bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacteriophage T4‐encoded Stp can be replaced as activator of anticodon nuclease by a normal host cell metabolite
Authors: Amitsur Michal , Benjamin Sima , Rosner Rachel , Chapman‐Shimshoni Daphne , Meidler Roberto , Blanga Shani , Kaufmann Gabriel 
Published: September 2003

SummaryThe bacterial tRNALys‐specific anticodon nuclease is known as a phage T4 exclusion system. In the uninfected host cell anticodon nuclease is kept latent due to the association of its core protein PrrC with the DNA restriction‐modification endonuclease EcoprrI. Stp, the T4‐encoded peptide inhibitor of EcoprrI activates the latent enzyme. Previous in vitro work indicated that the activation by Stp is sensitive to DNase and requires added nucleotides. Biochemical and mutational data reported here suggest that Stp activates the latent holoenzyme when its EcoprrI component is tethered to a cognate DNA substrate. Moreover, the activation is driven by GTP hydrolysis, possibly mediated by the NTPase domain of PrrC. The data also reveal that Stp can be replaced as the activator of latent anticodon nuclease by certain pyrimidine nucleotides, the most potent of which is dTTP. The activation by dTTP likewise requires an EcoprrI DNA substrate and GTP hydrolysis but involves a different form of the latent holoenzyme/DNA complex. Moreover, whereas Stp relays its activating effect through EcoprrI, dTTP targets PrrC. The activation of the latent enzyme by a normal cell constituent hints that anticodon nuclease plays additional roles, other than warding off phage T4 infection.
Shifting fungal reproductive mode by manipulation of mating type genes: obligatory heterothallism of Gibberella zeae
Authors: Lee Jungkwan , Lee Theresa , Lee Yin‐Won , Yun Sung‐Hwan , Turgeon B. Gillian 
Published: September 2003

SummaryFungi capable of sexual reproduction use heterothallic (self‐sterile) or homothallic (self‐fertile) mating strategies. In most ascomycetes, a single mating type locus, MAT, with two alternative forms (MAT1‐1 and MAT1‐2) called idiomorphs, controls mating ability. In heterothallic ascomycetes, these alternative idiomorphs reside in different nuclei. In contrast, most homothallic ascomycetes carry both MAT1‐1 and MAT1‐2 in a single nucleus, usually closely linked. An example of the latter is Gibberella zeae, a species that is capable of both selfing and outcrossing. G. zeae is a devastating cereal pathogen of ubiquitous geographical distribution, and also a producer of mycotoxins that threaten human and animal health. We asked whether G. zeae could be made strictly heterothallic by manipulation of MAT. Targeted gene replacement was used to differentially delete MAT1‐1 or MAT1‐2 from a wild‐type haploid MAT1‐1; MAT1‐2 strain, resulting in MAT1‐1; mat1‐2, mat1‐1; MAT1‐2 strains that were self‐sterile, yet able to cross to wild‐type testers and, more importantly, to each other. These results indicated that differential deletion of MAT idiomorphs eliminates selfing ability of G. zeae, but the ability to outcross is retained. They also indicated that both MAT idiomorphs are required for self‐fertility. To our knowledge, this is the first report of complete conversion of fungal reproductive strategy from homothallic to heterothallic by targeted manipulation of MAT. Practically, this approach opens the door to simple and efficient procedures for obtaining sexual recombinants of G. zeae that will be useful for genetic analyses of pathogenicity and other traits, such as the ability to produce mycotoxins.
Titration of the Escherichia coli DnaA protein to excess datA sites causes destabilization of replication forks, delayed replication initiation and delayed cell division
Authors: Morigen  , Løbner‐Olesen Anders , Skarstad Kirsten 
Published: September 2003

SummaryIn Escherichia coli, the level of the initiator protein DnaA is limiting for initiation of replication at oriC. A high‐affinity binding site for DnaA, datA, plays an important role. Here, the effect of extra datA sites was studied. A moderate increase in datA dosage (≈ fourfold) delayed initiation of replication and cell division, but increased the rate of replication fork movement about twofold. At a further increase in the datA gene dosage, the SOS response was induced, and incomplete rounds of chromosome replication were detected. Overexpression of DnaA protein suppressed the SOS response and restored normal replication timing and rate of fork movement. In the presence of extra datA sites, cells showed a dependency on PriA and RecA proteins, indicating instability of the replication fork. The results suggest that wild‐type replication fork progression normally includes controlled pausing, and that this is a prerequisite for normal replication fork function.
Negative feedback regulation ofdnaK,clpBandlonexpression by the DnaK chaperone machine inStreptomyces coelicolor, identified by transcriptome andin vivoDnaK‐depletion analysis
Authors: Bucca Giselda , Brassington Anna M. E. , Hotchkiss Graham , Mersinias Vassilios , Smith Colin P. 
Published: September 2003

SummaryThednaKoperon ofStreptomyces coelicolorencodes the DnaK chaperone machine and the negative autoregulator HspR, which confers repression of the operon by binding to several inverted repeat sequences in the promoter region,dnaKp. Previousin vitrostudies demonstrated that DnaK forms a specific complex with HspR bound to its operator sequences indnaKp, and a model was proposed in which DnaK functions as a corepressor of thednaKoperon (Bucca, G., Brassington, A., Schonfeld, H.J., and Smith, C.P. (2000)Mol Microbiol38: 1093–1103). Here we reportin vivoDnaK depletion experiments which demonstrate that DnaK is a negative regulator of thednaKoperon. Cellular depletion of the DnaK chaperone leads to high‐level transcription fromdnaKpat the normal growth temperature. DNA microarray‐based analysis of gene expression in wild‐type andhspR‐disruption mutant strains has identified a core cluster of genes regulated by HspR: thednaKandclpB‐SCO3660operons andlon. These three transcription units are considered to be the direct targets of HspR. Significantly, analysis of the entire genome sequence revealed that the promoter regions ofdnaK,clpBandlonare the only sequences that contain the HspR consensus binding sequence 5′‐TTGAGY‐N7‐ACTCAA. S1 nuclease mapping confirmed that transcription of bothclpBandlonis substantially enhanced at ambient temperature in strains depleted of DnaK, providing further evidence that these genes are members of the DnaK‐HspR regulon. From transcriptome analysis, 17 genes were shown to be upregulated more than twofold in anhspRdisruption mutant. This included the seven genes encoded by thednaK,clpBandlontranscription units. Significantly, the other 10 genes are not heat‐shock inducible in the wild type and their upregulation in thehspRmutant is considered to be an indirect consequence of enhanced synthesis of one or more components of the HspR regulon (the DnaK chaperone machine, ClpB and Lon protease).
Large‐scale essential gene identification in Candida albicans and applications to antifungal drug discovery
Authors: Roemer Terry , Jiang Bo , Davison John , Ketela Troy , Veillette Karynn , Breton Anouk , Tandia Fatou , Linteau Annie , Sillaots Susan , Marta Catarina , Martel Nick , Veronneau Steeve , Lemieux Sebastien , Kauffman Sarah , Becker Jeff , Storms Reginald , Boone Charles , Bussey Howard 
Published: September 2003

Summary Candida albicans is the primary fungal pathogen of humans. Despite the need for novel drugs to combat fungal infections [Sobel, J.D. (2000) Clin Infectious Dis 30: 652], antifungal drug discovery is currently limited by both the availability of suitable drug targets and assays to screen corresponding targets. A functional genomics approach based on the diploid C. albicans genome sequence, termed GRACETM (gene replacement and conditional expression), was used to assess gene essentiality through a combination of gene replacement and conditional gene expression. In a systematic application of this approach, we identify 567 essential genes in C. albicans. Interestingly, evaluating the conditional phenotype of all identifiable C. albicans homologues of the Saccharomyces cerevisiae essential gene set [Giaever, G., Chu, A.M., Ni, L., Connelly, C., Riles, L., Veronneau, S., et al. (2002) Nature 418: 387–391] by GRACE revealed only 61% to be essential in C. albicans, emphasizing the importance of performing such studies directly within the pathogen. Construction of this conditional mutant strain collection facilitates large‐scale examination of terminal phenotypes of essential genes. This information enables preferred drug targets to be selected from the C. albicans essential gene set by phenotypic information derived both in vitro, such as cidal versus static terminal phenotypes, as well as in vivo through virulence studies using conditional strains in an animal model of infection. In addition, the combination of phenotypic and bioinformatic analyses further improves drug target selection from the C. albicans essential gene set, and their respective conditional mutant strains may be directly used as sensitive whole‐cell assays for drug screening.
CcpA regulation of aerobic and respiration growth in Lactococcus lactis
Authors: Gaudu Philippe , Lamberet Gilles , Poncet Sandrine , Gruss Alexandra 
Published: September 2003

SummaryThe catabolic control protein CcpA is the highly conserved regulator of carbon metabolism in Gram‐positive bacteria. We recently showed that Lactococcus lactis, a fermenting bacterium in the family of Streptococcaceae, is capable of respiration late in growth when haem is added to aerated cultures. As the start of respiration coincides with glucose depletion from the medium, we hypothesized that CcpA is involved in this metabolic switch and investigated its role in lactococcal growth under aeration and respiration conditions. Compared with modest changes observed in fermentation growth, inactivation of ccpA shifts metabolism to mixed acid fermentation under aeration conditions. This shift is due to a modification of the redox balance via derepression of NADH oxidase, which eliminates oxygen and decreases the NADH pool. CcpA also plays a decisive role in respiration metabolism. Haem addition to lag phase ccpA cells results in growth arrest and cell mortality. Toxicity is due to oxidative stress provoked by precocious haem uptake. We identify the repressor of the haem transport system and show that it is a target of CcpA activation. We propose that CcpA‐mediated repression of haem uptake is a means of preventing oxidative damage at the start of exponential growth. CcpA thus appears to govern a regulatory network that coordinates oxygen, iron and carbon metabolism.
The Vibrio fischeri quorum‐sensing systems ain and lux sequentially induce luminescence gene expression and are important for persistence in the squid host
Authors: Lupp Claudia , Urbanowski Mark , Greenberg E. Peter , Ruby Edward G. 
Published: September 2003

SummaryBacterial quorum sensing using acyl‐homoserine lactones (acyl‐HSLs) as cell‐density dependent signalling molecules is important for the transcriptional regulation of many genes essential in the establishment and the maintenance of bacteria–host associations. Vibrio fischeri, the symbiotic partner of the Hawaiian bobtail squid Euprymna scolopes, possesses two distinct acyl‐HSL synthase proteins, LuxI and AinS. Whereas the cell density‐dependent regulation of luminescence by the LuxI‐produced signal is a well‐described phenomenon, and its role in light organ symbiosis has been defined, little is known about the ain system. We have investigated the impact of the V. fischeri acyl‐HSL synthase AinS on both luminescence and symbiotic colonization. Through phenotypic studies of V. fischeri mutants we have found that the AinS‐signal is the predominant inducer of luminescence expression in culture, whereas the impact of the LuxI‐signal is apparent only at the high cell densities occurring in symbiosis. Furthermore, our studies revealed that ainS regulates activities essential for successful colonization of E. scolopes, i.e. the V. fischeri ainS mutant failed to persist in the squid light organ. Mutational inactivation of the transcriptional regulator protein LuxO in the ainS mutant partially or completely reversed all the observed phenotypes, demonstrating that the AinS‐signal regulates expression of downstream genes through the inactivation of LuxO. Taken together, our results suggest that the two quorum‐sensing systems in V. fischeri, ain and lux, sequentially induce the expression of luminescence genes and possibly other colonization factors.
Predicting yield loss in maize fields and developing decision support for post‐emergence herbicide applications
Authors: Lemieux C , Vallée L , Vanasse A 
Published: September 2003

SummaryThis work was initiated to integrate an image analysis system and a prediction equation to support decisions for post‐emergence herbicide applications under field conditions. Data were collected from 1999 to 2001 in 32 commercial fields to obtain weed cover data at the three to four leaf stage of maize (Zea mays L.), and crop yield at maturity. Relative crop yield was predicted using a non‐linear sigmoidal equation with relative weed cover as the predictor variable (P < 0.0001; R2 = 0.39). The decision procedure consists of using the equation within the limits of a yield loss threshold that represents the loss one is willing to tolerate. The tolerance threshold (TT) allows determination of a weed threshold (WT). The procedure considers the variability around the prediction equation by setting the WT at the intersection between the lower 95% confidence interval of the prediction line and the TT. It also considers the variability around the weed cover estimate. For a given field, the decision is made by comparing the average weed cover corrected for sampling error, to the WT. We tested the performance of the decision procedure and found it could lead to a saving of 25% of herbicide use. We also computed a probability table showing the chances of getting relative yield above or below the TT. We suggest using the probability table in combination with the decision procedure to manage risks. The proposed approach does not offer a set ‘yes’ or ‘no’ answer but rather provides a framework to support decisions by producers who ultimately must manage the risks.
Mechanisms of resistance to simazine in Sonchus oleraceus
Authors: Fraga M I , Tasende M G 
Published: September 2003

Summary Sonchus oleraceus biotypes resistant to simazine were identified by chlorophyll fluorescence analysis of intact leaves. The mechanisms of resistance were determined on the basis of cpDNA and glutathione S‐transferase (GST) activity analyses. The results of the cpDNA analysis showed that most of the resistant biotypes had a Ser 264 Gly mutation in the psbA gene, which is responsible for an amino acid substitution in the D‐1 protein sequence. The cpDNA fragments were amplified by polymerase chain reaction and digested with restriction enzyme MaeI. Two restriction bands of 338 and 75 bp were recorded in biotypes with the target mutation, while three bands (218, 120 and 75 bp) were present in biotypes without this mutation. A second mechanism of resistance in this species was through the detoxification of simazine by conjugation with glutathione. In resistant biotypes without the above‐mentioned mutation, the average level of GST (simazine) activity in leaves was 4.5‐fold greater than in the resistant biotypes with the target mutation and 8.3‐fold greater than in the susceptible biotypes. Resistance as a result of the target mutation was more common than that achieved through detoxification by glutathione conjugation of simazine.
Natural tolerance of Cuscuta campestris to herbicides inhibiting amino acid biosynthesis
Authors: Nadler‐Hassar T , Rubin B 
Published: September 2003

SummaryThe response of Cuscuta campestris Yuncker, a non‐specific above‐ground holoparasite, to amino acid biosynthesis inhibitor (AABI) herbicides, was compared with other resistant and sensitive plants in dose–response assays carried out in Petri dishes. Cuscuta campestris was found to be much more resistant to all AABI herbicides tested. The I50 value of C. campestris growth inhibition by glyphosate was eightfold higher than that of transgenic, glyphosate‐resistant cotton (RR‐cotton). The I50 value for C. campestris shoot growth inhibition by sulfometuron was above 500 μM, whereas that of sorghum roots was only 0.004 μM. Cuscuta campestris exposed to glyphosate gradually accumulated shikimate, confirming herbicide penetration into the parasite and interaction with an active form of the target enzyme of the herbicide, 5‐enolpyruvylshikimate‐3‐phosphate synthase. More than half of the C. campestris plants associated with transgenic, glyphosate‐resistant sugarbeet (RR‐sugarbeet) treated with glyphosate or with transgenic, sulfometuron‐resistant tomato (SuR‐tomato) treated with sulfometuron recovered and resumed regular growth 20–30 days after treatment. New healthy stems developed, followed by normal flowering and seed setting. The results of the current study demonstrate the unique capacity of C. campestris to tolerate high rates of AABI. The mechanism of this phenomenon is yet to be elucidated.
Changes in the abundance of weeds in spring cereal fields in Finland
Authors: Hyvönen T , Ketoja E , Salonen J 
Published: September 2003

SummaryThe data of two weed surveys of spring cereals (conducted in 1982–84 and 1997–99) in Finland were applied to study changes in the total abundance (the number of individuals and dry weight) of the weed community as well as in the abundance and frequency of occurrence of single species. The estimated overall mean for the differences in total dry weight was 31.1 kg ha−1 and the differences in the total number of individuals was 46.6 individuals m−2 with higher numbers in the 1990s. Most of the overall variability in dry weight (63%) and in number of individuals (57%) was attributable to variability between fields within the same farm. None of the environmental variables could explain the variability in the difference in dry weight, or in the number of individuals between decades. Descriptive analysis of the single species data revealed a higher abundance and frequency of occurrence of most species in the 1990s than in the 1980s. No statistically significant differences were detected in the number of individuals of species tolerant of sulfonylureas (pooled data on Galium spurium and Viola arvensis) between decades. The results are discussed in relation to changes in the use of herbicides.
Combining physical, cultural and biological methods: prospects for integrated non‐chemical weed management strategies
Authors: Hatcher P E , Melander B 
Published: September 2003

SummaryPhysical, cultural and biological methods for weed control have developed largely independently and are often concerned with weed control in different systems: physical and cultural control in annual crops and biocontrol in extensive grasslands. We discuss the strengths and limitations of four physical and cultural methods for weed control: mechanical, thermal, cutting, and intercropping, and the advantages and disadvantages of combining biological control with them. These physical and cultural control methods may increase soil nitrogen levels and alter microclimate at soil level; this may be of benefit to biocontrol agents, although physical disturbance to the soil and plant damage may be detrimental. Some weeds escape control by these methods; we suggest that these weeds may be controlled by biocontrol agents. It will be easiest to combine biological control with fire and cutting in grasslands; within arable systems it would be most promising to combine biological control (especially using seed predators and foliar pathogens) with cover‐cropping, and mechanical weeding combined with foliar bacterial and possibly foliar fungal pathogens. We stress the need to consider the timing of application of combined control methods in order to cause least damage to the biocontrol agent, along with maximum damage to the weed and to consider the wider implications of these different weed control methods.
The control of Achillea millefolium in the Snowy Mountains of Australia
Authors: Sanecki G M , Sanecki K L , Wright G T , Johnston F M 
Published: September 2003

SummaryThe response of Achillea millefolium L. to herbicides was measured to determine the effectiveness of the current recommendations and to test alternative herbicides. Five plots at each of the three replicate sites were selected and randomly treated with one of the four herbicides: dicamba/2,4‐D, glyphosate, metsulfuron‐methyl and triclopyr/picloram. After 12 months, the recommended treatment, dicamba/2,4‐D, did not cause a significant reduction in aerial biomass compared with untreated controls and the number of flowering stems was significantly increased in treated plots. Metsulfuron‐methyl and triclopyr/picloram caused a significant reduction in A. millefolium aerial biomass but did not affect the number of flowering stems. Glyphosate produced a significant reduction in aerial biomass and was less effective. These results suggest that the current recommendation for A. millefolium might be improved. Site‐specific effects such as aspect may also influence the effectiveness of herbicides on this species.
Deposition of spray liquid on the soil below cereal crops after applications during the growing season
Authors: Jensen P K , Spliid N H 
Published: September 2003

SummaryThe aim of this study was to investigate how big a proportion of the spray liquid applied in a typical application was deposited on the soil surface below the crop. From an agronomical point of view this part of the spray is an undesirable loss of foliar acting pesticides during application and it also constitutes a primary source of leaching and surface run‐off. The investigation was carried out during 1998–2001 in winter wheat and in spring barley. Applications were carried out at approximate intervals of 10 days during the whole growing season in the two cereal crops. The results showed that a high proportion of the spray liquid reaches the soil below the crop during applications at early growth stages corresponding to the growth stages where weed control on farms is carried out. At later growth stages soil deposition declined and reached values below 5% of the applied dose in winter wheat after inflorescence emergence (50–59 BBCH). The spring barley crops remained more open and minimum soil deposit values were approximately 15% of the applied dose at growth stages (50–59 BBCH). During ripening soil deposition values increased again as crop cover decreased.
Herbicides used in combination can reduce the probability of herbicide resistance in finite weed populations
Authors: Diggle A J , Neve P B , Smith F P 
Published: September 2003

SummaryA simulation study was conducted to examine the effect of pattern of herbicide use on development of resistance to two herbicides with different modes of action in finite weed populations. The effects of the size of the treatment area (analogous to initial weed population), germination fraction and degree of self‐pollination in the weed were investigated. The results indicate that the probability of developing resistance to one or both herbicides decreases as the size of the area/initial population decreases. For treatment areas of 100 ha or less with an initial weed seedbank of 100 seeds m−2 and initial frequencies of the resistance genes of 10−6, development of resistance to both herbicides (double‐resistance) is uncommon within 50 years for all types of weeds if both herbicides are used in all years (used in combination). If herbicides are used in alternate years (rotated) double‐resistance almost always occurs in 100 ha areas but is uncommon in areas of 1 ha or less. The results suggest that adoption of practices that limit movement of weeds in conjunction with using herbicides in combination rather than in rotation can substantially delay development of herbicide resistance.