bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genotypical Differences in Aluminum Resistance of Maize Are Expressed in the Distal Part of the Transition Zone. Is Reduced Basipetal Auxin Flow Involved in Inhibition of Root Elongation by Aluminum?
Authors: Kollmeier Malte , Felle Hubert H. , Horst Walter J. 
Published: July 2002

Abstract
Short-term Al treatment (90 μm Al at pH 4.5 for 1 h) of the distal transition zone (DTZ; 1–2 mm from the root tip), which does not contribute significantly to root elongation, inhibited root elongation in the main elongation zone (EZ; 2.5–5 mm from the root tip) to the same extent as treatment of the entire maize (Zea mays) root apex. Application of Al to the EZ had no effect on root elongation. Higher genotypical resistance to Al applied to the entire root apex, and specifically to the DTZ, was expressed by less inhibition of root elongation, Al accumulation, and Al-induced callose formation, primarily in the DTZ. A characteristic pH profile along the surface of the root apex with a maximum of pH 5.3 in the DTZ was demonstrated. Al application induced a substantial flattening of the pH profile moreso in the Al-sensitive than in the Al-resistant cultivar. Application of indole-3-acetic acid to the EZ but not to the meristematic zone significantly alleviated the inhibition of root elongation induced by the application of Al to the DTZ. Basipetal transport of exogenously applied [3H]indole-3-acetic acid to the meristematic zone was significantly inhibited by Al application to the DTZ in the Al-sensitive maize cv Lixis. Our results provide evidence that the primary mechanisms of genotypical differences in Al resistance are located within the DTZ, and suggest a signaling pathway in the root apex mediating the Al signal between the DTZ and the EZ through basipetal auxin transport.
Comparative Analysis of Expressed Sequences in Phytophthora sojae
Authors: Qutob Dinah , Hraber Peter T. , Sobral Bruno W.S. , Gijzen Mark 
Published: July 2002

Abstract
Phytophthora sojae (Kaufmann and Gerdemann) is an oomycete that causes stem and root rot on soybean (Glycine max L. Merr) plants. We have constructed three cDNA libraries using mRNA isolated from axenically grown mycelium and zoospores and from tissue isolated from plant hypocotyls 48 h after inoculation with zoospores. A total of 3,035 expressed sequence tags (ESTs) were generated from the three cDNA libraries, representing an estimated 2,189 cDNA transcripts. The ESTs were classified according to putative function based on similarity to known proteins, and were analyzed for redundancy within and among the three source libraries. Distinct expression patterns were observed for each library. By analysis of the percentage G+C content of the ESTs, we estimate that two-thirds of the ESTs from the infected plant library are derived from P. sojae cDNA transcripts. The ESTs originating from this study were also compared with a collection of Phytophthora infestans ESTs and with all other non-human ESTs to assess the similarity of the P. sojae sequences to existing EST data. This collection of cDNA libraries, ESTs, and accompanying annotation will provide a new resource for studies on oomycetes and on soybean responses to pathogen challenge.
Aluminum Accumulation at Nuclei of Cells in the Root Tip. Fluorescence Detection Using Lumogallion and Confocal Laser Scanning Microscopy
Authors: Silva Ivo R. , Smyth T. Jot , Moxley Dana F. , Carter Thomas E. , Allen Nina S. , Rufty Thomas W. 
Published: July 2002

Abstract
The mechanistic basis for Al toxicity effects on root growth is still a matter of speculation, but it almost certainly involves decreased cell division at the root apex. In this series of experiments, we attempt to determine whether Al enters meristematic cells and binds to nuclei when roots are exposed to a low Al3+ activity in solution. The methodology involved the use of the Al-sensitive stain lumogallion (3-[2,4 dihydroxyphenylazo]-2-hydroxy-5-chlorobenzene sulfonic acid), the DNA stain 4′,6-diamino-phenylindole, and confocal laser scanning microscopy. Soybean (Glycine max L. Merr.) cv Young (Al-sensitive) and PI 416937 (Al-tolerant) genotypes were exposed to 1.45 μm Al3+ for periods ranging from 30 min to 72 h, and then washed with 10 mm citrate to remove apoplastic Al. Fluorescence images show that within 30 min Al entered cells of the sensitive genotype and accumulated at nuclei in the meristematic region of the root tip. Substantial Al also was present at the cell periphery. The images indicated that the Al-tolerant genotype accumulated lower amounts of Al in meristematic and differentiating cells of the root tip and their cell walls. Collectively, the results support an important role for exclusion in Al tolerance.
Characterization of Auxin Conjugates in Arabidopsis. Low Steady-State Levels of Indole-3-Acetyl-Aspartate, Indole-3-Acetyl-Glutamate, and Indole-3-Acetyl-Glucose
Authors: Tam Yuen Yee , Epstein Ephraim , Normanly Jennifer 
Published: July 2002

Abstract
Amide-linked indole-3-acetic acid (IAA) conjugates constitute approximately 90% of the IAA pool in the dicot Arabidopsis, whereas ester-linked conjugates and free IAA account for approximately 10% and 1%, respectively when whole seedlings are measured. We show here that IAA-aspartate Asp, IAA-glutamate (Glu), and IAA-glucose (Glc) are present at low levels in Arabidopsis. Nine-day-old wild-type Arabidopsis seedlings yielded 17.4 ± 4.6 ng g−1fresh weight IAA-Asp and 3.5 ± 1.6 ng g−1 fresh weight IAA-Glu, and IAA-Glc was present at 7 to 17 ng g−1fresh weight in 12-d-old wild-type seedlings. Total IAA content in 9-d-old Arabidopsis seedlings was 1,200 ± 178 ng g−1fresh weight, so these three IAA conjugates together made up only 3% of the conjugate pool throughout the whole plant. We detected less than wild-type levels of IAA-Asp and IAA-Glu (7.8 ± 0.4 ng g−1 fresh weight and 1.8 ± 0.3 ng g−1fresh weight, respectively) in an Arabidopsis mutant that accumulates conjugated IAA. Our results are consistent with IAA-Asp, IAA-Glu, and IAA-Glc being either minor, transient, or specifically localized IAA metabolites under normal growth conditions and bring into question the physiological relevance of IAA-Asp accumulation in response to high concentrations of exogenous IAA.
The Mechanical Properties and Molecular Dynamics of Plant Cell Wall Polysaccharides Studied by Fourier-Transform Infrared Spectroscopy
Authors: Wilson Reginald H. , Smith Andrew C. , Kačuráková Marta , Saunders Paul K. , Wellner Nikolaus , Waldron Keith W. 
Published: July 2002

Abstract
Polarized one- and two-dimensional infrared spectra were obtained from the epidermis of onion (Allium cepa) under hydrated and mechanically stressed conditions. By Fourier-transform infrared microspectroscopy, the orientation of macromolecules in single cell walls was determined. Cellulose and pectin exhibited little orientation in native epidermal cell walls, but when a mechanical stress was placed on the tissue these molecules showed distinct reorientation as the cells were elongated. When the stress was removed the tissue recovered slightly, but a relatively large plastic deformation remained. The plastic deformation was confirmed in microscopic images by retention of some elongation of cells within the tissue and by residual molecular orientation in the infrared spectra of the cell wall. Two-dimensional infrared spectroscopy was used to determine the nature of the interaction between the polysaccharide networks during deformation. The results provide evidence that cellulose and xyloglucan associate while pectin creates an independent network that exhibits different reorientation rates in the wet onion cell walls. The pectin chains respond faster to oscillation than the more rigid cellulose.
How Alfalfa Root Hairs Discriminate between Nod Factors and Oligochitin Elicitors
Authors: Felle Hubert H. , Kondorosi Éva , Kondorosi Ádam , Schultze Michael 
Published: July 2002

Abstract
Using ion-selective microelectrodes, the problem of how signals coming from symbiotic partners or from potential microbial intruders are distinguished was investigated on root hairs of alfalfa (Medicago sativa). The Nod factor, NodRm-IV(C16:2,S), was used to trigger the symbiotic signal and (GlcNAc)8 was selected from (GlcNAc)4-8, to elicit defense-related reactions. To both compounds, root hairs responded with initial transient depolarizations and alkalinizations, which were followed by a hyperpolarization and external acidification in the presence of (GlcNAc)8. We propose that alfalfa recognizes tetrameric Nod factors and N-acetylchitooligosaccharides (n = 4–8) with separate perception sites: (a) (GlcNAc)4 and (GlcNAc)6 reduced the depolarization response to (GlcNAc)8, but not to NodRm-IV(C16:2,S); and (b) depolarization and external alkalization were enhanced when NodRm-IV(C16:2,S) and (GlcNAc)8 were added jointly without preincubation. We suggest further that changes in cytosolic pH and Ca2+ are key events in the transduction, as well as in the discrimination of signals leading to symbiotic responses or defense-related reactions. To (GlcNAc)8, cells responded with a cytosolic acidification, and they responded to NodRm-IV(C16:2,S) with a sustained alkalinization. When both agents were added jointly, the cytosol first alkalized and then acidified. (GlcNAc)8 and NodRm-IV(C16:2,S) transiently increased cytosolic Ca2+ activity, whereby the response to (GlcNAc)8 exceeded the one to NodRm-IV(C16:2,S) by at least a factor of two.
The Effect of Exogenous Abscisic Acid on Stomatal Development, Stomatal Mechanics, and Leaf Gas Exchange inTradescantia virginiana
Authors: Franks Peter J. , Farquhar Graham D. 
Published: July 2002

AbstractGas exchange parameters and stomatal physical properties were measured in Tradescantia virginiana plants grown under well-watered conditions and treated daily with either distilled water (control) or 3.0 mm abscisic acid (ABA). Photosynthetic capacity (CO2 assimilation rate for any given leaf intercellular CO2 concentration [c i]) and relative stomatal sensitivity to leaf-to-air vapor-pressure difference were unaffected by the ABA treatment. However, at an ambient CO2 concentration (c a) of 350 μmol mol−1, ABA-treated plants operated with significantly lowerc i. ABA-treated plants had significantly smaller stomata and higher stomatal density in their lower epidermis. Stomatal aperture versus guard cell pressure (P g) characteristics measured with a cell pressure probe showed that although the form of the relationship was similar in control and ABA-treated plants, stomata of ABA-treated plants exhibited more complete closure atP g = 0 MPa and less than half the aperture of stomata in control plants at any givenP g. Scaling from stomatal aperture versusP g to stomatal conductance versusP g showed that plants grown under ABA treatment would have had significantly lower maximum stomatal conductance and would have operated with lower stomatal conductance for any given guard cell turgor. This is consistent with the observation of lower c i/c a in ABA-treated plants with a c a of 350 μmol mol−1. It is proposed that the ABA-induced changes in stomatal mechanics and stomatal conductance versusP g characteristics constitute an improvement in water-use efficiency that may be invoked under prolonged drought conditions.
Silencing on the Spot. Induction and Suppression of RNA Silencing in the Agrobacterium-Mediated Transient Expression System
Authors: Johansen Lisa K. , Carrington James C. 
Published: July 2002

Abstract
The Agrobacterium-mediated transient expression assay in intact tissues has emerged as a rapid and useful method to analyze genes and gene products in plants. In many cases, high levels of active protein can be produced without the need to produce transgenic plants. In this study, a series of tools were developed to enable strong or weak induction of RNA silencing and to suppress RNA silencing in the absence of stable transgenes. Transient delivery of a gene directing production of a double-stranded green fluorescent protein (GFP) transcript rapidly induced RNA silencing of a codelivered GFP reporter gene, effectively preventing accumulation of GFP protein and mRNA. RNA silencing triggered by the strong dsGFP inducer was partially inhibited by the tobacco etch virus silencing suppressor, P1/HC-Pro. In the absence of the strong double-stranded GFP inducer, the functional GFP gene served as a weak RNA silencing inducer in the transient assay, severely limiting accumulation of the GFP mRNA over time. The weak silencing induced by the GFP gene was suppressed by P1/HC-Pro. These results indicate RNA silencing can be triggered by a variety of inducers and analyzed entirely using transient gene delivery systems. They also indicate that RNA silencing may be a significant limitation to expression of genes in theAgrobacterium-mediated transient assay but that this limitation can be overcome by using RNA silencing suppressors.
Characterization of the N‐terminal repeat domain of Escherichia coli ClpA—A class I Clp/HSP100 ATPase
Authors: Lo John H. , Baker Tania A. , Sauer Robert T. 
Published: July 2002

AbstractThe ClpA, ClpB, and ClpC subfamilies of the Clp/HSP100 ATPases contain a conserved N‐terminal region of ∼150 residues that consists of two approximate sequence repeats. This sequence from the Escherichia coli ClpA enzyme is shown to encode an independent structural domain (the R domain) that is monomeric and ∼40% α‐helical. A ClpA fragment lacking the R domain showed ATP‐dependent oligomerization, protein‐stimulated ATPase activity, and the ability to complex with the ClpP peptidase and mediate degradation of peptide and protein substrates, including casein and ssrA‐tagged proteins. Compared with the activities of the wild‐type ClpA, however, those of the ClpA fragment missing the R domain were reduced. These results indicate that the R domain is not required for the basic recognition, unfolding, and translocation functions that allow ClpA‐ClpP to degrade some protein substrates, but they suggest that it may play a role in modulating these activities.
Development of a cytokine analog with enhanced stability using computational ultrahigh throughput screening
Authors: Luo Peizhi , Hayes Robert J. , Chan Cheryl , Stark Diane M. , Hwang Marian Y. , Jacinto Jonathan M. , Juvvadi Padmaja , Chung Helen S. , Kundu Anirban , Ary Marie L. , Dahiyat Bassil I. 
Published: July 2002

AbstractGranulocyte‐colony stimulating factor (G‐CSF) is used worldwide to prevent neutropenia caused by high‐dose chemotherapy. It has limited stability, strict formulation and storage requirements, and because of poor oral absorption must be administered by injection (typically daily). Thus, there is significant interest in developing analogs with improved pharmacological properties. We used our ultrahigh throughput computational screening method to improve the physicochemical characteristics of G‐CSF. Improving these properties can make a molecule more robust, enhance its shelf life, or make it more amenable to alternate delivery systems and formulations. It can also affect clinically important features such as pharmacokinetics. Residues in the buried core were selected for optimization to minimize changes to the surface, thereby maintaining the active site and limiting the designed protein's potential for antigenicity. Using a structure that was homology modeled from bovine G‐CSF, core designs of 25–34 residues were completed, corresponding to 1021–1028 sequences screened. The optimal sequence from each design was selected for biophysical characterization and experimental testing; each had 10–14 mutations. The designed proteins showed enhanced thermal stabilities of up to 13°C, displayed five‐to 10‐fold improvements in shelf life, and were biologically active in cell proliferation assays and in a neutropenic mouse model. Pharmacokinetic studies in monkeys showed that subcutaneous injection of the designed analogs results in greater systemic exposure, probably attributable to improved absorption from the subcutaneous compartment. These results show that our computational method can be used to develop improved pharmaceuticals and illustrate its utility as a powerful protein design tool.
Substrate Specificities of MexAB-OprM, MexCD-OprJ, and MexXY-OprM Efflux Pumps in
Pseudomonas aeruginosa
Authors: Masuda Nobuhisa , Sakagawa Eiko , Ohya Satoshi , Gotoh Naomasa , Tsujimoto Hideto , Nishino Takeshi 
Published: July 2002

ABSTRACT

To find the exact substrate specificities of three species of tripartite efflux systems of
Pseudomonas aeruginosa
, MexAB-OprM, MexCD-OprJ, and MexXY-OprM, we constructed a series of isogenic mutants, each of which constitutively overproduced one of the three efflux systems and lacked the other two, and their isogenic mutants, which lacked all these systems. Comparison of the susceptibilities of the constructed mutants to 52 antimicrobial agents belonging to various groups suggested the following substrate specificities. All of the efflux systems extrude a wide variety of antimicrobial agent groups, i.e., quinolones, macrolides, tetracyclines, lincomycin, chloramphenicol, most penicillins (all but carbenicillin and sulbenicillin), most cephems (all but cefsulodin and ceftazidime), meropenem, and S-4661, but none of them extrude polymyxin B or imipenem. Extrusion of aminoglycosides is specific to MexXY-OprM, and extrusion of a group of the β-lactams, i.e., carbenicillin, sulbenicillin, ceftazidime, moxalactam, and aztreonam, is specific to MexAB-OprM. Moreover, MexAB-OprM and MexCD-OprJ extrude novobiocin, cefsulodin, and flomoxef, while MexXY-OprM does not. These substrate specificities are distinct from those reported previously.
Quinupristin-Dalfopristin Resistance among Gram-Positive Bacteria in Taiwan
Authors: Luh Kwen-Tay , Hsueh Po-Ren , Teng Lee-Jene , Pan Hui-Ju , Chen Yu-Chi , Lu Jang-Jih , Wu Jiunn-Jong , Ho Shen-Wu 
Published: July 2002

ABSTRACT

To understand quinupristin-dalfopristin resistance among clinical isolates of gram-positive bacteria in Taiwan, where this agent is not yet available for clinical use, we evaluated 1,287 nonduplicate isolates recovered from January 1996 to December 1999 for in vitro susceptibility to quinupristin-dalfopristin and other newer antimicrobial agents. All methicillin-susceptible
Staphylococcus aureus
(MSSA) isolates were susceptible to quinupristin-dalfopristin. High rates of nonsusceptibility to quinupristin-dalfopristin (MICs, ≥2 μg/ml) were demonstrated for the following organisms: methicillin-resistant
S. aureus
(MRSA) (31%), coagulase-negative staphylococci (CoNS) (16%),
Streptococcus pneumoniae
(8%), viridans group streptococci (51%), vancomycin-susceptible enterococci (85%), vancomycin-resistant
Enterococcus faecalis
(100%), vancomycin-resistant
Enterococcus faecium
(66%),
Leuconostoc
spp. (100%),
Lactobacillus
spp. (50%), and
Pediococcus
spp. (87%). All isolates of MSSA, MRSA,
S. pneumoniae
, and viridans group streptococci were susceptible to vancomycin and teicoplanin. The rates of nonsusceptibility to vancomycin and teicoplanin were 5 and 7%, respectively, for CoNS, ranging from 12 and 18% for
S. simulans
to 0 and 0% for
S. cohnii
and
S. auricularis
. Moxifloxacin and trovafloxacin had good activities against these isolates except for ciprofloxacin-resistant vancomycin-resistant enterococci and methicillin-resistant staphylococci. In Taiwan, virginiamycin has been used in animal husbandry for more than 20 years, which may contribute to the high rates of quinupristin-dalfopristin resistance.
Syringomycin E Inhibition of
Saccharomyces cerevisiae
: Requirement for Biosynthesis of Sphingolipids with Very-Long-Chain Fatty Acids and Mannose- and Phosphoinositol-Containing Head Groups
Authors: Stock Stephen D. , Hama Hiroko , Radding Jeffrey A. , Young Debra A. , Takemoto Jon Y. 
Published: July 2002

ABSTRACT

Syringomycin E is an antifungal cyclic lipodepsinonapeptide that inhibits the growth of
Saccharomyces cerevisiae
by interaction with the plasma membrane. A screen conducted to find the yeast genes necessary for its fungicidal action identified two novel syringomycin E response genes,
SYR3
and
SYR4
. A
syr3
mutant allele was complemented by
ELO2
and
ELO3
. These genes encode enzymes that catalyze the elongation of sphingolipid very long chain fatty acids. Tetrad analysis showed that
SYR3
was
ELO2
. Strains with deletions of
SYR3/ELO2
and
ELO3
were resistant to syringomycin E, and lipid analyses of both mutants revealed shortened fatty acid chains and lower levels of sphingolipids.
SYR4
was identified by Tn
5
inactivation of genomic library plasmids that complemented a
syr4
mutant allele.
SYR4
was found to be identical to
IPT1
, which encodes the terminal sphingolipid biosynthetic enzyme, mannosyl-diinositolphosphoryl-ceramide synthase. Deletion Δ
syr4/ipt1
strains were viable, were resistant to syringomycin E, did not produce mannosyl-diinositolphosphoryl-ceramide, and accumulated mannosyl-inositolphosphoryl-ceramide. Accumulation of mannosyl-inositolphosphoryl-ceramide was not responsible for resistance since a temperature-sensitive secretory pathway mutant (

sec14-3
ts

) accumulated this sphingolipid and was sensitive to syringomycin E. Finally, Δ
csg1/sur1
and Δ
csg2
strains defective in the transfer of mannose to inositolphosphoryl-ceramide were resistant to syringomycin E. These findings show that syringomycin E growth inhibition of yeast is promoted by the production of sphingolipids with fully elongated fatty acid chains and the mannosyl and terminal phosphorylinositol moieties of the polar head group.
Occurrence of a
Salmonella enterica
Serovar Typhimurium DT104-Like Antibiotic Resistance Gene Cluster Including the
floR
Gene in
S. enterica
Serovar Agona
Authors: Cloeckaert Axel , Sidi Boumedine Karim , Flaujac Geraldine , Imberechts Hein , D'Hooghe Inge , Chaslus-Dancla Elisabeth 
Published: July 2002

ABSTRACT

Recently a chromosomal locus possibly specific for
Salmonella enterica
serovar Typhimurium DT104 has been reported that contains a multiple antibiotic resistance gene cluster. Evidence is provided that
Salmonella enterica
serovar Agona strains isolated from poultry harbor a similar gene cluster including the newly described
floR
gene, conferring cross-resistance to chloramphenicol and florfenicol.