bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-Term Growth of Ginkgo with CO2 Enrichment Increases Leaf Ice Nucleation Temperatures and Limits Recovery of the Photosynthetic System from Freezing
Authors: Terry Andrew C. , Quick W. Paul , Beerling David J. 
Published: July 2002

Abstract
The importance of subzero temperature interactions with elevated CO2 on plant carbon metabolism has received rather little attention, despite their likely role in influencing future vegetation productivity and dynamics. Here we focused on the critical issues of CO2-enrichment effects on leaf-freezing temperatures, subsequent membrane damage, and recovery of the photosynthetic system. We show that growth in elevated CO2 (70 Pa) results in a substantial and significant (P &lt; 0.01) increase (up to 4°C) in the ice nucleation temperature of leaves of Maidenhair tree (Ginkgo biloba), which was observed consistently throughout the 1999 growing season relative to their ambient CO2 (35 Pa) counterparts. We suggest that increased sensitivity of leaves to ice damage after growth in elevated CO2 provides an explanation for increased photoinhibition observed in the field early and late in the growing season when low nighttime temperatures are experienced. This new mechanism is proposed in addition to the earlier postulated explanation for this phenomenon involving a reduction in the rate of triose-P utilization owing to a decrease in the rate of carbohydrate export from the leaf.
Aux/IAA Proteins Are Phosphorylated by Phytochrome in Vitro
Authors: Colón-Carmona Adán , Chen Donna L. , Yeh Kuo-Chen , Abel Steffen 
Published: July 2002

AbstractAuxin/indole-3-acetic acid (Aux/IAA) genes encode short-lived transcription factors that are induced as a primary response to the plant growth hormone IAA or auxin. Gain-of-function mutations in Arabidopsis genes,SHY2/IAA3, AXR3/IAA17, andAXR2/IAA7 cause pleiotropic phenotypes consistent with enhanced auxin responses, possibly by increasing Aux/IAA protein stability. Semidominant mutations shy2-1D,shy2-2, axr3-1, and axr2-1induce ectopic light responses in dark-grown seedlings. Because genetic studies suggest that the shy2-1D andshy2-2 mutations bypass phytochrome requirement for certain aspects of photomorphogenesis, we tested whether SHY2/IAA3 and related Aux/IAA proteins interact directly with phytochrome and whether they are substrates for its protein kinase activity. Here we show that recombinant Aux/IAA proteins from Arabidopsis and pea (Pisum sativum) interact in vitro with recombinant phytochrome A from oat (Avena sativa). We further show that recombinant SHY2/IAA3, AXR3/IAA17, IAA1, IAA9, and Ps-IAA4 are phosphorylated by recombinant oat phytochrome A in vitro. Deletion analysis of Ps-IAA4 indicates that phytochrome A phosphorylation occurs on the N-terminal half of the protein. Metabolic labeling and immunoprecipitation studies with affinity-purified antibodies to IAA3 demonstrate increased in vivo steady-state levels of mutant IAA3 in shy2-2 plants and phosphorylation of the SHY2-2 protein in vivo. Phytochrome-dependent phosphorylation of Aux/IAA proteins is proposed to provide one molecular mechanism for integrating auxin and light signaling in plant development.
Structures of ruthenium-modified Pseudomonas aeruginosa azurin and [Ru(2,2′-bipyridine)2(imidazole)2]SO4·10H2O
Authors: Faham Salem , Day Michael W. , Connick William B. , Crane Brian R. , Di Bilio Angel J. , Schaefer William P. , Rees Douglas C. , Gray Harry B. 
Published: July 2002

The crystal structure of Ru(2,2′-bipyridine)2(imidazole)(His83)azurin (RuAz) has been determined to 2.3 Å resolution by X-ray crystallography. The spectroscopic and thermodynamic properties of both the native protein and [Ru(2,2′-bipyridine)2(imidazole)2]2+ are maintained in the modified protein. Dark-green RuAz crystals grown from PEG 4000, LiNO3, CuCl2 and Tris buffer are monoclinic, belong to the space group C2 and have cell parameters a = 100.6, b = 35.4, c = 74.7 Å and β = 106.5°. In addition, [Ru(2,2′-bipyridine)2(imidazole)2]SO4·10H2O was synthesized, crystallized and structurally characterized by X-ray crystallography. Red–brown crystals of this complex are monoclinic, space group P21/n, unit-cell parameters a = 13.230 (2), b = 18.197 (4), c = 16.126 (4) Å, β = 108.65 (2)°. Stereochemical parameters for the refinement of Ru(2,2′-bipyridine)2(imidazole)(His83) were taken from the atomic coordinates of [Ru(2,2′-bipyridine)2(imidazole)2]2+. The structure of RuAz confirms that His83 is the only site of chemical modification and that the native azurin structure is not perturbed significantly by the ruthenium label.
Unusual evolutionary history of the tRNA splicing endonuclease EndA: Relationship to the LAGLIDADG and PD‐(D/E)XK deoxyribonucleases
Authors: Bujnicki Janusz M. , Rychlewski Leszek 
Published: July 2002

AbstractThe tRNA splicing endoribonuclease EndA from Methanococcus jannaschii is a homotetramer formed via heterologous interaction between the two pairs of homodimers. Each monomer consists of two α/β domains, the N‐terminal domain (NTD) and the C‐terminal domain (CTD) containing the RNase A‐like active site. Comparison of the EndA coordinates with the publicly available protein structure database revealed the similarity of both domains to site‐specific deoxyribonucleases: the NTD to the LAGLIDADG family and the CTD to the PD‐(D/E)XK family. Superposition of the NTD on the catalytic domain of LAGLIDADG homing endonucleases allowed a suggestion to be made about which amino acid residues of the tRNA splicing nuclease might participate in formation of a presumptive cryptic deoxyribonuclease active site. On the other hand, the CTD and PD‐(D/E)XK endonucleases, represented by restriction enzymes and a phage λ exonuclease, were shown to share extensive similarities of the structural framework, to which entirely different active sites might be attached in two alternative locations. These findings suggest that EndA evolved from a fusion protein with at least two distinct endonuclease activities: the ribonuclease, which made it an essential “antitoxin” for the cells whose RNA genes were interrupted by introns, and the deoxyribonuclease, which provided the means for homing‐like mobility. The residues of the noncatalytic CTDs from the positions corresponding to the catalytic side chains in PD‐(D/E)XK deoxyribonucleases map to the surface at the opposite side to the tRNA binding site, for which no function has been implicated. Many restriction enzymes from the PD‐(D/E)XK superfamily might have the potential to maintain an additional active or binding site at the face opposite the deoxyribonuclease active site, a property that can be utilized in protein engineering.
Solution structure of the DNA‐binding domain of the TyrR protein of Haemophilus influenzae
Authors: Wang Yunjun , Zhao Shimin , Somerville Ronald L. , Jardetzky Oleg 
Published: July 2002

AbstractThe TyrR protein of Haemophilus influenzae is a 36‐kD transcription factor whose major function is to control the expression of genes important in the biosynthesis and transport of aromatic amino acids. Using 1H and 15N NMR spectroscopy, we have determined the 3D solution structure of the TyrR C‐terminal DNA‐binding domain (DBD) containing residues from 258 to 318 (TyrR[258–318]). The NMR results show that this segment of TyrR consists of a potential hinge helix at its N terminus (residues 263–270) as well as three well‐defined α‐helices extending from residues 277–289 (HR‐2), 293–300 (HR‐1), and 304–314 (HR). Helix HR‐1 and HR fold in a typical helix–turn–helix (HTH) motif. The three helices and the hinge helix are tightly bound together by hydrophobic interaction and hydrogen bonds. Several hydrophilic residues whose side chains may directly interact with DNA are identified. A hydrophobic patch that may be part of the interaction surface between the domains of TyrR protein is also observed. Comparisons with the structures of other HTH DNA‐binding proteins reveal that in terms of the spatial orientation of the three helices, this protein most closely resembles the cap family.
A Sensitive Amphotericin B Immunoassay for Pharmacokinetic and Distribution Studies
Authors: Machard Sophie , Theodoro Frederic , Benech Henri , Grognet Jean-Marc , Ezan Eric 
Published: July 2002

ABSTRACT

Since currently used assays of amphotericin B (AMB) lack sensitivity or are not easily adaptable in all laboratories, we have developed an enzyme immunoassay for AMB in biological fluids and tissues. Antibodies to AMB were raised in rabbits after administration of an AMB-bovine serum albumin conjugate. The enzymatic tracer was obtained by coupling AMB via its amino group to acetylcholinesterase (EC
3.1.1.7
). These reagents were used for the development of a competitive immunoassay performed on microtitration plates. The limit of quantification was 100 pg/ml in plasma and 1 ng/g in tissues. The plasma assay was performed directly without extraction on a minimal volume of 0.1 ml. The intra- and interassay coefficients of variation were in the range of 5 to 17%, and the recoveries were 92 to 111% for AMB added to human plasma. The assay was applied to a pharmacokinetic study with mice given AMB intraperitoneally at the dose of 1 mg/kg. The drug distribution in selected compartments (plasma, liver, spleen, lung, and brain) was monitored until 72 h after administration. In conclusion, our assay is at least 100-fold more sensitive than previously described bioassays or chromatographic determinations of AMB and may be useful in studying the tissue pharmacokinetics of new AMB formulations and in drug monitoring in clinical situations.
In Vivo Antimalarial Activity of the Beta-Carboline Alkaloid Manzamine A
Authors: Ang Kenny K. H. , Holmes Michael J. , Higa Tatsuo , Hamann Mark T. , Kara Ursula A. K. 
Published: July 2002

ABSTRACT

Manzamine A, a β-carboline alkaloid present in several marine sponge species, inhibits the growth of the rodent malaria parasite
Plasmodium berghei
in vivo. More than 90% of the asexual erythrocytic stages of
P. berghei
were inhibited after a single intraperitoneal injection of manzamine A into infected mice. A remarkable aspect of manzamine A treatment is its ability to prolong the survival of highly parasitemic mice, with 40% recovery 60 days after a single injection. Oral administration of an oil suspension of manzamine A also produced significant reductions in parasitemia. The plasma manzamine A concentration peaked 4 h after injection and remained high even at 48 h. Morphological changes of
P. berghei
were observed 1 h after treatment of infected mice. (−)-8-Hydroxymanzamine A also displayed antimalarial activity, whereas manzamine F, a ketone analog of manzamine A, did not. Our results suggest that manzamine A and (−)-8-hydroxymanzamine A are promising new antimalarial agents.
Antileishmanial Activities of Aphidicolin and Its Semisynthetic Derivatives
Authors: Kayser O. , Kiderlen A. F. , Bertels S. , Siems K. 
Published: July 2002

ABSTRACT

Aphidicolin and a series of semisynthetic aphidicolan derivatives have been identified in in vitro tests as novel drugs with antiparasitic potential. All compounds have been tested against extracellular promastigotes of
Leishmania donovani
,
L. infantum
,
L. enriettii
, and
L. major
and against intracellular amastigotes of
L. donovani
in murine macrophages. The compounds showed antileishmanial activity at concentrations in the microgram range (50% effective concentration [EC
50
] = 0.02 to 1.83 μg/ml). The most active derivative (aphidicolin-17-glycinate hydrochloride) had EC
50
s of 0.2 μg/ml against extracellular and 0.02 μg/ml against intracellular
L. donovani
parasites. To validate the pharmacological potential of tested drugs, pharmacological safety was determined by testing all compounds against two neoplastic cell lines (squamous carcinoma [KB] and melanoma [SK-Mel]) and against murine bone marrow-derived macrophages as host cells. With minor exceptions only for macrophages, tested aphidicolans did not show significant cytotoxicity (EC
50
> 25.0 μg/ml). Structure-activity relationships of these aphidicolan derivatives are discussed.
AmpD Is Required for Regulation of Expression of NmcA, a Carbapenem-Hydrolyzing β-Lactamase ofEnterobacter cloacae
Authors: Naas Thierry , Massuard Sandrine , Garnier Fabien , Nordmann Patrice 
Published: July 2002

ABSTRACTTo further elucidate the induction process of the carbapenem-hydrolyzing β-lactamase of Ambler class A, NmcA,ampDgenes of the wild-type (WT) strain and of ceftazidime-resistant mutants ofEnterobacter cloacaeNOR-1 were cloned and tested in transcomplementation experiments. Ceftazidime-resistantE.cloacaeNOR-1 mutants exhibited derepressed expression of the AmpC-type cephalosporinase and of the carbapenem-hydrolyzing β-lactamase NmcA. TheampDgenes ofEscherichia coliandE.cloacaeWT NOR-1 transcomplemented the ceftazidime-resistantE.cloacaeNOR-1 mutants to the WT level of β-lactamase expression, while the mutatedampDalleles ofE.cloacaeNOR-1 failed to do so. The deducedE.cloacaeNOR-1 WT AmpD protein exhibited 95 and 91% amino acid identity with theE.cloacaeO29 andE.cloacae14 WT AmpD proteins, respectively. Of the 12 ceftazidime-resistantE.cloacaeNOR-1 strains, 3 had AmpD proteins with amino acid changes, while the others had truncated AmpD proteins. Most of these mutations were located outside the conserved regions that link the AmpD proteins to the cell wall hydrolases. AmpD fromE.cloacaeNOR-1 is involved in the regulation of expression of both β-lactamases (NmcA and AmpC), suggesting that structurally unrelated genes may be under the control of an identical genetic system.
Potent Anti-
Trypanosoma cruzi
Activities of Oxidosqualene Cyclase Inhibitors
Authors: Buckner Frederick S. , Griffin John H. , Wilson Aaron J. , Van Voorhis Wesley C. 
Published: July 2002

ABSTRACT

Trypanosoma cruzi
is the protozoan agent that causes Chagas' disease, a major health problem in Latin America. Better drugs are needed to treat infected individuals. The sterol biosynthesis pathway is a potentially excellent target for drug therapy against
T. cruzi
. In this study, we investigated the antitrypanosomal activities of a series of compounds designed to inhibit a key enzyme in sterol biosynthesis, oxidosqualene cyclase. This enzyme converts 2,3-oxidosqualene to the tetracyclic product, lanosterol. The lead compound,
N
-(4
E
,8
E
)-5,9, 13-trimethyl-4,8, 12-tetradecatrien-1-ylpyridinium, is an electron-poor aromatic mimic of a monocyclized transition state or high-energy intermediate formed from oxidosqualene. This compound and 27 related compounds were tested against mammalian-stage
T. cruzi
, and 12 inhibited growth by 50% at concentrations below 25 nM. The lead compound was shown to cause an accumulation of oxidosqualene and decreased production of lanosterol and ergosterol, consistent with specific inhibition of the oxidosqualene cyclase. The data demonstrate potent anti-
T. cruzi
activity associated with inhibition of oxidosqualene cyclase.
Anticandida Activity Is Retained in P-113, a 12-Amino-Acid Fragment of Histatin 5
Authors: Rothstein David M. , Spacciapoli Peter , Tran Linh T. , Xu Tao , Roberts F. Donald , Dalla Serra Mauro , Buxton Deborah K. , Oppenheim Frank G. , Friden Phillip 
Published: July 2002

ABSTRACT

Through the analysis of a series of 25 peptides composed of various portions of the histatin 5 sequence, we have identified P-113, a 12-amino-acid fragment of histatin 5, as the smallest fragment that retains anticandidal activity comparable to that of the parent compound. Amidation of the P-113 C terminus increased the anticandidal activity of P-113 approximately twofold. The three histidine residues could be exchanged for three hydrophobic residues, with the fragment retaining anticandidal activity. However, the change of two or more of the five basic (lysine and arginine) residues to uncharged residues resulted in a substantial loss of anticandidal activity. A synthetic
d
-amino-acid analogue, P-113D, was as active against
Candida albicans
as the
l
-amino-acid form. In vitro MIC tests in low-ionic-strength medium showed that P-113 has potent activity against
Candida albicans, Candida glabrata, Candida parapsilosis
, and
Candida tropicalis
. These results identify P-113 as a potential antimicrobial agent in the treatment of oral candidiasis.
Inhibition of Fumarate Reductase in
Leishmania major
and
L. donovani
by Chalcones
Authors: Chen Ming , Zhai Lin , Christensen Søren Brøgger , Theander Thor G. , Kharazmi Arsalan 
Published: July 2002

ABSTRACT

Our previous studies have shown that chalcones exhibit potent antileishmanial and antimalarial activities in vitro and in vivo. Preliminary studies showed that these compounds destroyed the ultrastructure of
Leishmania
parasite mitochondria and inhibited the respiration and the activity of mitochondrial dehydrogenases of
Leishmania
parasites. The present study was designed to further investigate the mechanism of action of chalcones, focusing on the parasite respiratory chain. The data show that licochalcone A inhibited the activity of fumarate reductase (FRD) in the permeabilized
Leishmania major
promastigote and in the parasite mitochondria, and it also inhibited solubilized FRD and a purified FRD from
L. donovani
. Two other chalcones, 2,4-dimethoxy-4′-allyloxychalcone (24m4ac) and 2,4-dimethoxy-4′-butoxychalcone (24mbc), also exhibited inhibitory effects on the activity of solubilized FRD in
L. major
promastigotes. Although licochalcone A inhibited the activities of succinate dehydrogenase (SDH), NADH dehydrogenase (NDH), and succinate- and NADH-cytochrome
c
reductases in the parasite mitochondria, the 50% inhibitory concentrations (IC
50
) of licochalcone A for these enzymes were at least 20 times higher than that for FRD. The IC
50
of licochalcone A for SDH and NDH in human peripheral blood mononuclear cells were at least 70 times higher than that for FRD. These findings indicate that FRD, one of the enzymes of the parasite respiratory chain, might be the specific target for the chalcones tested. Since FRD exists in the
Leishmania
parasite and does not exist in mammalian cells, it could be an excellent target for antiprotozoal drugs.
Clinafloxacin Pharmacokinetics in Subjects with Various Degrees of Renal Function
Authors: Randinitis Edward J. , Koup Jeffery R. , Rausch George , Abel Robert , Bron Nicola J. , Hounslow Neil J. , Vassos Artemios B. , Sedman Allen J. 
Published: July 2002

ABSTRACT

As the primary route for elimination of clinafloxacin is renal clearance (CL
R
) of unchanged drug, studies were conducted to determine the pharmacokinetic profile of clinafloxacin following administration to young and elderly subjects, subjects with various degrees of renal function, and subjects requiring dialysis. These were open-label studies in which subjects received single oral clinafloxacin doses. Sixteen young subjects (18 to 35 years old) and 16 elderly subjects (>65 years old) were enrolled in a study comparing pharmacokinetic profiles of clinafloxacin in young and elderly subjects. Twenty subjects having various degrees of renal function were enrolled into one of three groups based on degree of renal function as measured by creatinine clearance (CL
CR
). Twelve subjects with severe renal impairment requiring dialysis enrolled in a third study. Clinafloxacin was generally well tolerated by all subjects. Clinafloxacin pharmacokinetic profiles in elderly subjects were dependent only on age-related decreases in renal function. Clinafloxacin maximum concentrations in plasma, areas under the concentration-time curves, and terminal elimination half-life values increased with decreasing CL
CR
values. Total apparent body clearance of clinafloxacin from the plasma after oral administration (CL
oral
) and CL
R
were dependent on CL
CR
according to the following relationships: CL
oral
= 2.3 · CL
CR
+ 77 and CL
R
= 1.74 · CL
CR
. Hemodialysis had no significant effect on clinafloxacin clearance. Based on the relationship between CL
CR
and clinafloxacin CL
oral
and CL
R
values, the clinafloxacin dose should be halved in patients having a CL
CR
of <40 ml/min. Further dose adjustment is not warranted in patients requiring hemodialysis.
Inactivation of a Novel Gene Produces a Phenotypic Variant Cell and Affects the Symbiotic Behavior of
Xenorhabdus nematophilus
Authors: Volgyi Antonia , Fodor Andras , Forst Steven 
Published: July 2002

ABSTRACT

Xenorhabdus nematophilus
is an insect pathogen that lives in a symbiotic association with a specific entomopathogenic nematode. During prolonged culturing, variant cells arise that are deficient in numerous properties. To understand the genetic mechanism underlying variant cell formation, a transposon mutagenesis approach was taken. Three phenotypically similar variant strains of
X. nematophilus
, each of which contained a single transposon insertion, were isolated. The insertions occurred at different locations in the chromosome. The variant strain, ANV2, was further characterized. It was deficient in several properties, including the ability to produce antibiotics and the stationary-phase-induced outer membrane protein, OpnB. Unlike wild-type cells, ANV2 produced lecithinase. The emergence of ANV2 from the nematode host was delayed relative to the emergence of the parental strain. The transposon in ANV2 had inserted in a gene designated
var1
, which encodes a novel protein composed of 121 amino acid residues. Complementation analysis confirmed that the pleiotropic phenotype of the ANV2 strain was produced by inactivation of
var1
. Other variant strains were not complemented by
var1
. These results indicate that inactivation of a single gene was sufficient to promote variant cell formation in
X. nematophilus
and that disruption of genetic loci other than
var1
can result in the same pleiotropic phenotype.
Small-Subunit rRNA Genotyping of Rhizobia Nodulating Australian
Acacia
spp
Authors: Lafay Bénédicte , Burdon Jeremy J. 
Published: July 2002

ABSTRACT

The structure of rhizobial communities nodulating
Acacia
in southeastern Australia from south Queensland to Tasmania was investigated by a molecular approach. A total of 118 isolates from nodule samples from 13 different
Acacia
species collected at 44 sites were characterized by small-subunit (SSU) ribosomal DNA (rDNA) PCR-restriction fragment length polymorphism analysis. Nine rhizobial genomospecies were identified, and these taxa corresponded to previously described genomospecies (B. Lafay and J. J. Burdon, Appl. Environ. Microbiol. 64:3989–3997, 1998). Eight of these genomospecies belonged to the
Bradyrhizobium
lineage and accounted for 96.6% of the isolates. The remaining genomospecies corresponded to
Rhizobium tropici
. For analysis of geographic patterns, results were grouped into five latitudinal regions regardless of host origin. In each region, as observed previously for rhizobial isolates taken from non-
Acacia
legumes (Lafay and Burdon, Appl. Environ. Microbiol. 64:3989–3997, 1998), rhizobial communities were dominated by one or two genomospecies, the identities of which varied from place to place. Despite this similarity in patterns, the most abundant genomospecies for
Acacia
isolates differed from the genomospecies found in the non-
Acacia
-derived rhizobial collection, suggesting that there is a difference in nodulation patterns of the Mimosoideae and the Papilionoideae. Only two genomospecies were both widespread and relatively abundant across the range of sites sampled. Genomospecies A was found in all regions except the most northern sites located in Queensland, whereas genomospecies B was not detected in Tasmania. This suggests that genomospecies A might be restricted to the more temperate regions of Australia, whereas in contrast, genomospecies B occurs in different climatic and edaphic conditions across the whole continent. The latter hypothesis is supported by the presence of genomospecies B in southwestern Australia, based on partial SSU rDNA sequence data (N. D. S. Marsudi, A. R. Glenn, and M. J. Dilworth, Soil Biol. Biochem. 31:1229–1238, 1998).