bluuebunny/crossref_metadata_2025 huggingface dataset:
Additional experiences to elucidate the microbial component of soil suppressiveness towards strawberry black root rot complex
Authors: MANICI L M , CAPUTO F , BARUZZI G
Published: August 2005

Several studies were carried out to investigate the soil microbial components involved in suppressing strawberry black rot root which occurs throughout the Italian strawberry growing region. Quantitative and qualitative evaluation of fungi involved in black root rot were combined with several soil microbial parameters involved in soil suppressiveness towards black root rot agents. The first survey, carried out in an intensively cultivated area of northern Italy, identified Rhizoctonia spp. as the main root pathogen together with several typical weak pathogens belonging to the well‐known black rot root complex of strawberry crop: Cylindrocarpondestructans, Fusarium oxysporum, F. solani, Pestalotia longiseta and others. The root colonisation frequency of strawberry plants increased strongly from autumn to spring at harvesting stage. Rhizoctonia spp. were the only pathogens which followed the rising trend of root colonisation with relative frequency; all the weak pathogens of strawberry black root rot complex did not vary their frequency. Only non‐pathogenic fungi decreased from autumn to spring when at least 60% of colonising fungi were represented by Rhizoctonia. These data suggested that the late vegetative stage was the best time to record the soil inoculum of root rot agents in strawberry using root infection frequency as a parameter of soil health. A further study was performed in two fields, chosen for their common soil texture and pH, but with significant differences in previous soil management: one (ALSIA) had been subjected to strawberry monoculture without organic input for several years; the other (CIF) has been managed according to a 4‐year crop rotation and high organic input. In this study Pythium artificially inoculated was adopted as an indicator for the behaviour of saprophytically living pathogens in bulk soil. Pythium showed a sharp, different response after inoculation in bulk soil from the two soil systems evaluated. Pythium was suppressed only in the CIF field where the highest levels of total fungi and fluorescent bacteria and highest variability were observed. The suppressiveness conditions towards Pythium, observed in the CIF and absent in the ALSIA field, corresponded with the root infection frequency recorded at the late vegetative stage on strawberry plants grown in the two fields: strawberry plants from the CIF field showed lower root colonisation frequency and higher variability than that recorded on those coming from the ALSIA field.
Soil solarisation, amendments and bio‐control agents for the control of Macrophomina phaseolina and Fusarium oxysporum f.sp. cumini in aridisols
Authors: ISRAEL S , MAWAR R , LODHA S
Published: August 2005

The effects of soil solarisation, residue incorporation, summer irrigation and biocontrol agents singly or in combination on survival of Macrophomina phaseolina and Fusarium oxysporum f.sp. cumini were ascertained in the 2000 and 2001 summer seasons. In amended plots, temperature increased by 2.5°C over non‐amended plots (42–51°C) at various soil depths. Combining amendments and soil solarisation elevated the soil temperatures by 0.5–5°C and 2.5–13.0°C compared to non‐amended solarised and non‐solarised plots, respectively. These treatment combinations significantly reduced M. phaseolina and Fusarium propagules compared to control. Of these, combining mustard pod residues with soil solarisation almost eliminated viable propagules of both the pathogens at 0–30 cm soil depth. However, a combination of mustard pod residue and oil‐cake (2.5 + 0.5 ton ha−1) with only one summer irrigation also caused pronounced reduction in pathogenic propagules, which was equal to that recorded in non‐amended solarised plots. The effect of surviving propagules of M. phaseolina and Fusarium on incidence of dry root rot on clusterbean and wilt on cumin was studied in subsequent rainy and winter seasons, respectively. Significant reductions in both diseases were recorded in residue and biocontrol amended plots with or without polyethylene mulching compared to non‐amended control. The lowest plant mortality in both the crops was recorded in mustard residue amended solarised plots in a two year field experiment. However, the disease indices in the plots having a combination of mustard residues and oil‐cake amendment with one summer irrigation was equal to that achieved in the treatment having polyethylene mulching. These results suggest that in hot arid regions use of Brassica residues can be a practical and feasible substitute for polyethylene mulching in managing soil‐borne diseases.
Control of purple spot of loquat fruit (Eriobotrya japonica) by means of mineral compounds
Authors: GARIGLIO N , MARTINEZ‐FUENTES A , MESEJO C , AGUSTÍ M
Published: August 2005

Treatments to control purple spot of loquat fruit (Eriobotrya japonica) were tested based on the hypothesis that the disorder appears as a consequence of water unbalance between flesh and epidermal tissues caused by their different ability for sugar accumulation. Calcium nitrate, calcium chloride, Ca‐EDTA, ammonium nitrate and potassium nitrate at a concentration of 150 mm applied 2 weeks before fruit colour break reduced significantly the proportion of purple‐spotted fruit, giving rise to a reduction of water potential of the epidermal tissue that allows it to retain water. The most favourable date of treatment was during the 2 weeks prior to fruit colour break.
Time and concentration dependent interactions of Beauveria bassiana with sublethal rates of imidacloprid against the aphid pests Macrosiphoniellasanborni and Myzus persicae
Authors: YE SU‐DAN , DUN YU‐HUI , FENG MING‐GUANG
Published: August 2005

A series of laboratory bioassays with each consisting of low, medium and high concentration treatments of the fungal biocontrol agent Beauveria bassiana alone or supplemented with an increasing sublethal rate of imidacloprid were conducted to quantify the fungal and chemical interactions on chrysanthemum aphid Macrosiphoniella sanborni (0.01‐0.05 a.i. μg mL−1) and green peach aphid Myzus persicae (0.05‐0.5 a.i. μg mL−1). During one week after exposure to a 1 mL spray onto a 95 cm2 area in a Potter Spray Tower, M. sanborni was either more susceptible to B. bassiana or more sensitive to imidacloprid than M. persicae. The time–concentration–mortality (TCM) responses of each aphid species in each of five bioassays fit well to a TCM model, indicating a strong dependence of the fungal and chemical interactions on both concentration and post‐spray time. Adding imidacloprid to B. bassiana sprays at the rates of 0.025–0.05 μg mL−1 against M. sanborni or 0.1–0.5 μg mL−1 against M. persicae significantly enhanced or accelerated the fungal action. Based on the LC50 or LC90 estimates and their variances determined by the fitted TCM relationships for each aphid species, the relative potencies of an imidacloprid‐inclusive bioassay over those with B. bassiana alone or together with a lower sublethal rate ranged from a few to hundreds of times and varied over days after spray. These results suggest an alternative tactic for practical control of the aphid pests by a combined formulation or application of B. bassiana and imidacloprid and manage aphid resistance to the chemical insecticide.
Age‐specific bioassays and fecundity of Phthorimaea operculella (Lepidoptera: Gelechiidae) reared on cry1Ac ‐transgenic potato plants
Authors: DAVIDSON M M , BUTLER R C , WRATTEN S D , CONNER A J
Published: August 2005

Variation in the susceptibility of lepidopterous pest larvae of different ages to transgenic crops and the potential for survivors to reproduce could have important consequences for the development of resistance in such pests. Experiments were undertaken in the laboratory to determine if larvae of the potato tuber moth, Phthorimaea operculella, of different ages (0 (< 1 day old), 3, 5, 7 days) varied in their susceptibility to cry1Ac9–transgenic potato (Solanum tuberosum) foliage grown in the glasshouse or field. The survival and fecundity of larvae reared on transgenic tubers was also determined in the laboratory. There were no apparent differences in susceptibility of larvae of different ages to transgenic foliage. Larvae fed glasshouse or field‐grown non‐transgenic foliage had significantly larger relative growth indices and more larvae pupated, than those fed transgenic foliage, regardless of larval age. Eggs from a laboratory colony were placed on transgenic or non‐transgenic tubers to measure survival and fecundity. Between 6% and 15% of eggs placed on transgenic tubers developed into pupae for three of the four transgenic potato lines tested. On one transgenic line, only six adults emerged from 1300 eggs. In contrast, between 71% and 97% of the eggs placed on non‐transgenic tubers developed into pupae. Male and female pupae from transgenic lines weighed less than those from non‐transgenic lines. The fecundity of females from two of four transgenic lines was lower than from the non‐transgenic parent cultivar. Although larvae of different ages did not exhibit any overall age‐dependent pattern of increasing or decreasing susceptibility to transgenic foliage of glasshouse or field‐grown plants, the ability of larvae to survive and reproduce on transgenic tubers suggests this pest has the ability to evolve resistance to the transgenic plants used in the present study.
The use of image analysis to monitor the germination of seeds of broccoli (Brassica oleracea) and radish (Raphanus sativus)
Authors: Dell'Aquila A
Published: August 2005

To study broccoli and radish seed germination under different temperature regimes the germination test has been used to assess final germination percentage, start and rate. This method has been integrated with a computer‐aided image analysis test which is more accurate in monitoring the extent of imbibition phases through the assessment of seed area increase and timing of radicle emergence detected on single seeds. In addition, seed area increase has been used also to establish a close relationship with radicle elongation rate in the time range when ‘visible germination’ is scored by a classical germination test. The results suggest that this image analysis parameter may be considered as a reliable seed imbibition marker to integrate the germination parameters obtained by a germination test.
Intra‐population diversity between citrus viroid II variants described as agents of cachexia disease
Authors: VIDALAKIS G , DAVIS J Z , SEMANCIK J S
Published: August 2005

The citrus viroid II (CVd‐II, Hop stunt viroid) variant, cachexia 909 (Ca‐909) has been designated as a “cachexia” disease isolate on the basis of inducing extremely mild symptoms on the cachexia indexing host Parson's Special mandarin (PSM). However, Ca‐909 lacks the six‐nucleotide cluster demonstrated to control the pathogenicity of cachexia inducing agents such as CVd‐IIc. Progeny populations of CVd‐IIc and Ca‐909 from the bioamplification host, Etrog citron, and the indexing host PSM were surveyed for clones with possible mutations in the locus of the “cachexia cluster”. The intra‐population diversity and the genealogical relationships among clones of CVd‐IIc and Ca‐909 populations were also analysed using principles of the coalescent theory. CVd‐IIc progeny was found not to mutate in the “cachexia cluster” and Ca‐909 did not acquire any mutations related to the nucleotide sites of the “cachexia cluster”. Specific mutations of the Ca‐909 progeny were found to be similar to the non‐cachexia variant, CVd‐IIa. Population profiles and genealogical patterns of CVd‐IIc and Ca‐909 in Etrog citron were not significantly different. However, although CVd‐IIc progeny were more conserved in PSM, Ca‐909 progeny displayed titre, population profiles, and genealogical patterns more uniform in selected tissues of Parson's Special mandarin than CVd‐IIc. These experimental approaches demonstrate the genetic stability of the cachexia‐agent CVd‐IIc and question the inclusion of Ca‐909 as a cachexia disease agent.
Examples of phenological change, past and present, in UK farming
Authors: SPARKS T H , CROXTON P J , COLLINSON N , TAYLOR P W
Published: August 2005

This paper examines a large number of agricultural and other phenological records kept by a farmer in Sussex, UK from 1980 to 2000. Twenty five of the 29 events were earlier in 1990‐2000 than in 1980‐1989. The average advancement of all 29 events was 5.5 days at a time when January‐March mean temperature increased by 1.4°C. In comparing the events with monthly mean temperatures, 18 of the events were significantly negatively related to temperatures of the three calendar months preceding the mean event date. Response rates to temperature varied between 4 and 12 days earlier for each °C warmer.

A comparison with historical farming records reveals that many of the current farming events appear as responsive to temperature now as they were 200 years ago.
Gamma-ray bursts from quark stars
Authors: Paczyński B. , Haensel P.
Published: August 2005

Long gamma-ray bursts (GRBs) are believed to be related to the explosion of Type Ic supernovae, which have been stripped of their hydrogen and helium envelopes. There appear to be two types of these explosions: those that are approximately spherical (GRB 980425/SN 1998bw), and which are associated with weak bursts; and the classical GRBs which generate ultrarelativistic jets (GRB 030329/SN 2003dh). If this bimodality is real, Swift will provide clear evidence for it.

We propose that classical powerful GRBs, which generate ultrarelativistic outflows, are a result of the formation of quark stars. Quark stars may provide additional energy for the explosion of Type Ic supernovae, but far more important is the creation of a surface which acts as a membrane that cannot be penetrated by baryons. A surface of a quark star allows only ultrarelativistic matter to escape: photons, neutrinos, electron–positron pairs and magnetic fields. The formation of a quark star follows several minutes after the initial core collapse. Possible evidence for this time delay is provided by BATSE precursors to GRBs, as analysed by Lazzati.
Constraints on the dark energy equation of state from the imprint of baryons on the power spectrum of clusters
Authors: Angulo R. , Baugh C. M. , Frenk C. S. , Bower R. G. , Jenkins A. , Morris S. L.
Published: August 2005

Acoustic oscillations in the baryon–photon fluid leave a signature in the matter power spectrum. The overall shape of the spectrum and the wavelength of the oscillations depend upon the sound horizon scale at recombination. Using the Λ cold dark matter Hubble Volume simulation, we show that the imprint of baryons is visible in the power spectrum of cluster-mass dark matter haloes, in spite of significant differences between the halo power spectrum and the prediction of linear perturbation theory. A measurement of the sound horizon scale can constrain the dark energy equation of state. We show that a survey of clusters at intermediate redshift (z∼ 1), like the Sunyaev–Zel'dovich survey proposed by the South Pole Telescope or a red sequence photometric survey with VISTA or the Dark Energy Survey, could potentially constrain the sound horizon scale to an accuracy of ∼2 per cent, in turn fixing the ratio of the pressure of the dark energy to its density (w) to better than ∼10 per cent. Our approach does not require knowledge of the cluster mass, unlike those that depend upon the abundance of clusters.
The origin of long-period Alfvén waves in the solar wind
Authors: Zaqarashvili T. V. , Belvedere G.
Published: August 2005

We suggest that the observed long-period Alfvén waves in the solar wind may be generated in the solar interior as a result of the pulsation of the Sun in the fundamental radial mode. The period of this pulsation is about 1 h. The pulsation causes a periodic variation of density and large-scale magnetic field, which affects the Alfvén speed in the solar interior. Consequently, Alfvén waves with half the frequency of pulsation (i.e. with double the period) can be parametrically amplified in the interior below the convection zone as a result of the recently suggested swing wave–wave interaction. Therefore the amplified Alfvén waves have periods of several hours. The waves can propagate upwards through the convection zone to the solar atmosphere and cause the observed long-period Alfvén oscillations in the solar wind.
Cosmic backgrounds from miniquasars
Authors: Salvaterra Ruben , Haardt Francesco , Ferrara Andrea
Published: August 2005

A large population of intermediate-mass black holes (IMBHs) might be produced at early cosmic times as a leftover of the evolution of the very massive first stars. Accretion on to IMBHs provides a source of (re)ionizing radiation. We show that the baryon mass fraction locked into IMBHs and their growth is strongly constrained by the observed residual soft X-ray background (SXRB) intensity. Thus, unless they are extremely X-ray quiet, miniquasars must be quite rare and/or have a short shining phase. As a byproduct, we find that miniquasars cannot be the only source of reionization and that their alleged contribution to the near-infrared bands is completely negligible.
An Integrated Approach to Identifying the Salinity Source Contaminating a Ground‐Water Supply
Authors: Knuth Martin , Jackson Jim L. , Whittemore Donald O.
Published: August 2005

An integrated approach involving geohydrological, geochemical, and geophysical methods was used to determine the source of salinity contaminating a ground‐water supply in an area of Ohio where three possible sources existed: road salting, naturally saline ground waters at depth, and formation brines placed in surface pits during drilling of a gas well. Changes in chloride concentrations during pumping tests of contaminated wells indicated that the main source of salinity was derived from within the water‐table aquifer. Mixing curves of Br/Cl versus chloride concentration were used to determine which of each of the three salinity sources was the primary source affecting different well waters. The major source affecting the ground‐water supply was found to be the formation brines associated with the gas well drilling.

Geophysical surveys using electromagnetic induction (Geonics EM–31) and dipole‐dipole electrical resistivity methods provided a three‐dimensional view of the brine contamination plume in the unsaturated and saturated zones in the area of the gas well. The plume location and orientation confirmed that the formation brine from the blow‐down pits used during drilling of a nearby gas well was the primary source polluting the ground‐water supply in the study area.
A Compatible Single‐Phase/Two‐Phase Numerical Model: 2. Application to a Coastal Aquifer in Mexico
Authors: Rivera Alfonso , Ledoux Emmanuel , Sauvagnac Serge
Published: August 2005

The application of a numerical model to a coastal aquifer is presented including the simulation of single‐phase and two‐phase fluid flow. The single‐phase part of the model solves the diffusivity equation and helps to identify certain parameters of the aquifer and to simulate the flow field (fresh water) under different conditions. The two‐phase part of the model solves the partial differential equations describing the motion of salt water and fresh water separated by a sharp interface.

The model was calibrated using the observed piezometry of the aquifer for the fresh‐water flow field. Simulations were made for both steady‐and unsteady‐state conditions to establish the position and movement of the interface under different schemes of pumping. Results show that the model reproduces very accurately the flow field of fresh water. It identifies the potential salt‐water intrusion (upconing) into some of the pumping wells, thus helping in the identification of optimal pumping schemes.
Hydrocarbon Thickness Fluctuations in Monitoring Wells
Authors: Kemblowski M. W. , Chiang C. Y.
Published: August 2005

Hydrocarbon thickness measurements in monitoring wells are used to estimate the hydrocarbon volume in the subsurface and to evaluate the efficiency of hydrocarbon recovery. It is commonly assumed that the formation hydrocarbon thickness is linearly related to the measured one. However, field data quite frequently show hydrocarbon thickness fluctuations that are not related to either hydrocarbon recovery or its release.

It is postulated that these fluctuations are related to hydrocarbon/ground‐water interface elevation changes, and can be explained by two mechanisms: (1) difference in the residual saturation of hydrocarbons entrapped below and above the “interface,” and (2) preferred flow of the liquids through the monitoring well.
The Chemical Evolution of Ground Water in the Milk River Aquifer, Canada
Authors: Hendry M. Jim , Schwartz Franklin W.
Published: August 2005

Well‐defined trends are observed in the ion composition of ground water from the Milk River aquifer. Ground water from the area of the subcrop has higher concentrations of Na+, SO42‐, Ca2+, and Mg2+ than immediately downgradient. Away from the area of subcrop, Na+, Cl‐, HCO3‐ + CO32‐, and CH4 concentrations increase systematically with increased residence time, pH decreases, and Mg2+ and Ca2+ concentrations are typically low (less than 0.1 mmol/1). Geologic changes play an important role in producing these chemical patterns. The first major geologic change was the erosion of the overlying confining beds in the recharge area about 5 × 105 years ago, enabling meteoric water with low concentrations of Na+ and Cl‐ to enter the aquifer and displace preexisting water. The second major change was the deposition of glacial till in the area of the Milk River about 30,000 to 40,000 years ago. Water recharging through the till to the aquifer developed characteristically high concentrations of Na+, SO42‐, Ca2+, and Mg2+. Downgradient of the area of subcrop, the trends in Na+ and Cl‐ are controlled by diffusion from the underlying confining shale. Analyses of ground‐water and gas samples for sulfate reducers and ground‐water and gas samples for sulfide and H2S, respectively, suggest that SO42‐ reduction is not a major process. Geochemical modeling suggests that CO2 gas is added to the ground water with increased residence time in the aquifer. The increase in CO2, CH4, and dissolved inorganic carbon can be attributed to methane fermentation. Geochemical modeling suggests that cation exchange plays a minor role in the chemical evolution of the ground waters.
The Convergence of Synthetic Organic and Polymer Chemistries
Authors: Hawker Craig J. , Wooley Karen L.
Published: August 2005

Several recent conceptual advances, which take advantage of the design criteria and practical techniques of molecular-level control in organic chemistry, allow preparation of well-defined polymers and nanostructured materials. Two trends are clear: the realization that synthesis of complex macromolecules poses major challenges and opportunities and the expectation that such materials will exhibit distinctive properties and functions. Polymer synthesis methods now being developed will yield well-defined synthetic macromolecules that are capable of mimicking many of the features of proteins (for example, three-dimensional folded structure) and other natural materials. These macromolecules have far-reaching potential for the study of molecular-level behavior at interfaces, in thin films, and in solution, while also enabling the development of encapsulation, drug-delivery, and nanoscale-patterning technologies.
Mitogenic Influence of Human R-Spondin1 on the Intestinal Epithelium
Authors: Kim Kyung-Ah , Kakitani Makoto , Zhao Jingsong , Oshima Takeshi , Tang Tom , Binnerts Minke , Liu Yi , Boyle Bryan , Park Emily , Emtage Peter , Funk Walter D. , Tomizuka Kazuma
Published: August 2005

Several described growth factors influence the proliferation and regeneration of the intestinal epithelium. Using a transgenic mouse model, we identified a human gene,
R-spondin1
, with potent and specific proliferative effects on intestinal crypt cells. Human R-spondin1 (hRSpo1) is a thrombospondin domain-containing protein expressed in enteroendocrine cells as well as in epithelial cells in various tissues. Upon injection into mice, the protein induced rapid onset of crypt cell proliferation involving β-catenin stabilization, possibly by a process that is distinct from the canonical Wnt-mediated signaling pathway. The protein also displayed efficacy in a model of chemotherapy-induced intestinal mucositis and may have therapeutic application in gastrointestinal diseases.
Contact-Dependent Inhibition of Growth in
Escherichia coli
Authors: Aoki Stephanie K. , Pamma Rupinderjit , Hernday Aaron D. , Bickham Jessica E. , Braaten Bruce A. , Low David A.
Published: August 2005

Bacteria have developed mechanisms to communicate and compete with each other for limited environmental resources. We found that certain
Escherichia coli
, including uropathogenic strains, contained a bacterial growth-inhibition system that uses direct cell-to-cell contact. Inhibition was conditional, dependent upon the growth state of the inhibitory cell and the pili expression state of the target cell. Both a large cell-surface protein designated
C
ontact-
d
ependent
i
nhibitor A (CdiA) and two-partner secretion family member CdiB were required for growth inhibition. The CdiAB system may function to regulate the growth of specific cells within a differentiated bacterial population.
The
yliA
, -
B
, -
C
, and -
D
Genes of
Escherichia coli
K-12 Encode a Novel Glutathione Importer with an ATP-Binding Cassette
Authors: Suzuki Hideyuki , Koyanagi Takashi , Izuka Shunsuke , Onishi Akiko , Kumagai Hidehiko
Published: August 2005

Glutathione protects cells and organisms from oxygen species and peroxides and is indispensable for aerobically living organisms. Moreover, it acts against xenobiotics and drugs by the formation and excretion of glutathione
S
conjugates. In this study, we show that the
yliA
, -
B
, -
C
, and -
D
genes of
Escherichia coli
K-12 encode a glutathione transporter with the ATP-binding cassette. The transporter imports extracellular glutathione into the cytoplasm in an ATP-dependent manner. This transporter, along with γ-glutamyltranspeptidase, has an important role in
E. coli
growth with glutathione as a sole sulfur source.
A LysR-Type Regulator, CidR, Is Required for Induction of the
Staphylococcus aureus cidABC
Operon
Authors: Yang Soo-Jin , Rice Kelly C. , Brown Raquel J. , Patton Toni G. , Liou Linda E. , Park Yong Ho , Bayles Kenneth W.
Published: August 2005

The
Staphylococcus aureus cidABC
and
lrgAB
operons have been shown to regulate murein hydrolase activity and affect antibiotic tolerance. The
cid
operon enhances murein hydrolase activity and antibiotic sensitivity, whereas the
lrg
operon inhibits these processes. Based on these findings and the structural similarities of the
cidA
and
lrgA
gene products to the bacteriophage holin family of proteins, we have proposed that the
cid
and
lrg
operons encode holin- and antiholin-like proteins, respectively, that function to control the murein hydrolase activity produced by the bacteria. Analysis of
cid
operon transcription revealed the presence of two transcripts, one spanning all three
cid
genes and whose expression is induced by growth in the presence of acetic acid and the other spanning
cidB
and
cidC
only that is produced in a sigma B-dependent manner. The
cidABC
operon lies immediately downstream from the
cidR
gene, encoding a potential LysR-type transcriptional regulator. In this study, we demonstrate that
cidR
is involved in the regulation of
cidABC
expression. Northern blot analyses revealed that the
cidR
gene product positively regulates
cidABC
expression by increasing transcription in the presence of acetic acid produced as a result of the metabolism of glucose. As expected for an operon that encodes a positive effector of murein hydrolase activity, the upregulation of
cidABC
expression resulted in increased murein hydrolase activity produced by these cells. Furthermore, it was demonstrated that antibiotic tolerance and stationary-phase survival of
S. aureus
are affected by the
cidR
gene. Taken together, these results demonstrate that the
cidR
gene product functions as a transcriptional activator of
cidABC
transcription in response to acetic acid accumulation in the growth medium.
ABC Transporter for Corrinoids inHalobacteriumsp. Strain NRC-1
Authors: Woodson Jesse D. , Reynolds April A. , Escalante-Semerena Jorge C.
Published: August 2005

We report evidence for the existence of a putative ABC transporter for corrinoid utilization in the extremely halophilic archaeonHalobacteriumsp. strain NRC-1. Results from genetic and nutritional analyses ofHalobacteriumshowed that mutants with lesions in open reading frames (ORFs) Vng1370G, Vng1371Gm, and Vng1369G required a 105-fold higher concentration of cobalamin for growth than the wild-type or parent strain. The data support the conclusion that these ORFs encode orthologs of the bacterial cobalamin ABC transporter permease (btuC; Vng1370G), ATPase (btuD; Vng1371Gm), and substrate-binding protein (btuF; Vng1369G) components. Mutations in the Vng1370G, Vng1371Gm, and Vng1369G genes were epistatic, consistent with the hypothesis that their products work together to accomplish the same function. Extracts ofbtuFmutant strains grown in the presence of cobalamin did not contain any cobalamin molecules detectable by a sensitive bioassay, whereasbtuCDmutant strain extracts did. The data are consistent with the hypothesis that the BtuF protein is exported to the extracellular side of the cell membrane, where it can bind cobalamin in the absence of BtuC and BtuD. Our data also provide evidence for the regulation of corrinoid transport and biosynthesis.Halobacteriumsynthesized cobalamin in a chemically defined medium lacking corrinoid precursors. To the best of our knowledge, this is the first genetic analysis of an archaeal corrinoid transport system.
Adaptation to Disruption of the Electron Transfer Pathway for Fe(III) Reduction in
Geobacter sulfurreducens
Authors: Leang Ching , Adams L. A. , Chin K.-J. , Nevin K. P. , Methé B. A. , Webster J. , Sharma M. L. , Lovley D. R.
Published: August 2005

Previous studies demonstrated that an outer membrane
c
-type cytochrome, OmcB, was involved in Fe(III) reduction in
Geobacter sulfurreducens
. An OmcB-deficient mutant was greatly impaired in its ability to reduce both soluble and insoluble Fe(III). Reintroducing
omcB
restored the capacity for Fe(III) reduction at a level proportional to the level of OmcB production. Here, we report that the OmcB-deficient mutant gradually adapted to grow on soluble Fe(III) but not insoluble Fe(III). The adapted OmcB-deficient mutant reduced soluble Fe(III) at a rate comparable to that of the wild type, but the cell yield of the mutant was only ca. 60% of that of the wild type under steady-state culturing conditions. Analysis of proteins and transcript levels demonstrated that expression of several membrane-associated cytochromes was higher in the adapted mutant than in the wild type. Further comparison of transcript levels during steady-state growth on Fe(III) citrate with a whole-genome DNA microarray revealed a significant shift in gene expression in an apparent attempt to adapt metabolism to the impaired electron transport to Fe(III). These results demonstrate that, although there are many other membrane-bound
c
-type cytochromes in
G. sulfurreducens
, increased expression of these cytochromes cannot completely compensate for the loss of OmcB. The concept that outer membrane cytochromes are promiscuous reductases that are interchangeable in function appears to be incorrect. Furthermore, the results indicate that there may be different mechanisms for electron transfer to soluble Fe(III) and insoluble Fe(III) oxides in
G. sulfurreducens
, which emphasizes the importance of studying electron transport to the environmentally relevant Fe(III) oxides.
E1 Enzyme of the Pyruvate Dehydrogenase Complex in
Corynebacterium glutamicum
: Molecular Analysis of the Gene and Phylogenetic Aspects
Authors: Schreiner Mark E. , Fiur Diana , Holátko Jiří , Pátek Miroslav , Eikmanns Bernhard J.
Published: August 2005

The E1p enzyme is an essential part of the pyruvate dehydrogenase complex (PDHC) and catalyzes the oxidative decarboxylation of pyruvate with concomitant acetylation of the E2p enzyme within the complex. We analyzed the
Corynebacterium glutamicum aceE
gene, encoding the E1p enzyme, and constructed and characterized an E1p-deficient mutant. Sequence analysis of the
C. glutamicum aceE
gene and adjacent regions revealed that
aceE
is not flanked by genes encoding other enzymes of the PDHC. Transcriptional analysis revealed that
aceE
from
C. glutamicum
is monocistronic and that its transcription is initiated 121 nucleotides upstream of the translational start site. Inactivation of the chromosomal
aceE
gene led to the inability to grow on glucose and to the absence of PDHC and E1p activities, indicating that only a single E1p enzyme is present in
C. glutamicum
and that the PDHC is essential for the growth of this organism on carbohydrate substrates. Surprisingly, the E1p enzyme of
C. glutamicum
showed up to 51% identity to homodimeric E1p proteins from gram-negative bacteria but no similarity to E1 α- or β-subunits of heterotetrameric E1p enzymes which are generally assumed to be typical for gram-positives. To investigate the distribution of E1p enzymes in bacteria, we compiled and analyzed the phylogeny of 46 homodimeric E1p proteins and of 58 α-subunits of heterotetrameric E1p proteins deposited in public databases. The results revealed that the distribution of homodimeric and heterotetrameric E1p subunits in bacteria is not in accordance with the rRNA-based phylogeny of bacteria and is more heterogeneous than previously assumed.
Heat Shock Response ofArchaeoglobus fulgidus
Authors: Rohlin Lars , Trent Jonathan D. , Salmon Kirsty , Kim Unmi , Gunsalus Robert P. , Liao James C.
Published: August 2005

The heat shock response of the hyperthermophilic archaeonArchaeoglobus fulgidusstrain VC-16 was studied using whole-genome microarrays. On the basis of the resulting expression profiles, approximately 350 of the 2,410 open reading frames (ORFs) (ca. 14%) exhibited increased or decreased transcript abundance. These span a range of cell functions, including energy production, amino acid metabolism, and signal transduction, where the majority are uncharacterized. One ORF called AF1298 was identified that contains a putative helix-turn-helix DNA binding motif. The gene product, HSR1, was expressed and purified fromEscherichia coliand was used to characterize specific DNA recognition regions upstream of twoA. fulgidusgenes, AF1298 and AF1971. The results indicate that AF1298 is autoregulated and is part of an operon with two downstream genes that encode a small heat shock protein, Hsp20, and cdc48, an AAA+ATPase. The DNase I footprints using HSR1 suggest the presence of acis-binding motif upstream of AF1298 consisting of CTAAC-N5-GTTAG. Since AF1298 is negatively regulated in response to heat shock and encodes a protein only distantly related to the N-terminal DNA binding domain of Phr ofPyrococcus furiosus, these results suggest that HSR1 and Phr may belong to an evolutionarily diverse protein family involved in heat shock regulation in hyperthermophilic and mesophilicArchaeaorganisms.
Gene Organization and Transcriptional Analysis of thetprJ,tprI,tprG, andtprFLoci inTreponema pallidumStrains Nichols and Sea 81-4
Authors: Giacani Lorenzo , Hevner Karin , Centurion-Lara Arturo
Published: August 2005

Thetprgene family ofTreponema pallidumsubsp.pallidum, the causative agent of syphilis, has recently become the focus of intensive investigation. TprF and TprI sequences are highly conserved among different isolates and are the targets of strong humoral and cellular immune responses of the host, and immunization with a recombinant peptide from the amino terminus of these antigens has been shown to alter significantly lesion development following homologous challenge. This indicates that these antigens are expressed during infection and strongly suggests a key functionality.tprFandtprIare located immediately downstream of thetprGandtprJgenes, respectively, separated by very short intergenic spacers (55 nucleotides forG-Fand 56 nucleotides forJ-I). Preliminary analysis using gene-specific primers failed to amplifytprJin the Sea 81-4 isolate. In this study, sequence and transcriptional analysis of these loci showed a similar gene organization in the Nichols and Sea 81-4 strains, a complex pattern of transcription, and the presence of G homopolymeric repeats of variable lengths upstream of thetprF,tprI,tprG, andtprJtranscriptional start sites. However, distinctive features were also identified in the Sea 81-4 isolate, including atprG-like open reading frame in thetprJlocus, a frameshift and a premature termination in thetprGcoding sequence, a longertprG-tprFintergenic spacer, and absence of cotranscription of thetprG-tprFgenes.
The Toxin-Antitoxin System of the Streptococcal Plasmid pSM19035
Authors: Zielenkiewicz Urszula , Cegłowski Piotr
Published: August 2005

pSM19035 of the pathogenic bacterium
Streptococcus pyogenes
is a low-copy-number plasmid carrying erythromycin resistance, stably maintained in a broad range of gram-positive bacteria. We show here that the ω
-ε-ζ
operon of this plasmid constitutes a novel proteic plasmid addiction system in which the ε and ζ genes encode an antitoxin and toxin, respectively, while ω plays an autoregulatory function. Expression of toxin Zeta is bactericidal for the gram-positive
Bacillus subtilis
and bacteriostatic for the gram-negative
Escherichia coli
. The toxic effects of ζ gene expression in both bacterial species are counteracted by proper expression of ε. The ε
-ζ
toxin-antitoxin cassette stabilizes plasmids in
E. coli
less efficiently than in
B. subtilis
.
Discordant 16S and 23S rRNA Gene Phylogenies for the Genus
Helicobacter
: Implications for Phylogenetic Inference and Systematics
Authors: Dewhirst Floyd E. , Shen Zeli , Scimeca Michael S. , Stokes Lauren N. , Boumenna Tahani , Chen Tsute , Paster Bruce J. , Fox James G.
Published: August 2005

Analysis of 16S rRNA gene sequences has become the primary method for determining prokaryotic phylogeny. Phylogeny is currently the basis for prokaryotic systematics. Therefore, the validity of 16S rRNA gene-based phylogenetic analyses is of fundamental importance for prokaryotic systematics. Discrepancies between 16S rRNA gene analyses and DNA-DNA hybridization and phenotypic analyses have been noted in the genus
Helicobacter
. To clarify these discrepancies, we sequenced the 23S rRNA genes for 55 helicobacter strains representing 41 taxa (>2,700 bases per sequence). Phylogenetic-tree construction using neighbor-joining, parsimony, and maximum likelihood methods for 23S rRNA gene sequence data yielded stable trees which were consistent with other phenotypic and genotypic methods. The 16S rRNA gene sequence-derived trees were discordant with the 23S rRNA gene trees and other data. Discrepant 16S rRNA gene sequence data for the helicobacters are consistent with the horizontal transfer of 16S rRNA gene fragments and the creation of mosaic molecules with loss of phylogenetic information. These results suggest that taxonomic decisions must be supported by other phylogenetically informative macromolecules, such as the 23S rRNA gene, when 16S rRNA gene-derived phylogeny is discordant with other credible phenotypic and genotypic methods. This study found
Wolinella succinogenes
to branch with the unsheathed-flagellum cluster of helicobacters by 23S rRNA gene analyses and whole-genome comparisons. This study also found intervening sequences (IVSs) in the 23S rRNA genes of strains of 12
Helicobacter
species. IVSs were found in helices 10, 25, and 45, as well as between helices 31′ and 27′. Simultaneous insertion of IVSs at three sites was found in
H. mesocricetorum.
Biodiversity-Based Identification and Functional Characterization of the Mannose-Specific Adhesin ofLactobacillus plantarum
Authors: Pretzer Gabriele , Snel Johannes , Molenaar Douwe , Wiersma Anne , Bron Peter A. , Lambert Jolanda , de Vos Willem M. , van der Meer Roelof , Smits Mari A. , Kleerebezem Michiel
Published: August 2005

Lactobacillus plantarumis a frequently encountered inhabitant of the human intestinal tract, and some strains are marketed as probiotics. Their ability to adhere to mannose residues is a potentially interesting characteristic with regard to proposed probiotic features such as colonization of the intestinal surface and competitive exclusion of pathogens. In this study, the variable capacity of 14L. plantarumstrains to agglutinateSaccharomyces cerevisiaein a mannose-specific manner was determined and subsequently correlated with anL. plantarumWCFS1-based genome-wide genotype database. This led to the identification of four candidate mannose adhesin-encoding genes. Two genes primarily predicted to code for sortase-dependent cell surface proteins displayed a complete gene-trait match. Their involvement in mannose adhesion was corroborated by the finding that a sortase (srtA) mutant ofL. plantarumWCFS1 lost the capacity to agglutinateS. cerevisiae. The postulated role of these two candidate genes was investigated by gene-specific deletion and overexpression inL. plantarumWCFS1. Subsequent evaluation of the mannose adhesion capacity of the resulting mutant strains showed that inactivation of one candidate gene (lp_0373) did not affect mannose adhesion properties. In contrast, deletion of the other gene (lp_1229) resulted in a complete loss of yeast agglutination ability, while its overexpression quantitatively enhanced this phenotype. Therefore, this gene was designated to encode the mannose-specific adhesin (Msa; gene name,msa) ofL. plantarum. Domain homology analysis of the predicted 1,000-residue Msa protein identified known carbohydrate-binding domains, further supporting its role as a mannose adhesin that is likely to be involved in the interaction ofL. plantarumwith its host in the intestinal tract.
Characterization of the Genome Composition of
Bartonella koehlerae
by Microarray Comparative Genomic Hybridization Profiling
Authors: Lindroos Hillevi L. , Mira Alex , Repsilber Dirk , Vinnere Olga , Näslund Kristina , Dehio Michaela , Dehio Christoph , Andersson Siv G. E.
Published: August 2005

Bartonella henselae
is present in a wide range of wild and domestic feline hosts and causes cat-scratch disease and bacillary angiomatosis in humans. We have estimated here the gene content of
Bartonella koehlerae
, a novel species isolated from cats that was recently identified as an agent of human endocarditis. The investigation was accomplished by comparative genomic hybridization (CGH) to a microarray constructed from the sequenced 1.93-Mb genome of
B. henselae
. Control hybridizations of labeled DNA from the human pathogen
Bartonella quintana
with a reduced genome of 1.58 Mb were performed to evaluate the accuracy of the array for genes with known levels of sequence divergence. Genome size estimates of
B. koehlerae
by pulsed-field gel electrophoresis matched that calculated by the CGH, indicating a genome of 1.7 to 1.8 Mb with few unique genes. As in
B. quintana
, sequences in the prophage and the genomic islands were reported absent in
B. koehlerae
. In addition, sequence variability was recorded in the chromosome II-like region, where
B. koehlerae
showed an intermediate retention pattern of both coding and noncoding sequences. Although most of the genes missing in
B. koehlerae
are also absent from
B. quintana
, its phylogenetic placement near
B. henselae
suggests independent deletion events, indicating that host specificity is not solely attributed to genes in the genomic islands. Rather, the results underscore the instability of the genomic islands even within bacterial populations adapted to the same host-vector system, as in the case of
B. henselae
and
B. koehlerae
.
Domain Structure of HrpE, the Hrp Pilus Subunit of
Xanthomonas campestris
pv. vesicatoria
Authors: Weber Ernst , Koebnik Ralf
Published: August 2005

The plant-pathogenic bacterium
Xanthomonas campestris
pv. vesicatoria possesses a type III secretion (TTS) system necessary for pathogenicity in susceptible hosts and induction of the hypersensitive response in resistant plants. This specialized protein transport system is encoded by a 23-kb
hrp
(hypersensitive response and pathogenicity) gene cluster.
X. campestris
pv. vesicatoria produces filamentous structures, Hrp pili, at the cell surface under
hrp
-inducing conditions. The Hrp pilus acts as a cell surface appendage of the TTS system and serves as a conduit for the transfer of bacterial effector proteins into the plant cell cytosol. The major pilus component, the HrpE pilin, is unique to xanthomonads and is encoded within the
hrp
gene cluster. In this study, functional domains of HrpE were mapped by linker-scanning mutagenesis and by reporter protein fusions to an N-terminally truncated avirulence protein (AvrBs3Δ2). Thirteen five-amino-acid peptide insertion mutants were obtained and could be grouped into six phenotypic classes. Three permissive mutations were mapped in the N-terminal half of HrpE, which is weakly conserved within the HrpE protein family. Four dominant-negative peptide insertions in the strongly conserved C-terminal region suggest that this domain is critical for oligomerization of the pilus subunits. Reporter protein fusions revealed that the N-terminal 17 amino acid residues act as an efficient TTS signal. From these results, we postulate a three-domain structure of HrpE with an N-terminal secretion signal, a surface-exposed variable region of the N-terminal half, and a C-terminal polymerization domain. Comparisons with a mutant study of HrpA, the Hrp pilin from
Pseudomonas syringae
pv. tomato DC3000, and hydrophobicity plot analyses of several nonhomologous Hrp pilins suggest a common architecture of Hrp pilins of different plant-pathogenic bacteria.
Presence of Multiple Sites Containing Polar Material in SphericalEscherichia coliCells That Lack MreB
Authors: Nilsen Trine , Yan Arthur W. , Gale Gregory , Goldberg Marcia B.
Published: August 2005

In rod-shaped bacteria, certain proteins are specifically localized to the cell poles. The nature of the positional information that leads to the proper localization of these proteins is unclear. In a screen for factors required for the localization of theShigellasp. actin assembly protein IcsA to the bacterial pole, a mutant carrying a transposon insertion inmreBdisplayed altered targeting of IcsA. The phenotype of cells containing a transposon insertion inmreBwas indistinguishable from that of cells containing a nonpolar mutation inmreBor that of wild-type cells treated with the MreB inhibitor A22. In cells lacking MreB, a green fluorescent protein (GFP) fusion to a cytoplasmic derivative of IcsA localized to multiple sites. Secreted full-length native IcsA was present in multiple faint patches on the surfaces of these cells in a pattern similar to that seen for the cytoplasmic IcsA-GFP fusion. EpsM, the polarVibrio choleraeinner membrane protein, also localized to multiple sites inmreBcells and colocalized with IcsA, indicating that localization to multiple sites is not unique to IcsA. Our results are consistent with the requirement, either direct or indirect, for MreB in the restriction of certain polar material to defined sites within the cell and, in the absence of MreB, with the formation of ectopic sites containing polar material.