 huggingface dataset:
Standardization of methods for detection of Ralstonia solanacearum in potato*
Authors: Elphinstone J. G. , Stead D. E. , Caffier D. , Janse J. D. , López M. M. , Mazzucchi U. , Müller P. , Persson P. , Rauscher E. , Schiessendoppler E. , Santos M. Sousa , Stefani E. , van Vaerenbergh J.
Published: April 2008

In support of EU Council Directive 98/57/EC on the control of potato brown rot disease, caused by Ralstonia solanacearum, a ring test was conducted to evaluate and standardize currently recommended methods for official testing of potato tubers. Test tubers were either naturally infected (symptomatic) or vacuum‐infiltrated with different R. solanacearum suspensions or water. Testing was performed independently in 19 EU plant health laboratories using standardized protocols based on those annexed to the Directive. With high pathogen concentrations, fully reliable results were obtained with dilution plating on a selective medium, immunofluorescent antibody staining (IFAS), enzyme‐linked immunosorbent assay (ELISA), fluorescent in situ hybridization and a tomato bioassay. The reliability of diagnoses across all laboratories decreased with inoculum concentration in asymptomatic tubers, irrespective of the methods used. Comparable results were obtained with 3 commercial antisera in IF AS or with 2 antisera in ELISA but the IFAS method was slightly more reliable. In several laboratories, diagnoses obtained using polymerase chain reaction (PCR) protocols were less reliable than those using the other methods. Independent optimization of PCR conditions in each laboratory and the introduction of internal positive PCR controls are recommended.
Genetic diversity of Erwinia carotovora strains isolated from infected plants grown in Poland*
Authors: Śledź W. , Jafra S. , Waleron M. , Lojkowska E.
Published: April 2008

The species Erwinia carotovora contains several subspecies, among which Erwinia carotovora subsp. atroseptica and Erwinia carotovora subsp. carotovora cause the highest losses of economically important plants. Potato blackleg, which is a tuber‐borne disease, occurs during the growing season and is caused by E. c. atroseptica. Soft rot of potato tubers is usually caused by E. c. carotovora and E. c. atroseptica. As a result of the absence of resistant cultivars, disease control relies primarily on the production and use of healthy seed potatoes. Selection and elimination of infected material is very difficult as infection almost always appears in conditions favourable for disease development. About 1500 strains of pectinolytic Erwinia were isolated from plants and tubers with disease symptoms obtained from Control Inspectors of the Polish State Inspection of Plant Protection. Biochemical, immunological and molecular methods were used to estimate E. c. atroseptica and E. c. carotovora. About 57% of the isolated bacteria belong to subspecies atroseptica. ELISA testing with monoclonal antibodies indicated that only about 65% of these E. c. atroseptica isolates belonged to serogroup I.
A comparison of molecular methods for the routine detection of viroids*
Authors: Mumford R. A. , Walsh K. , Boonham N.
Published: April 2008

Viroids, such as Chrysanthemum stunt viroid (CSVd) and Potato spindle tuber viroid (PSTVd), are important plant pathogens. However, because of their unique biological properties, viroids have proved, in the past, difficult to diagnose. The use of molecular methods has now changed this and this paper reports the comparison of three such methods (dot‐blot hybridization using DIG‐labelled cRNA probes, reverse transcription‐polymerase chain reaction (RT‐PCR) and TaqMan), which have been developed for routine detection of CSVd. Sensitivity comparisons show that the TaqMan assay is more sensitive than either RT‐PCR (100 times) and hybridization (1000 times). RT‐PCR and TaqMan assays have also been developed to detect PSTVd. In addition to the development of sensitive detection methods, considerable emphasis has been placed on making these assays amenable to mass‐scale detection through the use of internal controls and the development of a rapid, reliable probe capture extraction system.
Use of fluorogenic Scorpions for fast and sensitive detection of plant viruses*
Authors: Sialer M.M. Finetti , Ciancio A. , Gallitelli D.
Published: April 2008

Very recently, a novel nucleic acid detection technology based on a primer with a quenched fluorophore and a probe complementary to an internal portion of the amplicon has been developed. The primer probe, named ‘Scorpion’, fluoresces only upon hybridization with its target, i.e. if the specific extension product of the primer is synthesized during the reaction. We have used Scorpion primers in RT‐PCR assays to detect Tomato spotted wilt tospovirus and Plum pox potyvirus in naturally infected plants. Amplified products of the expected size were detected either by real‐time measurements or by visual estimation of fluorescence emission from tubes placed over an ultraviolet light source at the end of the Scorpion‐RT‐PCR. In serially diluted plant sap, the visual method allowed detection of 7.5 pg of infected plant tissue and proved at least as sensitive as visual estimation of ethidium bromide‐stained amplicons separated by gel electrophoresis.
Comparison of serological and molecular techniques for detection of Tomato yellow leaf curl begomovirus*
Authors: Dalmon A. , Cailly M. , David C.
Published: April 2008

Tomato yellow leaf curl begomovirus (TYLCV) causes severe damage to tomato crops. The virus is not considered as established in France, although a single outbreak (subjected to eradication measures) occurred in 1999. Since the vector of TYLCV, the whitefly Bemisia tabaci, is already present in France and the virus is present in several neighbouring Mediterranean countries, there is a high risk of introduction into France. To prevent spread of the disease, systematic detection is essential. Samples of tomato and Eustoma grandiflorum were tested, and different methods were compared to determine which is the best for regular tests. Classical serological methods (TAS‐ELISA and immuno‐printing) were compared with molecular hybridization (which is specially suitable for the single‐stranded DNA genome of Geminiviridae), and PCR. Tissue‐printing methods, which avoid time‐consuming sample preparation, gave consistent results with hybridization. In contrast, immunoprinting detection confirmed only 61 % of samples found positive with TAS‐ELISA. Furthermore, a comparison of signal intensities obtained with TYLCV‐IL or TYLCV‐Sar probes provided indications on viral strain(s) detected. The efficiency, reliability and feasibility of serological and molecular techniques for routine official testing are discussed.
Molecular detection of olive viruses*
Authors: Grieco F. , Alkowni R. , Saponari M. , Savino V. , Martelli G. P.
Published: April 2008

Olive hosts 13 viruses belonging in seven different genera. Additional non‐mechanically transmissible viruses probably infect olive in nature, as suggested by the widespread occurrence of double‐stranded RNAs (dsRNAs) in trees from which no viruses can be recovered by manual inoculation. Because sanitary selection appears to be the only measure for restraining virus dissemination through propagating material, detection methods are needed which are more sensitive and reliable than those currently available (biological and serological). The following molecular techniques have therefore been used and their efficiency compared: (1) dsRNA analysis; (2) dot‐blot hybridization with digoxigenin‐labelled riboprobes in separate reactions or in mixture; and (3) reverse transcription‐polymerase chain reaction (RT‐PCR). It was found that: (1) dsRNAs were detected in 210 out of 286 olive accessions (73.4%) coming from six different Italian regions; (2) one‐step RT‐PCR yielded much better results using TNA extracts than crude sap; and (3) dot‐blot hybridization of denatured dsRNAs with digoxigenin‐labelled virus‐specific riboprobes was the most reliable detection method available.
Satellite DNA used as a species‐specific probe for identification ofBursaphelenchus xylophilus*
Authors: Abad P.
Published: April 2008

The phytoparasitic nematodeBursaphelenchus xylophilusis the causal agent of pine wilt disease. However, it is difficult to differentiate isolates ofB. xylophilusfrom the closely related speciesB. mucronatus, which is not pathogenic to pine trees under field conditions. Here, we describe the development of a species‐specific DNA probe using a satellite DNA sequence fromB. xylophilus.This unusually abundant satellite DNA constitutes up to 30% of the nematode genome. It is represented as a tandemly repeatedMspI site‐containing sequence with a monomeric unit of 160 bp. We show that thisMspI satDNA probe is effective directly on a single squashedB. xylophilusnematode spotted onto a filter or by using polymerase chain reaction (PCR) amplification. Thus, in the pine wood‐nematode species complex, identification of the plant pathogenic speciesB. xylophilusmay be accomplished both rapidly and reliably.
Use of satellite DNA for specific diagnosis of the quarantine root‐knot nematodes Meloidogyne chitwoodi and M. fallax*
Authors: Castagnone‐Sereno P.
Published: April 2008

The root‐knot nematodes Meloidogyne chitwoodi and M. fallax are potato parasites that have recently been designated as quarantine pests in Europe. The related and more widely distributed species M. hapla may be found associated with them in field conditions. Because of their morphological resemblance, specific diagnosis of these three species is a difficult task. Therefore, simple and reliable diagnostic tools are urgently needed, for both routine identification of these nematodes and implementation of efficient management strategies and/or phytosanitary regulations. Here is presented an overview of the research recently conducted at INRA Antibes (FR) in order to develop molecular tools for the characterization of these nematodes, based on satellite DNA sequences isolated from their genome.
Diagnostics of cyst nematodes and tephritid fruit flies using mitochondrial and ribosomal DNA*
Authors: Fleming C. C. , Rao J. , Moreland B. , Craig D. , Turner S. J.
Published: April 2008

The accurate identification of invertebrates intercepted by European phytosanitary authorities is an important step in monitoring and controlling the movement of potential pests of EU agriculture, forestry and horticulture. Nematodes and tephritid fruit flies pose particular problems, with many intercepted specimens not identified to species level. Polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) analysis of mitochondrial and ribosomal DNA genes have been used to assess interspecific variability in the Tephritidae and in cyst nematodes, thus developing more effective diagnostic procedures for these invertebrate pests. PCR‐RFLP targeting the ribosomal DNA and mitochondrial DNA can be used to identify 10 tephritid species commonly detected in imported materials. Similarly, rDNA variation can be used to discriminate routinely between cyst nematodes of the genera Heterodera, Punctodera and Globodera. The integration of traditional morphology‐based diagnostics with a molecular approach is regarded as the most effective way of enhancing phytosanitary diagnostics in the future.
Collar rot of Chlorophytum borivilianum caused by Corticium rolfsii: a new disease
Authors: Singh H. B. , Singh A. , Tripathi A. , Tiwari S. K. , Johri J. K.
Published: April 2008

A new disease of Chlorophytum borivilianum, characterized by symptoms of collar rot, has been observed in experimental farms of the National Botanical Research Institute, Lucknow, India. The pathogen has been isolated and identified as Corticium rolfsii.
Bursaphelenchus species in conifers in Europe: distribution and morphological relationships
Authors: Braasch H.
Published: April 2008

The morphological relationship between European Bursaphelenchus species living in conifers was studied in order to provide key characters for their taxonomic identification. Several species have been newly described or recorded in Europe during the past few years and were morphologically investigated. Among the 28 conifer‐inhabiting European species, four groups can be distinguished from each other by the number of lateral incisures, number and position of anal papillae of males and presence and size of a vulval flap of females. Two groups, each containing just one species show two and six lateral lines, respectively, whereas most Bursaphelenchus species belong to two groups, possessing either three or four incisures. Each of the last two groups can be divided into three subgroups, which can be differentiated by spicule shape, number and position of caudal papillae, presence and size of a vulval flap and some other features. A fifth group includes species with unclear group affiliation due to insufficient knowledge of their morphology. The B. xylophilus group (B. xylophilus, B. mucronatus, B. fraudulentus) with four lateral lines, unique spicule shape and characteristic position of the caudal papillae can clearly be differentiated from all other groups by morphology, also using only light microscopy. Within this group, B. xylophilus can clearly be differentiated morphologically from the other species, provided that adult specimens of both sexes are found and also provided that the round‐tailed form of the species remains the only form present, as in Europe. Figures showing the important identification features of spicule shape and female tail shape are given for 28 species. A table shows the complete range of the most important morphometric measurements of these species. Data on the occurrence, host range and, as far as known, the vectors of these species were collected throughout Europe and references are given for each record.
Identification des espèces fongiques associées à la pourriture du pied du blé et étude de leur répartition selon les étages bioclimatiques en Tunisie
Authors: Gargouri S. , Hajlaoui M. R. , Guermech A. , Marrakchi M.
Published: April 2008

Des prospections ont été faites durant les mois d'avril et de mai 2000 dans 174 parcelles réparties sur six étages et sous‐étages bioclimatiques afin d'identifier les champignons associés à la pourriture du pied du blé en Tunisie. Environ 1600 isolats ont été obtenus à partir de la base des plantes de blé malades. Les champignons les plus fréquemment isolés ont étéFusarium culmorum (70%) et Gibberella zeae (21,5%). Gibberella avenacea et Cochliobolus sativus ont été isolés à la fréquence respective de 5,3% et 4,1%. L'identification moléculaire par PCR a été utilisée afin de distinguer entre les groupes 1 et 2 de G. zeae. Seuls les membres du groupe 1 ont été isolés au cours de ces prospections. Les fréquences de F. culmorum et G. zeae groupe 1 a varié en fonction des régions climatiques. F. culmorum a été dominant dans l'humide, tandis que G. zeae groupe 1 a été absent de cette région et sa fréquence a augmenté en allant vers les étages semiaride et aride.
Detection of Grapevine A vitivirus in Tunisian grapevines
Authors: M'hirsi S. , Fattouch S. , Acheche H. , Marrakchi M. , Marzouki N.
Published: April 2008

Grapevine A vitivirus (GVA), Grapevine B vitivirus (GVB), Grapevine leaf‐roll associated closterovirus 3 (GLRaV3) and Grapevine fanleaf nepovirus (GFLV) were detected by DAS‐ELISA in samples of grapevine showing symptoms of rugose wood from different viticultural areas of Tunisia. After optimization of experimental conditions, PCR and IC‐RT–PCR were found to be more efficient and sensitive than DAS‐ELISA for the detection of GVA.
Sediment shear properties from seafloor compliance measurements: Faroes‐Shetland basin case study
Authors: Crawford Wayne C. , Singh Satish C.
Published: April 2008

Shear properties provide important information about the lithology, fluid content and stability of sediments but are difficult to measure using conventional seismics in the marine environment. Seafloor compliance measurements are sensitive to subsurface shear properties but have only been used in the Pacific Ocean and on shallow coastal shelves, where the source wave energy is known to be strong. We show here that seafloor compliance measurements can provide useful information about shear properties of marine sediments in less energetic settings and under high noise conditions caused by strong seafloor currents. We measured compliance at three sites in the Faroes‐Shetland sedimentary basin north of the Atlantic ocean. The sites have 1000 times higher noise levels than quiet seafloor sites and the source wave power is highly variable, but the data still reveal significant differences in sediment properties between two sites down to 2 kilometres beneath the seafloor. The first site, at the northern end of the basin, has an average shear velocity of 400 m/s in the upper 0.6 kilometres beneath the seafloor, increasing to approximately 2100 m/s at 2 kilometres beneath the seafloor. The second site, further south and to the west of the basin axis, has an average shear velocity of 150 m/s in the upper 0.6 kilometres beneath the seafloor, increasing to 1400 m/s at 2 kilometres beneath the seafloor. The sediments are probably unconsolidated in the upper 0.6 kilometres beneath the seafloor at both sites, with a mean grain size of 1 μm at the southern site and 20 μm at the northern site. The southern site has higher porosity at all depths and a higher risk of borehole collapse during drilling.
Receiver function method in reflection seismology
Authors: Edme Pascal , Singh Satish C.
Published: April 2008

The receiver function method was originally developed to analyse earthquake data recorded by multicomponent (3C) sensors and consists in deconvolving the horizontal component by the vertical component. The deconvolution process removes travel path effects from the source to the base of the target as well as the earthquake source signature. In addition, it provides the possibility of separating the emergent P and PS waves based on adaptive subtraction between recorded components if plane waves of constant ray parameters are considered. The resulting receiver function signal is the local PS wave's impulse response generated at impedance contrasts below the 3C receiver.We propose to adapt this technique to the wide‐angle multi‐component reflection acquisition geometry. We focus on the simplest case of land data reflection acquisition. Our adapted version of the receiver function approach consists in a multi‐step procedure that first removes the P wavefield recorded on the horizontal component and next removes the source signature. The separation step is performed in the τ−p domain while the source designature can be achieved in either the τ−p or the t−x domain. Our technique does not require any a priori knowledge of the subsurface. The resulting receiver function is a pure PS‐wave reflectivity response, which can be used for amplitude versus slowness or offset analysis. Stack of the receiver function leads to a high‐quality S wave image.
Finite‐difference modelling of S‐wave splitting in anisotropic media
Authors: Bansal Reeshidev , Sen Mrinal K.
Published: April 2008

We have implemented a 3D finite‐difference scheme to simulate wave propagation in arbitrary anisotropic media. The anisotropic media up to orthorhombic symmetry were modelled using a standard staggered grid scheme and beyond (monoclinic and triclinic) using a rotated staggered grid scheme. The rationale of not using rotated staggered grid for all types of anisotropic media is that the rotated staggered grid schemes are more expensive than standard staggered grid schemes. For a 1D azimuthally anistropic medium, we show a comparison between the seismic data generated by our finite‐difference code and by the reflectivity algorithm; they are in excellent agreement.

We conducted a study on zero‐offset shear‐wave splitting using the finite‐difference modelling algorithm using the rotated staggered grid scheme. Our S‐wave splitting study is mainly focused on fractured media. On the scale of seismic wavelenghts, small aligned fractures behave as an equivalent anisotropic medium. We computed the equivalent elastic properties of the fractures and the background in which the fractures were embedded, using low‐frequency equivalent media theories. Wave propagation was simulated for both rotationally invariant and corrugated fractures embedded in an isotropic background for one, or more than one, set of fluid‐filled and dry fractures. S‐wave splitting was studied for dipping fractures, two vertical non‐orthogonal fractures and corrugated fractures. Our modelling results confirm that S‐wave splitting can reveal the fracture infill in the case of dipping fractures. S‐wave splitting has the potential to reveal the angle between the two vertical fractures. We also notice that in the case of vertical corrugated fractures, S‐wave splitting is sensitive to the fracture infill.
Sleep quality and morningness–eveningness of shift nurses
Authors: Chung Min‐Huey , Chang Fwu‐Mei , Yang Cheryl CH , Kuo Terry BJ , Hsu Nanly
Published: April 2008

Aim and objective.  The aim of the study was to analyse, while controlling for identified covariates, the effects of morningness–eveningness on sleep quality for shift nurses.

Background.  Shift nurses had greater difficulty falling asleep or staying asleep, thus resulting in higher rates of retiring from hospital. Existing research has addressed the effects of manpower demand and personal preferences on shift assignment; however, the concept of endogenous rhythms is rarely considered.

Methods.  This analysis included 137 nurses between the ages of 21–58. Nurses completed the Horne and Ostberg questionnaire to assess morningness‐eveningness and the Pittsburgh Sleep Quality Index (PSQI) questionnaire to measure self‐reported sleep quality over the last month. The 18‐point Chinese version had a Cronbach's reliability coefficient of 0·79 overall and 0·86 respectively. This study analysed correlates of sleep quality by comparing the groups with better or worse sleep quality according to the median of PSQI. Univariate and multivariate analyses were used for the risk factors of worse sleep quality.

Results.  The result showed that the strongest predictor of sleep quality was morningness–eveningness not the shift schedule or shift pattern for nurses under controlling the variable of age. Greater age and longer years employed in nursing significantly decreased the risk of worse sleep quality. The confounding age factor was properly controlled; evening types working on changing shifts had higher risk of poor sleep quality compared to morning types.

Conclusions.  Morningness–eveningness was the strongest predictor of sleep quality under controlling the variable of age in shift nurses.

Implications for clinical practice.  Our results suggested that determining if nurses were attributed to morning or evening types is an important sleep issue before deciding the shift assignment.
Epidemiology of hepatitis C virus infection in HIV‐infected individuals
Authors: Thomson Emma C. , Main Janice
Published: April 2008

Summary.  Many individuals are infected with both HIV and hepatitis C virus (HCV) infection. More rapid progression of liver disease is seen, higher levels of HCV RNA encourage transmission and sustained virological responses are lower in coinfected patients. The management of these patients is further complicated by potential interactions between antiretroviral therapy and peginterferon and ribavirin.
Communally breeding Bechstein's bats have a stable social system that is independent from the postglacial history and location of the populations
Authors: KERTH GERALD , PETROV BOYAN , CONTI ANDREJ , ANASTASOV DANIJELA , WEISHAAR MANFRED , GAZARYAN SUREN , JAQUIÉRY JULIE , KÖNIG BARBARA , PERRIN NICOLAS , BRUYNDONCKX NADIA
Published: April 2008

Investigating macro‐geographical genetic structures of animal populations is crucial to reconstruct population histories and to identify significant units for conservation. This approach may also provide information about the intraspecific flexibility of social systems. We investigated the history and current structure of a large number of populations in the communally breeding Bechstein's bat (Myotis bechsteinii). Our aim was to understand which factors shape the species’ social system over a large ecological and geographical range. Using sequence data from one coding and one noncoding mitochondrial DNA region, we identified the Balkan Peninsula as the main and probably only glacial refugium of the species in Europe. Sequence data also suggest the presence of a cryptic taxon in the Caucasus and Anatolia. In a second step, we used seven autosomal and two mitochondrial microsatellite loci to compare population structures inside and outside of the Balkan glacial refugium. Central European and Balkan populations both were more strongly differentiated for mitochondrial DNA than for nuclear DNA, had higher genetic diversities and lower levels of relatedness at swarming (mating) sites than in maternity (breeding) colonies, and showed more differentiation between colonies than between swarming sites. All these suggest that populations are shaped by strong female philopatry, male dispersal, and outbreeding throughout their European range. We conclude that Bechstein's bats have a stable social system that is independent from the postglacial history and location of the populations. Our findings have implications for the understanding of the benefits of sociality in female Bechstein's bats and for the conservation of this endangered species.
Mini‐III, a fourth class of RNase III catalyses maturation of the Bacillus subtilis 23S ribosomal RNA
Authors: Olmedo Gabriela , Guzmán Plinio
Published: April 2008

Ribonuclease III (RNase III) type of enzymes are double‐stranded RNA (dsRNA)‐specific endoribonucleases that have important roles in RNA maturation and mRNA decay. They are involved in processing precursors of ribosomal RNA (rRNA) in bacteria as well as precursors of short interfering RNAs (siRNAs) and microRNAs (miRNAs) in eukaryotes. RNase III proteins have been grouped in three major classes according to their domain organization. In this issue of Molecular Microbiology, Redko et al. identified a novel class of bacterial RNase III, named Mini‐III, consisting only of the RNase III catalytic domain and functioning in the maturation of the 23S rRNA in Bacillus subtilis. Its absence from proteobacteria reveals that this step is mechanistically different from the corresponding step in Escherichia coli. The fact that Mini‐III orthologues are present in unicellular photosynthetic eukaryotes and in plants opens new opportunities for functional studies of this type of RNases.
Fold and function of polypeptide transport‐associated domains responsible for delivering unfolded proteins to membranes
Authors: Knowles Timothy J. , Jeeves Mark , Bobat Saeeda , Dancea Felician , McClelland Darren , Palmer Tracy , Overduin Michael , Henderson Ian R.
Published: April 2008

Membranes of Gram‐negative bacteria, mitochondria and chloroplasts receive and fold β‐barrel transmembrane proteins through the action of polypeptide transport‐associated (POTRA) domains. In Escherichia coli, folding substrates are inserted into the outer membrane by the essential protein YaeT, a prototypic Omp85 protein. Here, the articulation between tandem POTRA domains in solution is defined by nuclear magnetic resonance (NMR) spectroscopy, indicating an unprecedented juxtaposition. The novel solution orientations of all five POTRA domains are revealed by small‐angle X‐ray scattering of the entire 46 kDa periplasmic region. NMR titration studies show that strands from YaeT's canonical folding substrate, PhoE, bind non‐specifically along alternating sides of its mixed β sheets, thus providing an ideal platform for helping to fold nascent outer‐membrane proteins. Together, this provides the first structural model of how multiple POTRA domains recruit substrates from the periplasmic solution into the outer membrane.
Trypanosoma brucei BRCA2 acts in antigenic variation and has undergone a recent expansion in BRC repeat number that is important during homologous recombination
Authors: Hartley Claire L. , McCulloch Richard
Published: April 2008

Antigenic variation in Trypanosoma brucei has selected for the evolution of a massive archive of silent Variant Surface Glycoprotein (VSG) genes, which are activated by recombination into specialized expression sites. Such VSG switching can occur at rates substantially higher than background mutation and is dependent on homologous recombination, a core DNA repair reaction. A key regulator of homologous recombination is BRCA2, a protein that binds RAD51, the enzyme responsible for DNA strand exchange. Here, we show that T. brucei BRCA2 has undergone a recent, striking expansion in the number of BRC repeats, a sequence element that mediates interaction with RAD51. T. brucei BRCA2 mutants are shown to be significantly impaired in antigenic variation and display genome instability. By generating BRCA2 variants with reduced BRC repeat numbers, we show that the BRC expansion is crucial in determining the efficiency of T. brucei homologous recombination and RAD51 localization. Remarkably, however, this appears not to be a major determinant of the activation of at least some VSG genes.
Lipid spirals in Bacillus subtilis and their role in cell division
Authors: Barák Imrich , Muchová Katarína , Wilkinson Anthony J. , O'Toole Peter J. , Pavlendová Nada
Published: April 2008

The fluid mosaic model of membrane structure has been revised in recent years as it has become evident that domains of different lipid composition are present in eukaryotic and prokaryotic cells. Using membrane binding fluorescent dyes, we demonstrate the presence of lipid spirals extending along the long axis of cells of the rod‐shaped bacterium Bacillus subtilis. These spiral structures are absent from cells in which the synthesis of phosphatidylglycerol is disrupted, suggesting an enrichment in anionic phospholipids. Green fluorescent protein fusions of the cell division protein MinD also form spiral structures and these were shown by fluorescence resonance energy transfer to be coincident with the lipid spirals. These data indicate a higher level of membrane lipid organization than previously observed and a primary role for lipid spirals in determining the site of cell division in bacterial cells.
Evolution of a new enzyme activity from the same motif fold
Authors: Leiman Petr G. , Molineux Ian J.
Published: April 2008

The host cell recognition protein of the Escherichia coli bacteriophage HK620 is a large homotrimeric tailspike that cleaves the O18A1 type O antigen. The crystal structure of HK620 tailspike determined in the apo and substrate‐bound form is reported by Barbirz et al. in this issue of Molecular Microbiology. Lacking detectable sequence similarity, the fold and overall organization of the HK620 tailspike are similar to those of the tailspikes of the related phages P22 and Sf6. The substrate‐binding site is intrasubunit in P22 and HK620 tailspikes, but intersubunit in Sf6, demonstrating how phages can adapt the same protein fold to recognize different substrates.
Co‐regulation of yeast purine and phosphate pathways in response to adenylic nucleotide variations
Authors: Gauthier Sébastien , Coulpier Fanny , Jourdren Laurent , Merle Michel , Beck Stefanie , Konrad Manfred , Daignan‐Fornier Bertrand , Pinson Benoît
Published: April 2008

Adenylate kinase (Adk1p) is a pivotal enzyme in both energetic and adenylic nucleotide metabolisms. In this paper, using a transcriptomic analysis, we show that the lack of Adk1p strongly induced expression of the PHO and ADE genes involved in phosphate utilization and AMP de novo biosynthesis respectively. Isolation and characterization of adk1 point mutants affecting PHO5 expression revealed that all these mutations also severely affected Adk1p catalytic activity, as well as PHO84 and ADE1 transcription. Furthermore, overexpression of distantly related enzymes such as human adenylate kinase or yeast UMP kinase was sufficient to restore regulation. These results demonstrate that adenylate kinase catalytic activity is critical for proper regulation of the PHO and ADE pathways. We also establish that adk1 deletion and purine limitation have similar effects on both adenylic nucleotide pool and PHO84 or ADE17 expression. Finally, we show that, in the adk1 mutant, upregulation of ADE1 depends on synthesis of the previously described effector(s) (S)AICAR ((N‐succinyl)‐5‐aminoimidazol‐4‐carboxamide ribotide), while upregulation of PHO84 necessitates the Spl2p positive regulator. This work reveals that adenylic nucleotide availability is a key signal used by yeast to co‐ordinate phosphate utilization and purine synthesis.
Fine‐tuned growth phase control of dps, encoding a DNA protection protein, by FIS and H‐NS
Authors: Schnetz Karin
Published: April 2008

Dps, a ferritin‐like DNA‐binding protein, protects bacterial DNA against oxidative stress and hyper‐compacts the nucleoid into a crystalline‐like structure. In Escherichia coli, transcription of dps from a single promoter is directed by σS‐RNA polymerase in stationary phase and by σ70‐RNA polymerase in fast‐dividing cells exposed to oxidative stress. In this issue of Molecular Microbiology, Grainger and co‐workers demonstrate that the nucleoid‐associated proteins, FIS and H‐NS, control sigma factor selection at the dps promoter by a novel mechanism. The finding suggests a simple mechanism of growth phase control of Dps production and has implications for the response to oxidative stress by pathogenic enterobacteria.
A Bowman‐Birk type protease inhibitor is involved in the tolerance to salt stress in wheat
Authors: SHAN LEI , LI CUILING , CHEN FANG , ZHAO SHUANGYI , XIA GUANGMIN
Published: April 2008

A salt‐responsive gene WRSI5 was characterized from salt‐tolerant cultivar Shanrong No. 3 (SR3), an introgression line via asymmetric somatic hybrid between Triticum aestivum L. cv. Jinan177 (JN177) and Thinopyrum ponticum Podp. The peptide encoded by WRSI5 contains a Bowman‐Birk domain sharing a high level of sequence identity to monocotyledonous protease inhibitors. When expressed in vitro, the WRSI5 gene product exhibited trypsin, but not chymotrypsin inhibition. The expression level of WRSI5 was increased in SR3 roots exposed to salt, drought or oxidative stress. In situ hybridization showed that it is induced in the endodermal cells of the mature region of the SR3 root tip, with no signal detectable in the corresponding region of the salt‐susceptible cultivar JN177. SR3 has a higher selectivity for K+ over Na+, and therefore limits the transport of Na+ from the root to the shoot. When overexpressed in Arabidopsis thaliana, WRSI5 improves the ability of seedlings to grow on a medium containing 150 mm NaCl. We suggest that WRSI5 plays an important role in regulating the plant growth rate or long‐distance Na+ transport in SR3 plants exposed to salt stress.
Unrelated cord blood transplantation for severe congenital neutropenia: Report of two cases with very different transplant courses
Authors: Markel Melissa K. , Haut Paul R. , Renbarger Jamie A. , Robertson Kent A. , Scott Goebel W.
Published: April 2008

Abstract:  SCN is characterized by neutropenia, life‐threatening infections, and progression to myelodysplastic syndrome/acute myelogenous leukemia. The only curative option is SCT, but few reports using UCB as a stem cell source exist. Here, we report two SCN patients transplanted with UCB. Patient 1 was transplanted at seven yr of age due to increasingly large injections of G‐CSF (>100 μg/kg/day) and the risk of developing leukemia. He engrafted promptly and is clinically well and immune reconstituted >2 yr post‐transplant. Patient 2 underwent UCB SCT at nine months of age for recurrent severe infections, despite high doses of G‐CSF. He rejected his first graft, having 100% host cells on day +35, and immediately underwent a second UCB SCT. He engrafted but experienced late graft rejection six months after the second transplant. He received a third UCB SCT following a more immunosuppressive conditioning regimen. His course was complicated by HHV‐6 viremia and gut GVHD, but he is now clinically well and has 99% donor engraftment >20 months post‐transplant. We conclude that UCB is an acceptable stem cell source for SCN patients, but conditioning must be adequately immunosuppressive to ensure engraftment in patients without prior chemotherapy.
Effect of Azolla on Irrigated Rice in Brazil
Authors: Gutbrod K. G.
Published: April 2008

A 1‐year study was conducted in 1983/84 at 2 experimental sites in Brazil to determine the effect of Azolla green‐manure (AO), A. intercrop (OA) and their combination (AA) on rice yield in comparison to mineral fertilization with urea. Nitrogen sources were combined with 4 rice sowing/planting systems.

On terraced terra‐roxa soil (Paleudalf) in subtropical northern Paraná State, transplanted rice (T) yielded 8.66 t · ha−1 compared to pregerminated (P), direct‐sown (D) and conventionally sown (C) rice with 7.92; 7.73 and 7.48 t · ha−1, respectively. N‐source treatments yielded 9.33; 8.54 and 7.34 t · ha−1 for AA, OA and AO compared to 8.46; 7.98 and 6.05 for 100, 50 and 0 kg N · ha−1, respectively. Fertilizer‐nitrogen equivalence (FNE) of Azolla treatments compared to urea broadcast in 3 applications ranged between 0 and more than 100 kg N · ha−1.

On hydromorphic latosol (Ustic Dystropept) in tropical Goiás State, rice yields were 4.07; 2.52; 1.46 and. 1.33 t · ha−1 for systems T, P, C and D, respectively. N‐source treatments yielded 2.79; 1.98 and 1.78 t · ha−1 for AA, AO and OA compared to 3.43; 2.63 and 1.46 t · ha−1 for 60; 30 and 0 kg N · ha−1 as urea broadcast in 2 applications, respectively. FNE of Azolla was between 0 and 56 kg N · ha−1.
Analytical Solutions of the Transient State Oxygen Diffusion Equation in Soils With a Production Term
Authors: Kanwar R. S.
Published: April 2008

Analytical solutions were developed to describe the nonsteady‐state transport of oxygen from the atmosphere into the soil media. These analyses are based on diffusion theory for oxygen diffusion in soils when oxygen is being consumed, either at a constant rate or consumption rate varies with time due to the biological and chemical processes occurring continuously in the soil media. The transport equations, and the initial and boundary conditions are set up to represent a field situation. Analytical solutions are obtained to calculate transient oxygen concentrations in the soil profile. The quantity of oxygen that might diffuse into the soil from atmosphere at any time, t, also can be found by using this method. Comparison with published data is made, and reasonably good agreement is obtained between oxygen concentrations at different depths and times computed from the analytical solutions and those actually measured.
Response of Yield Attributes of Isogenic Tall, Semidwarf, and Doubledwarf Winter Wheats to Nitrogen Fertilizer and Seeding Rates
Authors: Kim Nam I. , Paulsen Gary M.
Published: April 2008

Relationships between grain yield attributes and response to agronomic practices of dwarf and tall genotypes in the major U.S. wheat region were investigated. Isogenic tall, semidwarf, and doubledwarf (Norin 10/5/Pawnee) ‘Pawnee’ winter wheat (Triticum aestivum L.) lines were planted in a split‐split‐plot design with nitrogen fertilizer rates of 0, 50, and 100 kg ha−1 as main plots and seeding rates of 30, 60, and 90 kg ha−1 as subplots in four replications at Hutchinson and Manhattan, Kansas, during 1980–1981. There was no evidence that dwarf lines responded better than the tall line to nitrogen fertilizer; however, percentage fertile spikelets, spike length, harvest index, and kernel number per spike of the semidwarf line were favored by high nitrogen rates. Grain yield was more responsive to seeding rate in the doubledwarf line than in the other lines, and test weight and spike number per unit area were more responsive to seeding rate in one or both dwarf lines than in the tall line. Grain yield of each genotype depended highly on the predominant yield attributes — usually spike number per unit area and/or kernel weight — at one or both locations.
Effect of Soil Temperature on the Carbohydrate Status in the Potato Plant (S. tuberosum L.)
Authors: Randeni G. , Caesar K.
Published: April 2008

Seed tubers of the variety Ostara were raised in growth chambers of 16°C air temperature continuously. The vessels were placed in a water bath of automatic temperature regulation so that soil temperatures of 16°C and 28°C could be maintained. Four weeks after emergence the plants were treated with 14CO2 and 24 hours later the plants were harvested. Three more treatments and time harvests followed in two weeks intervals. C‐14 activity was determined in soluble carbohydrates, in insoluble carbohydrates, and in non extractable residues respectively of the various plant parts in order to obtain information about the translocation of assimilates in the plant.

While the plants at 28°C soil temperature reduced the soluble sugar levels to 50% up to 70 days after emergence, the plants at 16° brought it down to 33% much faster. — The C‐14 activity in insoluble carbohydrates amounted to only 50 % in the plants at 28°C while at 16°C it was more than 2/3 (Tables 1 and 2). — The C‐14 activity in non extractable residues is much less at 28°C than at 16°C (Tables 3 and 4). — The starch weight reaches only 30% of the value obtained at lower temperature 70 days after emergence (Table 5). — At the higher temperature starch is also increasingly transferred to the tubers but to a much lesser extent and not from the stems and stolons (Table 6).

Possible causes, particularly the role of phytohormones, and consequences are discussed.
Effect of Cold Hardening on Growth and Essential Oil Content of Mentha piperita L.
Authors: El‐Moursi A. , Shedeed M. R. , Reda F. , El‐Din K. Gamal
Published: April 2008

Divisions of running rhizomes of peppermint plants were planted in loamy clay soil in the experimental farm of National Research Centre, Dokki, Cairo, Egypt. After 21 days, the plants were exposed to low temperature 4, 7°C for 6, 9 and 12 days in controlled chamber before transplanting to large pots in winter season. Three cuttings were taken from the plants of different treatments during the season after 4, 7 and 10 months from transplanting. Representative samples of 6 replicates from each treatment were taken for the determination of vegetative growth and oil content in the leaves and branches.

The results obtained indicated that the highest fresh and dry weight of leaves and branches was recorded in the second cutting, however, it markedly decreased in the third one. The highest favourable effect of cold hardening on vegetative growth was observed at 4°C for 12 days exposure in the second cutting. The percentage of volatile oil in the leaves recorded the highest values in treatment of 7°C for 6 days in the second sampling date. Cold hardening either at 4°C or 7°C resulted in pronounced increase in the essential oil yield produced by the plant with the superiority of 4°C for 12 days which recorded the highest value.

It can be concluded from the obtained results that hardening peppermint plants with low temperature, particularly 4°C for 12 days before transplanting improved plant growth and considerably increased the volatile oil content in plant leaves and branches.
Genetic Variability, Genotypic and Phenotypic Correlations and Path‐Coefficient Analysis in Egyptian Clover (Trifolium alexandrinum L.)
Authors: Bakheit Bahy R.
Published: April 2008

Fifty‐six accessions of multi‐cut Egyptian clover were compared at four experiments under different environmental conditions; i.e. location and season. Considerable variation existed for all the characters studied. The genetic variance exceeded the environmental variance for all the studied traits. Heritability was high for all characters studied. The expected genetic advance from selection of the superior 10.7% of the accessions as calculated from the combined data reached to 16.10, 17.50, 5.20, 20.60, 3.52 and 21.00 for mean plant height, seasonal fresh forage yield, mean dry matter percentage, seasonal dry forage yield, mean protein percentage, and seasonal protein yield, respectively. Both phenotypic and genotypic correlations among traits showed that mean plant height was positively correlated with each of seasonal fresh forage yield, seasonal dry forage yield, mean dry matter percentage and seasonal protein yield, but negatively correlated with mean protein percentage. Negative correlation were also found between mean protein percentage with seasonal fresh and dry forage yield.

Over all experiments, pat‐coefficient analysis revealed that seasonal fresh forage yield had the highest positive direct effect on seasonal protein yield (0.841), followed by mean dry matter percentage (0.461). The mean protein percentage showed the minimum direct (0.172) and indirect influence on seasonal protein yield.
Transport of Anion Towards Root as Influenced by Soil Compaction
Authors: Bhadoria P. B. S.
Published: April 2008

This experiment was conducted in metal container of 2 liters capacity in the glass house to find out the effect of different bulk densities on the movement of non‐adsorbed anion (Cl) towards the root. It is inferred from the study that at low moisture content, compaction to a certain degree can increase movement of nutrients to the root due to increase in moisture content per unit volume of soil, further increase in compaction may however affect nutrient availability to the roots. This has a far greater significance in No3 movement. But from the salinity point of view, plant roots in soil containing salt will be exposed to a much higher salt concentration than that may be obtained from the analysis of the bulk soil.
Relationship Between Digestibility of Bromus inermis Plant Parts
Authors: Ugherughe P. O.
Published: April 2008

The change in leaf to stem ratio with advancing maturity is perhaps the greatest contributing factor in forages to decreased nutritive value. However, the relationship between the digestibility of plant parts has not been determined in most forage grasses. The objective of this study was to investigate the relationship between digestibility of smooth bromegrass (Bromus inermis Leyss.) plant parts and that between them and whole plant digestibility. Thirty genotypes grown as solid stands and spaced plants were used for the study. The leaves, stems, panicles, and whole plants were evaluated for digestibility using the acid‐pepsin dry matter disappearance (APDMD) technique. Genotypes were significantly different in leaf, stem, and panicle APDMD in each cutting under the two planting patterns. Significant differences were also found among APDMD of the first cutting (APDMD‐1) of leaves, stems, panicles, and whole plants, respectively, over the two‐year period. The APDMD of leaves, stems, panicles, and whole plants were less variable in the second and third cuttings than in the first cutting. Among the plant parts, the APDMD of leaves correlated best with whole plant APDMD. Furthermore, leaf APDMD also correlated better with stem APDMD than with panicle APDMD. Useful regression equations for the prediction of whole plant APDMD from leaf APDMD were obtained.