bluuebunny/crossref_metadata_2025 huggingface dataset:
MpcT is the transducer for membrane potential changes in Halobacterium salinarum
Authors: Koch Matthias K. , Oesterhelt Dieter
Published: March 2005

In Halobacterium salinarum mutants containing either of the light‐driven ion pumps bacteriorhodopsin (H+) or halorhodopsin (Cl–) as their only retinal protein, a decrease of irradiance in the absence of respiration causes a phototactic response. The conversion of the causal event, a decrease of proton motive force across the cell membrane, into a reversal of flagellar motor rotational direction was expected to involve a transducer. Via deletion analysis of all 18 known and putative halobacterial transducer (htr) genes, we found that Htr14, a methylatable membrane‐bound transducer lacking an extracellular domain, mediates the biological response, which includes adaptive methylation. Based on a minimal stimulus length of 200 ms and the determined cytoplasmic buffering capacity, we conclude that the change in the membrane potential (ΔΨ), and not that of the internal pH, is the signal‐generating event. Htr14 was therefore renamed to Membrane potential change Transducer, or MpcT. It is the first transducer for which the causative stimulus could be narrowed to a change in ΔΨ, as opposed to a change in pH or cellular redox state.
Integration and excision by the large serine recombinase φRv1 integrase
Authors: Bibb Lori A. , Hancox Maria I. , Hatfull Graham F.
Published: March 2005

The Mycobacterium tuberculosis prophage‐like element φRv1 encodes a site‐specific recombination system utilizing an integrase of the serine recombinase family. Recombination occurs between a putative attP site and the host chromosome, but is unusual in that the attB site lies within a redundant repetitive element (REP13E12)  of  which  there  are  seven  copies  in  the M. tuberculosis genome; four of these elements contain attB sites suitable for φRv1 integration in vivo. Although the mechanism of directional control of large serine integrases is poorly understood, a recombination directionality factor (RDF) has been identified that is required for φRv1 integrase‐mediated excisive recombination in vivo. Here we describe defined in vitro recombination reactions for both φRv1 integrase‐mediated integration and excision and show that the φRv1 RDF is not only required for excision but inhibits integrative recombination; neither reaction requires DNA supercoiling, host factors, or high‐energy cofactors. Integration, excision and excise‐mediated inhibition of integration require simple substrates sites, indicating that the control of directionality does not involve the manipulation of higher‐order protein–DNA architectures as described for the tyrosine integrases.
Functional analysis of the Campylobacter jejuni N‐linked protein glycosylation pathway
Authors: Linton Dennis , Dorrell Nick , Hitchen Paul G. , Amber Saba , Karlyshev Andrey V. , Morris Howard R. , Dell Anne , Valvano Miguel A. , Aebi Markus , Wren Brendan W.
Published: March 2005

We describe in this report the characterization of the recently discovered N‐linked glycosylation locus of the human bacterial pathogen Campylobacter jejuni, the first such system found in a species from the domain Bacteria. We exploited the ability of this locus to function in Escherichia coli to demonstrate through mutational and structural analyses that variant glycan structures can be transferred onto protein indicating the relaxed specificity of the putative oligosaccharyltransferase PglB. Structural data derived from these variant glycans allowed us to infer the role of five individual glycosyltransferases in the biosynthesis of the N‐linked heptasaccharide. Furthermore, we show that C. jejuni‐ and E. coli‐derived pathways can interact in the biosynthesis of N‐linked glycoproteins. In particular, the E. coli encoded WecA protein, a UDP‐GlcNAc: undecaprenylphosphate GlcNAc‐1‐phosphate transferase involved in glycolipid biosynthesis, provides for an alternative N‐linked heptasaccharide biosynthetic pathway bypassing the requirement for the C. jejuni‐derived glycosyltransferase PglC. This is the first experimental evidence that biosynthesis of the N‐linked glycan occurs on a lipid‐linked precursor prior to transfer onto protein. These findings provide a framework for understanding the process of N‐linked protein glycosylation in Bacteria and for devising strategies to exploit this system for glycoengineering.
Neisseria gonorrhoeae secretes chromosomal DNA via a novel type IV secretion system
Authors: Hamilton Holly L. , Domínguez Nadia M. , Schwartz Kevin J. , Hackett Kathleen T. , Dillard Joseph P.
Published: March 2005

The process of DNA donation for natural transformation of bacteria is poorly understood and has been assumed to involve bacterial cell death. Recently in Neisseria gonorrhoeae we found that mutations in three genes in the gonococcal genetic island (GGI) reduced the ability of a strain to act as a donor in transformation and to release DNA into the culture. To better characterize the GGI and the process of DNA donation, the 57 kb genetic island was cloned, sequenced and subjected to insertional mutagenesis. DNA sequencing revealed that the GGI has characteristics of a horizontally acquired genomic island and encodes homologues of type IV secretion system proteins. The GGI was found to be incorporated near the chromosomal replication terminus at the dif site, a sequence targeted by the site‐specific recombinase XerCD. Using a plasmid carrying a small region of the GGI and the associated dif site, we demonstrated that this model island could be integrated at the dif site in strains not carrying the GGI and was spontaneously excised from that site. Also, we were able to delete the entire 57 kb region by transformation with DNA from a strain lacking the GGI. Thus the GGI was likely acquired and integrated into the gonococcal chromosome by site‐specific recombination and may be lost by site‐specific recombination or natural transformation. We made mutations in six putative type IV secretion system genes and assayed these strains for the ability to secrete DNA. Five of the mutations greatly reduced or completely eliminated DNA secretion. Our data indicate that N. gonorrhoeae secretes DNA via a specific process. Donated DNA may be used in natural transformation, contributing to antigenic variation and the spread of antibiotic resistance, and it may modulate the host immune response.
Tethering the Z ring to the membrane through a conserved membrane targeting sequence in FtsA
Authors: Pichoff Sebastien , Lutkenhaus Joe
Published: March 2005

The cytokinetic Z ring is required for bacterial cell division. It consists of polymers of FtsZ, the bacterial ancestor of eukaryotic tubulin, linked to the cytoplasmic membrane. Formation of a Z ring in Escherichia coli occurs as long as one of two proteins, ZipA or FtsA, is present. Both of these proteins bind FtsZ suggesting that they might function to tether FtsZ filaments to the membrane. Although ZipA has a transmembrane domain and therefore can function as a membrane anchor, interaction of FtsA with the membrane has not been explored. In this study we demonstrate that FtsA, which is structurally related to eukaryotic actin, has a conserved C‐terminal amphipathic helix that is essential for FtsA function. It is required to target FtsA to the membrane and subsequently to the Z ring. As FtsA is much more widely conserved in bacteria than ZipA, it is likely that FtsA serves as the principal membrane anchor for the Z ring.
Targeted deletion of Plasmodium knowlesi Duffy binding protein confirms its role in junction formation during invasion
Authors: Singh Agam P. , Ozwara Hastings , Kocken Clemens H. M. , Puri Sunil K. , Thomas Alan W. , Chitnis Chetan E.
Published: March 2005

Red cell invasion by Plasmodium merozoites involves multiple steps such as attachment, apical reorientation, junction formation and entry into a parasitophorous vacuole. These steps are mediated by specific molecular interactions. P. vivax and the simian parasite P. knowlesi require interaction with the Duffy blood group antigen to invade human erythrocytes. P. vivax and P. knowlesi Duffy binding proteins (PvDBP and PkDBP), which bind the Duffy antigen during invasion, share regions of sequence homology and belong to a family of erythrocyte binding proteins (EBPs). By deletion of the gene that encodes PkDBP, we demonstrate that interaction of PkDBP with the Duffy antigen is absolutely necessary for invasion of human erythrocytes by P. knowlesi. Electron microscopy studies reveal that PkDBP knockout parasites are unable to form a junction with human erythrocytes. The interaction of PkDBP with the Duffy antigen is thus necessary for the critical step of junction formation during invasion. These studies provide support for development of intervention strategies that target EBPs to inhibit junction formation and block erythrocyte invasion by malaria parasites.
Qri2/Nse4, a component of the essential Smc5/6 DNA repair complex
Authors: Hu Bin , Liao Chunyan , Millson Stefan H. , Mollapour Mehdi , Prodromou Chrisostomos , Pearl Laurence H. , Piper Peter W. , Panaretou Barry
Published: March 2005

We demonstrate a role for Qri2 in the essential DNA repair function of the Smc5/6 complex inSaccharomyces cerevisiae. We generated temperature‐sensitive (ts) mutants inQRI2and characterized their properties. The mutants arrest after S phase and prior to mitosis. Furthermore, the arrest is dependant on the Rad24 checkpoint, and is also accompanied by phosphorylation of the Rad53 checkpoint effector kinase. The mutants also display genome instability and are sensitive to agents that damage DNA. Two‐hybrid screens reveal a physical interaction between Qri2 and proteins that arenon‐Smcelements of the Smc5/6 DNA repair complex, which is why we propose the nameNSE4for the open reading frame previously known asQRI2. A key role for Nse4 in Smc5/6 function is likely, as overexpressing known subunits of the Smc5/6 complex suppressesnse4tscell cycle arrest. Thense4tsgrowth arrest is non‐lethal and unlike the catastrophic nuclear fragmentation phenotype ofsmc6tsmutants, the nucleus remains intact; replicative intermediates and sheared DNA are not detected. This could imply a role for Nse4 in maintenance of higher order chromosome structure.
Lithospheric structure beneath the south‐eastern Zagros Mountains, Iran: recent slab break‐off?
Authors: Molinaro M. , Zeyen H. , Laurencin X.
Published: March 2005

Integrated lithospheric modelling, based on the combined interpretation of gravity, geoid and topography data sets, highlights a previously undocumented lithospheric thinning beneath the Zagros collisional belt (Iran), which we propose to relate to recent slab break‐off at the continent–ocean transitional lithosphere. Recent published data on the distribution of seismicity at depth support this interpretation. In agreement with other published models for the Zagros Mountains, the overlying crust exhibits, by contrast, a noticeable thickening, reaching a maximum of 52 km. The consequent thermal uplift expected from slab break‐off is suggested to have modified the Zagros wedge taper and triggered the recently documented switch from thin‐skinned to thick‐skinned deformation in the Zagros Fold–Thrust Belt.
A tephra‐based correlation between the Faroe Islands and the Norwegian Sea raises questions about chronological relationships during the last interglacial
Authors: Wastegård Stefan , Björck Svante , Greve Charlotte , Rasmussen Tine L.
Published: March 2005

Marine ash zones from the last interglacial period have been described from cores from the North Atlantic and an ash zone from the middle part of the interglacial has been observed in connection with a major cooling event. Here we present evidence for a coeval ash zone in a terrestrial site on the Faroe Islands. The investigated sediments are correlated with the upper part of oxygen isotope stage 5e and the beginning of stage 5d. The Eemian climatic optimum is represented in the lower part of the sequence close to the first occurrence of the ash zone. A tephra‐based correlation suggests that the climatic optimum was synchronous with the marine record from the Norwegian Sea, but several thousand years later than in Eemian sections of west central Europe. However, many questions on the chronological relationship between the Eemian and oxygen isotope stage 5e still remain to be answered.
Long‐runout pyroclastic surge on a Cretaceous alluvial plain, Republic of Korea
Authors: Sohn Y. K. , Jeong J. O. , Son M.
Published: March 2005

Pyroclastic surge is a dilute and turbulent flow of volcanic gas and tephra that is commonly generated during explosive volcanic eruptions and can threaten lives along its flow paths. Assessing its travel distance and delineating future volcanic hazards have therefore been major concerns of volcanologists. Historical eruptions show that most pyroclastic surges travel a few tens of kilometres or less from their sources. Aeolian or aquagene processes have therefore been evoked for the emplacement of supposed surge deposits much beyond this distance. Here we show that a Cretaceous tuff bed in Korea was emplaced by an exceptionally powerful pyroclastic surge that flowed as far as the most powerful pyroclastic flows that formed the low‐aspect‐ratio ignimbrites (LARI). This has significant implications for interpreting ancient volcanic eruptions and delineating volcanic hazards by pyroclastic surges, and casts intriguing questions on the eruption dynamics and physics of long‐runout pyroclastic surges and their distinction from LARI‐forming pyroclastic flows.
Mountain building‐enhanced continental weathering and organic carbon burial as major causes for climatic cooling at the Frasnian–Famennian boundary (c. 376 Ma)?
Authors: Averbuch O. , Tribovillard N. , Devleeschouwer X. , Riquier L. , Mistiaen B. , Van Vliet‐Lanoe B.
Published: March 2005

The Late Devonian was a period of drastic environmental changes, as exemplified by a major biotic crisis at the Frasnian–Famennian boundary (FFB) and the onset in Famennian times of glaciations across southern Gondwana. Worldwide evidence for the coeval development of the major Acadian–Eovariscan belt led us to propose a model relating the Late Frasnian–Famennian environmental perturbations to extensive continental uplift through two atmospheric CO2‐depleting mechanisms: (1) the intensification of silicate weathering on the continental areas as attested by a major rise in the87Sr/86Sr composition of sea water at the FFB; and (2) the massive burial of organic carbon (Kellwasser events) in partially confined basins due to the collisional‐induced reduction of equatorial oceanic communications between the Palaeotethysian and Panthalassic oceans. This process is also suggested to have been controlled by an important primary productivity connected to an increased nutrient availability triggered by the enhanced continental run‐off.
Movements detection of deep seated gravitational slope deformations by means of InSAR data and photogeological interpretation: northern Sicily case study
Authors: Saroli M. , Stramondo S. , Moro M. , Doumaz F.
Published: March 2005

We investigated the northern‐central portion of Sicily region (southern Italy) using aerial photographs and Synthetic Aperture Radar (SAR) data obtained by ERS1 and ERS2 satellites. This area shows a geological‐structural setting generated by the tectonic superposition of Apenninic‐Maghrebian carbonatic structures on terrigenous deposits. Such a structural setting favoured the development of large‐scale gravity‐driven phenomena (known in the geological literature as deep‐seated gravitational slope deformations) that are mostly responsible for the landscape evolution of the whole area. Morphological evidences such as landslides, sacking or rock‐flow, lateral spread and block slide can be detected from photogeological analysis. In order to understand the temporal behaviour and spatial distribution of such deformations we applied the interferometric SAR (InSAR) technique. Interferograms show fringe patterns spatially coinciding with some of the large‐scale gravitative phenomena previously identified by means of aerial‐photo analysis. The comparison between photogeological data and InSAR results allows delimiting the active sectors in the study area.
Growth, interaction and seismogenic potential of coupled active normal faults (Isernia Basin, central‐southern Italy)
Authors: Bucci Daniela Di , Naso Giuseppe , Corrado Sveva , Villa Igor M.
Published: March 2005

The inception and growth of the active Carpino‐Le Piane Basin Fault System (CLPBFS; central‐southern Apennines, Italy) was analysed with respect to the neighbouring Isernia and Surrounding (ISFS) and Boiano Basin (BBFS) extensional Fault Systems.39Ar–40Ar dating showed that the BBFS was already active 649 ± 21 ka bpand that the ISFS was active at least 476 ±10 kabp, whereas the activity of the CLPBFS started certainly later than 253 ± 22 kabp, and very probably as recently as <28 kabp. These ages, combined with structural data (geometry and kinematics of the fault systems), indicate that the inception and development of the CLPBFS could be strictly related to the stress changes caused by earthquakes occurring on the BBFS.
Thermal maturity of the axial zone of the southern Apennines fold‐and‐thrust belt (Italy) from multiple organic and inorganic indicators
Authors: Corrado S. , Aldega L. , Di Leo P. , Giampaolo C. , Invernizzi C. , Mazzoli S. , Zattin M.
Published: March 2005

The reconstruction of the thermal history of folded and thrust units is crucial to define the pattern of tectonic loading and the time‐space evolution of an orogen where tectonic exhumation processes occurred at shallow crustal levels. In the present study, a well‐constrained reconstruction of the thermal maturity in the axial zone of the southern Apennines has been achieved by the combined use of different thermal indicators in diagenesis. The major results are: (i) documentation of a jump in thermal maturity from the Apenninic Platform derived tectonic unit (from immature to early mature stages of hydrocarbon maturation) to the Lagonegro Basin derived tectonic units (late diagenetic zone); (ii) documentation of along‐strike slighter variations in the Lagonegro units, concerning thermal maturity (thus maximum burial temperatures). This can be related to changes in amounts of tectonic burial and erosion/exhumation because of the lack of cylindricity of contractional structures; (iii) recognition of an independent thermal evolution of the allochthonous chain compared with the Apulian Platform tectonic unit with Mt Alpi area (in the late mature stage of hydrocarbon generation) interpreted as a sector of localized, intense exhumation within the External Zone of the orogen.
Structural softening of the lithosphere
Authors: Schmalholz Stefan M. , Podladchikov Yuri Y. , Jamtveit Bjørn
Published: March 2005

Structural softening is a decrease in the amount of stress needed to deform the lithosphere at a particular rate because of its structural reorganization while all true rheological properties remain constant. Structural softening is fundamentally different than material softening, where the decrease in stress is generated by a change in rheological properties with progressive deformation, such as grain size reduction resulting from large shearing strain. We study structural softening generated by folding of the crust‐mantle boundary, which is a structural instability that inevitably develops during compression of the mechanically layered lithosphere. For ductile rheologies, the stress decrease represents a decrease of the effective lithospheric viscosity, which is proportional to the ratio of stress to lithospheric shortening strain rate. We present analytical and numerical results quantifying the decrease in stress and effective viscosity that occur during shortening at a constant rate. The decrease in effective viscosity can be up to 10‐fold.
Direct observation of adakite melts generated in the lower continental crust, Fiordland, New Zealand
Authors: Stevenson James A. , Daczko Nathan R. , Clarke Geoffrey L. , Pearson Norman , Klepeis Keith A.
Published: March 2005

Adakites have a distinct chemistry that links them to melting of a mafic source at high pressure. They have been attributed to melting of subducted oceanic crust or melting of the mafic crustal roots of thick continental arcs, and are an important contrast to mantle wedge melting as a means of generating continental crust. We report the first direct evidence for the generation of adakitic melts in mafic lower continental crust, in an exhumed Cretaceous arc in the South Island of New Zealand. The lower crustal Pembroke Granulite has the bulk chemistry and partial melting textures involving peritectic garnet appropriate for a source region for an adakitic melt. The melt migrated from the area through a fracture network now filled with trondhjemitic veins. Emplacement of the melt was in the upper crust of the Cretaceous section, illustrated by the presence of coeval adakites in the upper crustal Nelson‐Westland region.
Giant sandstone pipes record basin‐scale liquefaction of buried dune sands in the Middle Jurassic of SE Utah
Authors: Huuse Mads , Shoulders Simon J. , Netoff Dennis I. , Cartwright Joe
Published: March 2005

Giant sandstone pipes crop out over a 20 000 km2 area of SE Utah. They range from metres to decametres in diameter and crosscut more than 100 m of continental sediments. New and published observations, encompassing all known pipe localities in SE Utah, suggest that the pipes formed by upward movement of groundwater, sand and sediment blocks in response to liquefaction of buried dune sands. Pipe formation was most likely triggered by seismicity during a phase of Cordilleran shortening and regional tectonic reorganization in the late Middle Jurassic. The depth of liquefaction recorded by the pipes far exceeds depths usually considered in earthquake engineering.
Life cycle and potential gene flow of volunteer oilseed rape in different tillage systems
Authors: GRUBER S , PEKRUN C , CLAUPEIN W
Published: March 2005

The study examined the effect of tillage (intensive vs. zero tillage) on potential gene flow during the life cycle of oilseed rape volunteers between July 2002 and August 2003. After growing oilseed rape, 4–29% of the seeds lost during harvest entered the soil seedbank when stubble tillage was performed immediately after the seed input. The seedbank was small (0–3%) when stubble tillage was delayed. Zero tillage resulted in seedbanks from 1 to 17% of the initial seed input. The seeds were distributed mainly in the upper soil layers after zero tillage or primary tillage with a rigid tine cultivator, whereas ploughing shifted most of the seeds into deeper layers. The highest number of volunteers (1 plant m−2) emerged and flowered in the following crop of winter wheat either when a large soil seedbank existed and/or the seedbank was located mainly in the upper soil layer. Outcrossing with other rape crops was unlikely as volunteers flowered 1 month later than rape crops sown at the normal timing. These volunteers produced a maximum of 8 viable seeds m−2. Ploughing preserved seeds in deep soil layers transferring the risk of gene flow to the future, whereas non‐inversion tillage can cause gene flow from high numbers of flowering volunteers within the first year following oilseed rape cultivation.
Competition between weeds and spring wheat for 15N‐labelled nitrogen applied in pig slurry
Authors: PETERSEN J
Published: March 2005

The changes in weed:crop competition as affected by the interaction of slurry distribution pattern with crop sowing pattern was examined, using the parameters dry matter (DM) production, nitrogen (N) uptake and recovery of applied N in spring wheat and weeds. Pig slurry enriched with isotopic nitrogen (15N) was applied either fully incorporated or in concentrated bands. The two slurry distribution patterns were combined with either crop density or distance between the slurry band and seed row. Spring wheat and weeds were sampled separately seven times during the season. A high and fast crop recovery of applied N coincident with a low recovery in weeds may be obtained by at least three management elements: sowing the crop with a high seed density, sowing the crop row close to the band‐applied slurry N, and early sowing. The effects on crop DM, N‐uptake and 15N recovery of a high crop density and a narrow distance between the slurry band and crop row appear clearly at the beginning of the spring wheat elongation phase. For weeds the effects were most pronounced for 15N recovery, and using DM as the only response variable may cause insignificant results. However, methods for N application may be part of a strategy controlling weeds, but to obtain satisfactory weed control the N management needs to be supplemented with chemical or mechanical weed management.
Atrazine behaviour in the different pedological horizons of two Argentinean non‐till soil profiles
Authors: HANG S , BARRIUSO E , HOUOT S
Published: March 2005

Atrazine behaviour was investigated in the different pedological horizons from profiles of two non‐tilled soils, a Typic Argiustoll and an Entic Haplustoll from the Argentinean pampas. As atrazine use in field conditions was associated with maize cropping, only one type of soil received atrazine every other year. Atrazine behaviour was characterized through the balance of 14C‐U‐ring atrazine radioactivity among the mineralized fraction, the extractable fraction and the non‐extractable bound residues. The composition of the extractable fraction was characterized. Atrazine mineralization was the main dissipation mechanism in the superficial horizon of the Argiustoll because of microbial adaptation after repeated atrazine applications. In contrast, little atrazine mineralization was found in the Haplustoll profile, and it decreased with depth. The capacity of the soil organic matter to form bound residues was characterized using soil‐size fractionation. Atrazine‐bound residues depended on the soil organic matter content and the size of the fraction. Organic matter in the largest size fractions had a higher capacity to form atrazine‐bound residues. In the Argiustoll profile, the atrazine degradation capacity decreased in the subsurface horizons (Bt1 and Bt2), where a large part of bound residues were formed. The deepest horizon (BC) of this profile had a high capacity to degrade atrazine reaching this horizon after a lag period. In the Haplustoll profile, atrazine mineralization and bound residue formation followed the organic carbon mineralization pattern.
Dormancy and viability of Phalaris minor seed in a rice–wheat cropping system
Authors: OM H , KUMAR S , DHIMAN S D
Published: March 2005

Seed placement, soil temperature and soil moisture content influenced the process of after‐ripening in Phalaris minor seeds. Seeds of P. minor collected from the soil just after wheat harvesting exhibited higher germination than seeds from P. minor threshed directly. There was a pronounced impact of periodic inhabitation of seed into the soil on germination after its dispersal. Germination was strongly inhibited when the seed was kept in soil at more than field capacity (FC) or in water. Maximum germination of seed incubated in soil at FC occurred at 30°C while a temperature of 40°C favoured after‐ripening of seed when mixed with dry soil or kept dry without any medium. Release from conditional dormancy was quicker in the seed retrieved from the soil kept at 20°C than at 10°C. Seed release from conditional dormancy and germination increased with a rise in temperature from 30 to 40°C when the seed was retrieved from incubation in soil at FC for 70 days. The seed kept immersed in water was least responsive to a rise in temperature. Seed recovered from dry soil, or kept without any medium, responded quickly at both temperatures. Light enhanced the germination of Phalaris minor seed. The seedbank subjected to rice (Oryza sativa) field management conditions lost vigour in comparison with the seed stored in laboratory. There was significant variability in seed viability when exposed to differential water management conditions in rice.
Productivity and persistence of perennial grass mixtures under competition from annual weeds in the alpine region of the Qinghai‐Tibetan Plateau
Authors: DONG S K , LONG R J , HU Z Z , KANG M Y
Published: March 2005

In the alpine region of the Qinghai‐Tibetan Plateau four indigenous perennial grass species Bromus inermis (BI), Elymus sibiricus (ES), Elymus nutans (EN) and Agropyron cristatum (AC) were cultivated as three mixtures with different compositions and seeding rates, BI + EN, BI + ES + AC and BI + ES + EN + AC. From 1998 to 2001 there were three different weeding treatments: never weeded (CK); weeded on three occasions in the first year (1‐y) and weeded on three occasions in both the first and second year (2‐y) and their effect of grass combination and interactions on sward productivity and persistence was measured. Intense competitive interference by weedy annuals reduced dry matter (DM) yield of the swards. Grass combination significantly affected sward DM yields, leaf area index (LAI) and foliar canopy cover and also species composition DM and LAI, and species plant cover. Interaction between weeding treatments and grass combination was significant for sward DM yield, LAI and canopy cover, but not on species composition for DM, LAI or species plant cover. Grass mixture BI + ES + EN + AC gave the highest sward DM yield and LAI for both weeding and non‐weeding treatments. Species ES and EN were competitively superior to the others. Annual weedy forbs must be controlled to obtain productive and stable mixtures of perennial grasses, and germination/emergence is the most important time for removal. Weeding three times (late May, late June and mid‐July) in the establishment year is enough to maintain the production and persistence of perennial grass mixtures in the following growing seasons. Extra weeding three times in the second growing year makes only a slight improvement in productivity.
Factors influencing the weed flora in the Gezira Scheme, Sudan
Authors: KARAR R O , MOHAMED B F , MARRS R H
Published: March 2005

Agriculture plays a major role in the economic and social development of Sudan. The most important agricultural area in Sudan is the irrigated Gezira Agricultural Scheme (GAS), which takes water from the Sennar Dam on the Blue Nile. This study investigated weed communities in relation to geographical location and crop rotation in 2000 and 2001. Five agricultural units were sampled from the central sector of the GAS; within each unit we surveyed weed communities in different phases of the crop rotation: cotton, groundnuts, sorghum, and a fallow. The distribution of weed species showed some similarities in the 2 years sampled, with most species being found in all agricultural units but their relative proportions differed. Broad‐leaved weeds were dominant, suggesting that herbicides selected for weed control in the Gezira scheme need to be effective against this group of species. Agricultural unit and crop type affected weed communities in both years. The weed flora was largest in cotton, intermediate in groundnuts and sorghum, and smallest in the fallow. Although most weeds were found in all agricultural units; however, their relative abundances differed greatly, either as a result of differences in management between the units, or some other spatial effect. As such, weed control programmes need to be tailored at the agricultural unit scale.
Early vigour and allelopathy – two useful traits for enhanced barley and wheat competitiveness against weeds
Authors: BERTHOLDSSON N‐O
Published: March 2005

The objectives of this study were to identify traits in spring barley (Hordeum vulgare) and spring wheat (Triticum aestivum) related to the competitive ability of the crop and to determine their importance. Weed biomass 1–2 weeks prior to ear emergence was used as a measure of genotypic differences in competitiveness against weeds. Crop trait measurements comprised early crop biomass, early shoot height, straw length, heading and maturity. Early crop biomass 1–2 weeks prior to ear emergence was used as an overall trait for the various characters related to early vigour. In addition to these morphological traits, the potential allelopathic activity of the tested cultivars was determined using an agar‐based bioassay with Lolium perenne (ryegrass). In both barley and wheat, multiple regression analysis revealed that early crop biomass and potential allelopathic activity were the only parameters that significantly contributed to competitiveness. In barley, early crop biomass explained 24–57% of the observed genotypic variance across 4 years, allelopathic activity explained 7–58% and combined they explained 44–69% of the observed genotypic variance. In wheat, the corresponding figures were lower: 14–21% for early biomass, 0–21% for allelopathic activity and 27–37% when combined. Model predictions suggested that new cultivars with increased early vigour and allelopathic activity offer a potential to further reduce weed interference.
Post‐dispersal seed predation of non‐target weeds in arable crops
Authors: MAUCHLINE A L , WATSON S J , BROWN V K , FROUD‐WILLIAMS R J
Published: March 2005

Field experiments were conducted to quantify the natural levels of post‐dispersal seed predation of arable weed species in spring barley and to identify the main groups of seed predators. Four arable weed species were investigated that were of high biodiversity value, yet of low to moderate competitive ability with the crop. These were Chenopodium album, Sinapis arvensis, Stellaria media and Polygonum aviculare. Exclusion treatments were used to allow selective access to dishes of seeds by different predator groups. Seed predation was highest early in the season, followed by a gradual decline in predation over the summer for all species. All species were taken by invertebrates. The activity of two phytophagous carabid genera showed significant correlations with seed predation levels. However, in general carabid activity was not related to seed predation and this is discussed in terms of the mainly polyphagous nature of many Carabid species that utilized the seed resource early in the season, but then switched to carnivory as prey populations increased. The potential relevance of post‐dispersal seed predation to the development of weed management systems that maximize biological control through conservation and optimize herbicide use, is discussed.
Using thermal and hydrothermal time to model seedling emergence of Avena sterilis ssp. ludoviciana in Spain
Authors: LEGUIZAMÓN E S , FERNANDEZ‐QUINTANILLA C , BARROSO J , GONZALEZ‐ANDUJAR J L
Published: March 2005

Historical records on the field emergence of seedlings of Avena sterilis in winter cereal crops were used to develop thermal/hydrothermal models to predict the emergence of this weed as a function of meteorological conditions. When water was not a limiting factor, a Weibull function provided a good description of the relationship between thermal time and seedling emergence. The variability in the rate of seedling emergence observed under these conditions was associated with variation in the differential between measured and base temperatures. When water was limiting in the soil, the rate of seedling emergence was reduced, a different function was required to describe the process. The use of a hydrothermal model enabled the use of a single function to describe the patterns of seedling emergence of the nine site‐years considered in the study. Using this model we can conclude that 70% seedling emergence will be reached, under very diverse conditions, within 300 hydrodegree days. The hydrothermal model proposed was validated with independent seedling emergence data, supporting the idea that this model is robust enough to be used as a predictive tool for seedling emergence of A. sterilis in a variety of conditions.
Linkage disequilibrium and selection response in two‐stage marker‐assisted selection of dairy cattle over several generations
Authors: Schulman N.F. , Dentine M.R.
Published: March 2005

A stochastic simulation was carried out to investigate the advantage of marker‐assisted selection (MAS) in comparison with traditional selection over several generations. The selection goal was a sex‐limited trait or a linear combination of traits with a polygenic component, two unlinked additive QTL and a non‐genetic component. The simulated QTL were moderate or large and the allele frequencies were varied. Two stages of selection among the male offspring were carried out. In the first stage marker information was used to select among full sibs (MAS) or one full sib was chosen at random. In the second stage young bulls were selected based on a progeny test. The response in total genetic gain was faster with MAS than with traditional selection and persisted over several generations. With a QTL of moderate size and initial allele frequencies of the favourable allele of 0.05 the response with MAS was 6% higher than with traditional selection in the sires selected after progeny test. MAS in a within‐family two‐stage selection scheme improved the genetic merit of selected bulls even when linkage disequilibrium between QTL and polygenes was initially increased.
Antifungal effect of 5‐aminolevulinic acid PDT in Trichophyton rubrum
Authors: Kamp H. , Tietz H.‐J. , Lutz M. , Piazena H. , Sowyrda P. , Lademann J. , Blume‐Peytavi U.
Published: March 2005

In the present investigation, we have shown for the first time that the onychomycosis‐inducing dermatophyte Trichophyton rubrum was able to metabolize 5‐aminolevulinic acid (ALA) to protoporphyrin IX (PpIX) in liquid culture medium. We have established and optimized the culture conditions and could show the typical PpIX‐induced red fluorescence which was evaluated qualitatively by Wood's light examination and fluorescent microscopic analysis. The optimum concentration of ALA was in the range of 1–10 mmol l−1. If used in higher concentrations, ALA leads to a significantly reduced growth rate and absence of PpIX formation due to highly acidic conditions. The first observation of red fluorescence was detected between 10 and 14 days poststimulation with ALA, increasing thereafter. Fluorescent microscopic examinations demonstrated that formation of PpIX was restricted to selected parts of the fungal mycelium. Repeated application of ALA in order to achieve the highest formation of PpIX in T. rubrum failed, probably due to the sustained low pH values. ALA treatment and irradiation of T. rubrum clearly demonstrated the growth‐inhibiting effect of ALA PDT, either leading to reduced numbers of colonies or reduced diameters of single fungal colonies. Summarizing our results, ALA PDT might be a promising approach in the reduction of T. rubrum colonization in onychomycosis.
OralCandidaspecies and betel quid‐associated oral lesions in Padaung women of Northern Thailand
Authors: Reichart P. A. , Khongkhunthian P. , Samaranayake L. P. , Yau J. , Patanaporn V. , Scheifele C.
Published: March 2005

Purpose of the present investigation was to study the association between the betel quid chewing (BQC) habits, the oral yeast flora and oral lesions in female Padaung of northern Thailand. Oral swabs were taken from the tongue and palate of 50 Padaung women with and 50 control individuals without BQC habit. The spectrum of oralCandidaspecies in both groups was determined microbiologically. In addition, oral mucosal lesions were registered in both groups. Mean age of BQ chewers was 35.4 years, of non‐chewers was 19.2 years.Candida parapsilosiswas the most commonCandidaspp. isolated both in BQ chewers (46%) and non‐chewers (44%).Candida albicanswas revealed in 24% of BQ chewers and 18% of non‐chewers. There was no significant difference in carriage ofCandidaspp. isolated between both groups. Forty‐four per cent of BQ chewers revealed betel chewers mucosa, 10% showed leukoedema. Isolated populations such as the Padaung may reveal different patterns of candidal flora, in this case a predominance ofCandida parapsilosis.
Mycological examinations on the fungal flora of the chicken comb
Authors: Gründer S. , Mayser P. , Redmann T. , Kaleta E. F.
Published: March 2005

A total of 500 combs of adult chickens from two different locations in Germany (Hessen and Schleswig‐Holstein) were clinically and mycologically examined. The chickens came from three battery cages (n = 79), one voliere system (n = 32), six flocks maintained on deep litter (n = 69) and 12 flocks kept on free outdoor range (n = 320). Twenty‐two of the 500 chicken combs (4.4%) were found to have clinical signs: only non‐specific lesions neither typical of mycosis nor of avian pox such as desquamation with crust formation, yellow to brown or black dyschromic changes, alopecia in the surrounding area and moist inflammation. Only seven of the 22 clinically altered combs showed a positive mycological result; the non‐pathogenic and geophilic Trichophyton terrestre in one case and non‐pathogenic yeast in six cases. The following fungi were seen in the different housing systems: 13 dermatophytes (2.6% of 500 samples): 12 × T. terrestre, 1 × Trichophyton mentagrophytes, 11 isolates of Chrysosporium georgiae (2.2% of 500 samples) and 149 isolates of yeasts (29.8%): Malassezia sympodialis: n = 52, Kloeckera apiculata: n = 33, Trichosporon capitatum (syn. Geotrichum capitatum): n = 23, Trichosporon cutaneum/Trichosporon mucoides: n = 12, Trichosporon inkin (syn. Sarcinosporon inkin): n = 8 and Candida spp.: n = 21, including pathogenic or possibly pathogenic species: Candida albicans: n = 3, Candida famata: n = 4, Candida guilliermondii: n = 3, Candida lipolytica: n = 3, Candida dattila: n = 2 and one isolate each of Candida glabrata, Candida parapsilosis, Candida aaseri, Candida catenulata sive brumpti, Candida fructus and Candida kefyr sive pseudotropicalis. There is no stringent correlation between the clinical symptoms diagnosed on the chicken combs and the species of yeasts isolated. The causative agent of favus in chickens, Trichophyton gallinae, and the saprophytic yeast in pigeons, Cr. neoformans were not isolated. The most frequently isolated yeasts M. sympodialis and Kloeckera apiculata are suggested to be classified as members of the resident flora of the chicken comb.
A novel mycological analysis valuable for evaluating therapeutic efficacy of antimycotics against experimental dermatophytosis in guinea pigs
Authors: Majima Toshiro , Masui Shigeki , Uchida Katsuhisa , Yamaguchi Hideyo
Published: March 2005

Although antimycotic effects are mainly evaluated with regard to whether or not the fungi grow from a specimen obtained from the drug‐treated skin, the potential for discrepancies in skin specimens in which the fungi are grown has not been evaluated, in the experimental tinea model. In this study, to evaluate the therapeutic effectiveness of antimycotic agents against fungal skin infection, a novel form of mycological assessment, which focuses on the size of colonies grown from skin specimens was examined and developed. When microconidia of Trichophyton mentagrophytes were inoculated onto a Sabouraud dextrose agar (SDA) plate and incubated at 27 °C for 5 days, a linear relationship was observed between the growth area of mycelia and the logarithm of the quantity of microconidia. This relationship between the growth area and the logarithm of the number of T. mentagrophytes microconidia did not change with the addition of skin homogenate and/or keratin powder. Next, the number of fungi in skin blocks attendant upon experimental, cutaneous infection in guinea pigs was evaluated and analyzed via a calibration curve, determined based on a microconidium suspension of T. mentagrophytes. Estimates of severity of dermatophytic infection in experimental animals were parallel to, but more reliable than, results obtained via the conventional mycological method (fungus‐positive skin ratio of treated skin) in culture studies of infected dermal tissues. This new analytical method may also be applicable to the in vivo assessment of the therapeutic effect against dermatophytosis experimentally produced in guinea pigs.
An overview of the antifungal properties of allicin and its breakdown products – the possibility of a safe and effective antifungal prophylactic
Authors: Davis Stephen R
Published: March 2005

Reports about the safe and successful intravenous (i.v.) use of garlic derivatives in China against invasive fungal infections have been made, but little has been done to seriously investigate the in vivo use of these derivatives in the West. Laboratories have demonstrated impressive in vitro MICs using allitridium, one of these derivatives, against a range of medically important fungi. In addition, it has been demonstrated that allitridium shows in vitro synergy with amphotericin B, one of the main i.v. antifungal agents. Some of the breakdown products of allicin, the main parent antifungal compound in garlic, have been investigated for their general antimicrobial, anticancer and anticholesterol properties, and it appears that there is a common mode of action that underlies these activities. It appears that these small molecules have the ability to cross cell membranes and combine with sulfur‐containing molecular groups in amino acids and proteins, thus interfering with cell metabolism. It has been suggested that the reason human cells are not poisoned by allicin derivatives is that they contain glutathione, a sulfur‐containing amino acid that combines with the allicin derivative, thus preventing cell damage. In addition to their biochemical mechanism, these derivatives appear to stimulate cellular immunity, an important ability lacking in conventional antifungal chemotherapy. These derivatives appear to be safe, cheap, wide‐spectrum and immunostimulatory, as well as possibly synergistic with conventional antifungal therapy, making them ideal candidates for investigation into their use as prophylactic antifungal agents.
Efficacy of caspofungin in prophylaxis and treatment of an adult leukemic patient with invasive pulmonary aspergillosis in allogeneic stem cell transplantation
Authors: Ifran Ahmet , Kaptan Kürşat , Beyan Cengiz
Published: March 2005

Invasive aspergillosis is a major problem in the management of immunocompromised patients, its prevalence is rising and it is still a major cause of death in this group. The clinical success rate with classical drugs is far away from expectations. New drugs are needed in the treatment of this complication. Belonging to the new class of echinocandins, caspofungin is a newly introduced and promising drug in this fatal situation. We report a patient with acute myeloid leukemia who had invasive pulmonary aspergillosis during induction therapy being treated with amphotericin B in first step and afterwards with caspofungin. The patient received consolidation therapy and allogeneic stem cell transplantation while using caspofungin, and did not experience any adverse effect related to drug. Many side effects, e.g. derangements in liver and kidney functions, hypokalemia, infusion‐related side effects and especially thrombocytopenia, which are common with amphotericin B treatment are no longer problem with caspofungin. The efficacy of caspofungin in terms of regression of pulmonary lesions and control of fever is quite successful. The optimal therapies for opportunistic fungal infections are still debated, and further evaluation is needed.
Varied clinical manifestations of Penicillium marneffei in patients with human immunodeficiency virus: a report from south India
Authors: Michael J. S. , Abraham O. C. , Mathai D. , Mathews M. S.
Published: March 2005

Penicillium marneffei is a dimorphic fungus endemic to northeast India. This is the first report of penicilliosis from a hospital in south India. Three patients with diverse clinical manifestations who presented to a tertiary care hospital are described. High index of clinical suspicion and knowledge of ‘local’ microbiology is paramount in early diagnosis and timely treatment.