bluuebunny/crossref_metadata_2025 huggingface dataset:
Metabolic Flux in Both the Purine Mononucleotide and Histidine Biosynthetic Pathways Can Influence Synthesis of the Hydroxymethyl Pyrimidine Moiety of Thiamine in
Salmonella enterica
Authors: Allen Shara , Zilles Julie L. , Downs Diana M.
Published: October 2002

Together, the biosyntheses of histidine, purines, and thiamine pyrophosphate (TPP) contain examples of convergent, divergent, and regulatory pathway integration. Mutations in two purine biosynthetic genes (
purI
and
purH
) affect TPP biosynthesis due to flux through the purine and histidine pathways. The molecular genetic characterization of
purI
mutants and their respective pseudorevertants resulted in the conclusion that <1% of the wild-type activity of the PurI enzyme was sufficient for thiamine but not for purine synthesis. The respective pseudorevertants were found to be informational suppressors. In addition, it was shown that accumulation of the purine intermediate aminoimidazole carboxamide ribotide inhibits thiamine synthesis, specifically affecting the conversion of aminoimidazole ribotide to hydroxymethyl pyrimidine.
Demonstration and Characterization of a Specific Interaction between Gonococcal Transferrin Binding Protein A and TonB
Authors: Kenney Christopher D. , Cornelissen Cynthia Nau
Published: October 2002

Iron scavenging byNeisseria gonorrhoeaeis accomplished by the expression of receptors that are specific for host iron-binding proteins, such as transferrin and lactoferrin. Efficient transferrin-iron acquisition is dependent on the combined action of two proteins, designated TbpA and TbpB. TbpA is a TonB-dependent outer membrane receptor, whereas TbpB is lipid modified and serves to increase the efficiency of transferrin-iron uptake. Both proteins, together or separately, can be isolated from the gonococcal outer membrane by using affinity chromatography techniques. In the present study, we identified an additional protein in transferrin-affinity preparations, which had an apparent molecular mass of 45 kDa. The ability to copurify this protein by transferrin affinity was dependent upon the presence of TbpA and not TbpB. The amino-terminal sequence of the 45-kDa protein was identical to the amino terminus of gonococcal TonB, indicating that TbpA stably interacted with TonB, without the addition of chemical cross-linkers. Using immunoprecipitation, we could recover TbpA-TonB complexes without the addition of transferrin, suggesting that ligand binding was not a necessary prerequisite for TonB interaction. In contrast, a characterized TonB box mutant of TbpA did not facilitate interaction between these two proteins such that complexes could be isolated. We generated an in-frame deletion of gonococcal TonB, which removed 35 amino acids, including aNeisseria-specific, glycine-rich domain. This mutant protein, like the parental TonB, energized TbpA to enable growth on transferrin. Consistent with the functionality of this deletion derivative, TbpA-TonB complexes could be recovered from this strain. The results of the present study thus begin to define the requirements for a functional interaction between gonococcal TbpA and TonB.
Proteins Released byHelicobacter pyloriIn Vitro
Authors: Kim Nayoung , Weeks David L. , Shin Jai Moo , Scott David R. , Young Mary K. , Sachs George
Published: October 2002

Secretion of proteins byHelicobacter pylorimay contribute to gastric inflammation and epithelial damage. An in vitro analysis was designed to identify proteins released by mechanisms other than nonspecific lysis. The radioactivity of proteins in the supernatant was compared with that of the intact organism by two-dimensional gel phosphorimaging following a 4-h pulse-chase. The ratio of the amount of UreB, a known cytoplasmic protein, in the supernatant to that in the pellet was found to be 0.25, and this was taken as an index of lysis during the experiments (n= 6). Ratios greater than that of UreB were used to distinguish proteins that were selectively released into the medium. Thus, proteins enriched more than 10-fold in the supernatant compared to UreB were identified by mass spectrometry. Sixteen such proteins were present in the supernatant: VacA; a conserved secreted protein (HP1286); putative peptidylcis-transisomerase (HP0175); six proteins encoded by HP0305, HP0231, HP0973, HP0721, HP0129, and HP0902; thioredoxin (HP1458); single-stranded-DNA-binding 12RNP2 precursor (HP0827); histone-like DNA-binding protein HU (HP0835); ribosomal protein L11 (HP1202); a putative outer membrane protein (HP1564); and outer membrane proteins Omp21 (HP0913) and Omp20 (HP0912). All except HP0902, thioredoxin, HP0827, HP0835, and HP1202 had a signal peptide. When nalidixic acid, a DNA synthesis inhibitor, was added to inhibit cell division but not protein synthesis, to decrease possible contamination due to outer membrane shedding, two outer membrane proteins (Omp21 and Omp20) disappeared from the supernatant, and the amount of VacA also decreased. Thus, 13 proteins were still enriched greater than 10-fold in the medium after nalidixic acid treatment, suggesting these were released specifically, possibly by secretion. These proteins may be implicated inH. pylori-induced effects on the gastric epithelium.
Involvement of Two Putative Alternative Sigma Factors in Stress Response of the Radioresistant Bacterium
Deinococcus radiodurans
Authors: Schmid Amy K. , Lidstrom Mary E.
Published: October 2002

Two genes bearing similarity to alternative sigma factors were identified in the
Deinococcus radiodurans
genome sequence and designated
sig1
and
sig2
. These genes were cloned and inactivated, and both were found to be important for survival during heat and ethanol stress, although the
sig1
mutants displayed a more severe phenotype than the
sig2
mutants. Reporter gene fusions to the
groESL
and
dnaKJ
operons transformed into these mutant backgrounds indicated that
sig1
is required for the heat shock induction of
groESL
and
dnaKJ
, whereas
sig2
mutants show a more moderate defect in
dnaKJ
induction and are not impaired for
groESL
induction. Essentiality tests suggested that neither
sig1
nor
sig2
is essential under all conditions. Sequence comparisons demonstrated that the
sig1
gene product is classed distinctly with extracytoplasmic function (ECF) sigma factors, whereas Sig2 appears to be a more divergent sigma factor ortholog. These results suggest that
sig1
encodes the major ECF-derived heat shock sigma factor in
D. radiodurans
and that it plays a central role in the positive regulation of heat shock genes.
sig2
, in contrast, appears to play a more minor role in heat shock protection and may serve to modulate the expression of some heat protective genes.
Inversions over the Terminus Region inSalmonellaandEscherichia coli: IS200s as the Sites of Homologous Recombination Inverting the Chromosome ofSalmonella entericaSerovar Typhi
Authors: Alokam Suneetha , Liu Shu-Lin , Said Kamal , Sanderson Kenneth E.
Published: October 2002

Genomic rearrangements (duplications and inversions) in enteric bacteria such asSalmonella entericaserovar Typhimurium LT2 andEscherichia coliK12 are frequent (10−3to 10−5) in culture, but in wild-type strains these genomic rearrangements seldom survive. However, inversions commonly survive in the terminus of replication (TER) region, where bidirectional DNA replication terminates; nucleotide sequences fromS. entericaserovar Typhimurium LT2,S. entericaserovar Typhi CT18,E. coliK12, andE. coliO157:H7 revealed genomic inversions spanning the TER region. Assuming thatS. entericaserovar Typhimurium LT2 represents the ancestral genome structure, we found an inversion of 556 kb in serovar Typhi CT18 between two of the 25 IS200elements and an inversion of about 700 kb inE. coliK12 andE. coliO157:H7. In addition, there is another inversion of 500 kb inE. coliO157:H7 compared withE. coliK12. PCR analysis confirmed that allS. entericaserovar Typhi strains tested, but not strains of otherSalmonellaserovars, have an inversion at the exact site of the IS200insertions. We conclude that inversions of the TER region survive because they do not significantly change replication balance or because they are part of the compensating mechanisms to regain chromosome balance after it is disrupted by insertions, deletions, or other inversions.
Effects of Environmental Changes on Expression of the Oligopeptide Permease (
opp
) Genes of
Borrelia burgdorferi
Authors: Wang Xing-Guo , Lin Bo , Kidder J. Michael , Telford Samuel , Hu Linden T.
Published: October 2002

We analyzed expression of a putative oligopeptide permease (Opp) of
Borrelia burgdorferi.
Unlike the
opp
operons of other bacteria for which there is a single substrate binding protein,
B. burgdorferi
codes for three substrate binding proteins (OppA-I to -III) in its
opp
operon and an additional two homologs on plasmids (OppA-IV and -V). Instead of a single promoter region regulating transcription of the entire operon, as seen in other bacterial
opp
operons, it appears that among
oppA-I
,
-II
, and -
III
, as well as
oppA-IV
and -
V
, each has a potential upstream promoter region. We tested the function of these putative promoter sequences by fusion to a promoterless β-galactosidase reporter gene in pCB182. Each of the promoter regions was found to be active. The level of activity in the reporter constructs closely paralleled the level of expression of each gene in in vitro-grown
B. burgdorferi
. Changes in carbon and nitrogen availability differentially affected individual promoters, but no changes in promoter activity were seen when
Escherichia coli
bacteria (with the promoter constructs) were grown in various concentrations of phosphate and leucine and changes in pH. Expression of specific
oppA
genes with
B. burgdorferi
varied significantly between its mouse and fed and unfed tick hosts. Differences in regulation of
opp
gene expression suggest a potential role in environmental response by the organism.
The IrrE Protein of
Deinococcus radiodurans
R1 Is a Novel Regulator of
recA
Expression
Authors: Earl Ashlee M. , Mohundro Michael M. , Mian I. Saira , Battista John R.
Published: October 2002

IRS24 is a DNA damage-sensitive strain of
Deinococcus radiodurans
strain 302 carrying a mutation in an uncharacterized locus designated
irrE
. Five overlapping cosmids capable of restoring ionizing radiation resistance to IRS24 were isolated from a genomic library. The ends of each cloned insert were sequenced, and these sequences were used to localize
irrE
to a 970-bp region on chromosome I of
D. radiodurans
R1. The
irrE
gene corresponds to coding sequence DR0167 in the R1 genome. The
irrE
gene encodes a 35,000-Da protein that has no similarity to any previously characterized peptide. The
irrE
locus of R1 was also inactivated by transposon mutagenesis, and this strain was sensitive to ionizing radiation, UV light, and mitomycin C. Preliminary findings indicate that IrrE is a novel regulatory protein that stimulates transcription of the
recA
gene following exposure to ionizing radiation.
Bacterial Outer Membrane Ushers Contain Distinct Targeting and Assembly Domains for Pilus Biogenesis
Authors: Thanassi David G. , Stathopoulos Christos , Dodson Karen , Geiger Dominik , Hultgren Scott J.
Published: October 2002

Biogenesis of a superfamily of surface structures by gram-negative bacteria requires the chaperone/usher pathway, a terminal branch of the general secretory pathway. In this pathway a periplasmic chaperone works together with an outer membrane usher to direct substrate folding, assembly, and secretion to the cell surface. We analyzed the structure and function of the PapC usher required for P pilus biogenesis by uropathogenic
Escherichia coli.
Structural analysis indicated PapC folds as a β-barrel with short extracellular loops and extensive periplasmic domains. Several periplasmic regions were localized, including two domains containing conserved cysteine pairs. Functional analysis of deletion mutants revealed that the PapC C terminus was not required for insertion of the usher into the outer membrane or for proper folding. The usher C terminus was not necessary for interaction with chaperone-subunit complexes in vitro but was required for pilus biogenesis in vivo. Interestingly, coexpression of PapC C-terminal truncation mutants with the chromosomal
fim
gene cluster coding for type 1 pili allowed P pilus biogenesis in vivo. These studies suggest that chaperone-subunit complexes target an N-terminal domain of the usher and that subunit assembly into pili depends on a subsequent function provided by the usher C terminus.
Helicobacter pyloriExpresses an Autolytic Enzyme: Gene Identification, Cloning, and Theoretical Protein Structure
Authors: Marsich Eleonora , Zuccato Pierfrancesco , Rizzi Sonia , Vetere Amedeo , Tonin Enrico , Paoletti Sergio
Published: October 2002

Helicobacter pyloriis an important pathogen of the gastric system. The clinical outcome of infection is thought to be correlated with some genetic features of the bacterium. However, due to the extreme genetic variability of this organism, it is hard to draw definitive conclusions concerning its virulence factors. Here we describe a novelH. pylorigene which expresses an autolytic enzyme that is also capable of degrading the cell walls of both gram-positive and gram-negative bacteria. We designated this genelys. We found this gene and observed its expression in a number of unrelated clinical strains, a fact that suggests that it is well conserved in the species. A comparison of the nucleotide sequences oflysand the hypothetical geneHP0339fromH. pyloristrain ATCC 26695 revealed almost total identity, except for the presence of an insertion consisting of 24 nucleotides in thelyssequence. The coding sequences oflysandHP0339show a high degree of homology with the coding sequence of bacteriophage T4 lysozyme. Because of this similarity, it was possible to model the three-dimensional structures of both thelysandHP0339products.
Functional Analysis by Site-Directed Mutagenesis of the NAD
+
-Reducing Hydrogenase from
Ralstonia eutropha
Authors: Burgdorf Tanja , De Lacey Antonio L. , Friedrich Bärbel
Published: October 2002

The tetrameric cytoplasmic [NiFe] hydrogenase (SH) of
Ralstonia eutropha
couples the oxidation of hydrogen to the reduction of NAD
+
under aerobic conditions. In the catalytic subunit HoxH, all six conserved motifs surrounding the [NiFe] site are present. Five of these motifs were altered by site-directed mutagenesis in order to dissect the molecular mechanism of hydrogen activation. Based on phenotypic characterizations, 27 mutants were grouped into four different classes. Mutants of the major class, class I, failed to grow on hydrogen and were devoid of H
2
-oxidizing activity. In one of these isolates (HoxH I64A), H
2
binding was impaired. Class II mutants revealed a high D
2
/H
+
exchange rate relative to a low H
2
-oxidizing activity. A representative (HoxH H16L) displayed D
2
/H
+
exchange but had lost electron acceptor-reducing activity. Both activities were equally affected in class III mutants. Mutants forming class IV showed a particularly interesting phenotype. They displayed O
2
-sensitive growth on hydrogen due to an O
2
-sensitive SH protein.
Characterization of the Two-Component Abortive Phage Infection Mechanism AbiT from
Lactococcus lactis
Authors: Bouchard Julie D. , Dion Eric , Bissonnette Frédéric , Moineau Sylvain
Published: October 2002

During the production of fermented dairy products, virulent bacteriophages infecting
Lactococcus lactis
can delay or stop the milk acidification process. A solution to this biological problem consists of introducing natural phage barriers into the strains used by the dairy industry. One such hurdle is called abortive infection (Abi) and causes premature cell death with no or little phage progeny. Here, we describe the isolation and characterization of a novel Abi mechanism encoded by plasmid pED1 from
L. lactis
. The system is composed of two constitutively cotranscribed genes encoding putative proteins of 127 and 213 amino acids, named AbiTi and AbiTii, respectively. Site-directed mutagenesis indicated that a hydrophobic region at the C-terminal extremity of AbiTi is essential to the antiphage phenotype. The AbiT system is effective against phages of the 936 and P335 species (efficiency of plaquing between 10
−5
and 10
−7
) and causes a 20-fold reduction in the efficiency to form centers of infection as well as a 10- to 12-fold reduction in the burst size. Its efficacy could be improved by raising the plasmid copy number, but changing the intrinsic ratio of AbiTi and AbiTii did not greatly affect the antiphage activity. The monitoring of the intracellular phage infection process by DNA replication, gene expression, and electron microscopy as well as the study of phage mutants by genome mapping indicated that AbiT is likely to act at a later stage of the phage lytic cycle.
Functional Analysis of TraA, the Sex Pheromone Receptor Encoded by pPD1, in a Promoter Region Essential for the Mating Response in
Enterococcus faecalis
Authors: Horii Takaaki , Nagasawa Hiromichi , Nakayama Jiro
Published: October 2002

Conjugative transfer of a bacteriocin plasmid, pPD1, of
Enterococcus faecalis
is induced in response to a peptide sex pheromone, cPD1, secreted from plasmid-free recipient cells. cPD1 is taken up by a pPD1 donor cell and binds to an intracellular receptor, TraA. Once a recipient cell acquires pPD1, it starts to produce an inhibitor of cPD1, termed iPD1, which functions as a TraA antagonist and blocks self-induction in donor cells. In this study, we discuss how TraA transduces the signal of cPD1 to the mating response. Gel mobility shift assays indicated that TraA is bound to a
traA
-
ipd
intergenic region, which is essential for cPD1 response. DNase I footprinting analysis suggested the presence of one strong (
tab1
) and two weak (
tab2
and
tab3
) TraA-binding sites in the intergenic region. Primer extension analysis implied that the transcriptional initiation sites of
traA
and
ipd
were located in the intergenic region. Northern analysis showed that cPD1 upregulated and downregulated transcription of
ipd
and
traA
, respectively. The circular permutation assay showed that TraA bent a DNA fragment corresponding to the
tab1
region, and its angle was changed in the presence of cPD1 or iPD1. From these data, we propose a model that TraA changes the conformation of the
tab1
region in response to cPD1 and upregulates the transcription of
ipd
, which may lead to expression of genes required for the mating response.
Enterococcus faecalis
Heme-Dependent Catalase
Authors: Frankenberg Lena , Brugna Myriam , Hederstedt Lars
Published: October 2002

Enterococcus faecalis
cells cannot synthesize porphyrins and do not rely on heme for growth but can take up heme and use it to synthesize heme proteins. We recently described a cytochrome
bd
in
E. faecalis
strain V583 and here report the identification of a chromosomal gene,
katA
, encoding a heme-containing cytoplasmic catalase. The 54-kDa KatA polypeptide shows sequence similarity to members of the family of monofunctional catalases. A hexahistidyl-tagged version of the catalase was purified, and major characteristics of the enzyme were determined. It contains one protoheme IX group per KatA polypeptide. Catalase activity was detected only in
E. faecalis
cells grown in the presence of heme in the medium; about 2 and 10 μM hemin was required for half-maximal and maximal production of catalase, respectively. Our finding of a catalase whose synthesis is dependent on the acquisition of heme in the opportunistic pathogen
E. faecalis
might be of clinical importance. Studies of cellular heme transport and heme protein assembly and in vivo synthesis of metalloprotein analogs for biotechnological applications are impeded by the lack of experimental systems. We conclude that the
E. faecalis
cell potentially provides such a desired system.
Evolution and Virulence of Serogroup 6 Pneumococci on a Global Scale
Authors: Robinson D. Ashley , Briles David E. , Crain Marilyn J. , Hollingshead Susan K.
Published: October 2002

To study the evolution and virulence of pneumococcal populations, we used multilocus sequence typing to identify the major clones among 212 carriage and invasive isolates expressing capsular serogroup 6 from 39 countries. The global population consisted of 8 major complexes and 6 minor complexes of related clones and 32 clones of diverse origin. Surprisingly, serotype 6A clones evolved by mutation nearly as often as by recombination, whereas serotype 6B clones evolved almost exclusively by recombination (
P
= 0.0029). This is the first report of population genetic differences among serotypes of this species. The largest clonal complex was associated with invasive disease (
P
= 0.019) and included a common ancestor for five previously identified drug-resistant clones. The putative ancestors of the major clonal complexes were represented by a greater proportion of carriage isolates than were their descendents (
P
= 0.001), and the ancestors tended to be less virulent than their descendents in a mouse model of infection. These data suggested that virulent serogroup 6 clones have evolved multiple times from less-virulent ancestral clones.
A Proline-Rich Region with a Highly Periodic Sequence in Streptococcal β Protein Adopts the Polyproline II Structure and Is Exposed on the Bacterial Surface
Authors: Areschoug Thomas , Linse Sara , Stålhammar-Carlemalm Margaretha , Hedén Lars-Olof , Lindahl Gunnar
Published: October 2002

Proline-rich regions have been identified in many surface proteins of pathogenic streptococci and staphylococci. These regions have been suggested to be located in cell wall-spanning domains and/or to be required for surface expression of the protein. Because little is known about these regions, which are found in extensively studied and biologically important surface proteins, we characterized the proline-rich region in one such protein, the β protein of group B streptococci. The proline-rich region in β, designated the XPZ region, has a proline at every third position, and the sequence is highly periodic in other respects. Immunochemical analysis showed that the XPZ region was not associated with the cell wall but was exposed on the bacterial surface. Moreover, characterization of a β mutant lacking the XPZ region demonstrated that this region was not required for surface expression of the β protein. Comparison of the XPZ region in different β proteins showed that it varied in size but always retained the typical sequence periodicity. Circular dichroism spectroscopy indicated that the XPZ region had the structure of a polyproline II helix, an extended and solvent-exposed structure with exactly three residues per turn. Because of the three-residue sequence periodicity in the XPZ region, it is expected to be amphipathic and to have distinct nonpolar and polar surfaces. This study identified a proline-rich structure with unique properties that is exposed on the surface of an important human pathogen.
Structural Heterogeneity of the Streptococcal C5a Peptidase Gene inStreptococcus pyogenes
Authors: Koroleva Irina V. , Efstratiou Androulla , Suvorov Alexander N.
Published: October 2002

The 3′ ends of the genes for the C-terminal region of C5a peptidase from 15Streptococcus pyogenesisolates were analyzed by PCR. Amplicons were found to differ in size. DNA sequence analysis revealed that the differences between PCR fragment sizes accorded with the number of R repeats in the C5a peptidase gene.
Protein Splicing of the
Deinococcus radiodurans
Strain R1 Snf2 Intein
Authors: Southworth Maurice W. , Perler Francine B.
Published: October 2002

Adjacent intein fragments fused to a Snf2/Rad54 helicase-related protein and Snf2/Rad54 helicase were reported for
Deinococcus radiodurans
R1, leading to the speculation that a frameshift was required for splicing or that
trans
splicing occurred. However, a type strain (ATCC 13939, RF18410) yielded a single protein that splices by the Ala1 protein splicing pathway, with splicing dependent on adjacent residues.
Bex, theBacillus subtilisHomolog of the EssentialEscherichia coliGTPase Era, Is Required for Normal Cell Division and Spore Formation
Authors: Minkovsky Natalie , Zarimani Arash , Chary Vasant K. , Johnstone Brian H. , Powell Bradford S. , Torrance Pamela D. , Court Donald L. , Simons Robert W. , Piggot Patrick J.
Published: October 2002

TheBacillus subtilis bexgene complemented the defect in anEscherichia coli eramutant. The Bex protein showed 39% identity and 67% similarity to theE. coliEra GTPase. In contrast toera,bexwas not essential in all strains.bexmutant cells were elongated and filled with diffuse nucleoid material. They grew slowly and exhibited severely impaired spore formation.
Genomewide Transcriptional Analysis of the Cold Shock Response in
Bacillus subtilis
Authors: Beckering Carsten L. , Steil Leif , Weber Michael H. W. , Völker Uwe , Marahiel Mohamed A.
Published: October 2002

Previous studies with two-dimensional gel electrophoresis techniques revealed that the cold shock response in
Bacillus subtilis
is characterized by rapid induction and accumulation of two classes of specific proteins, which have been termed cold-induced proteins (CIPs) and cold acclimatization proteins (CAPs), respectively. Only recently, the
B. subtilis
two-component system encoded by the
desKR
operon has been demonstrated to be essential for the cold-induced expression of the lipid-modifying desaturase Des, which is required for efficient cold adaptation of the membrane in the absence of isoleucine. At present, one of the most intriguing questions in this research field is whether DesKR plays a global role in cold signal perception and transduction in
B. subtilis
. In this report, we present the first genomewide transcriptional analysis of a cold-exposed bacterium and demonstrate that the
B. subtilis
two-component system DesKR exclusively controls the desaturase gene
des
and is not the cold-triggered regulatory system of global relevance. In addition to this, we identified a set of genes that might participate as novel players in the cold shock adaptation of
B. subtilis
. Two cold-induced genes, the elongation factor homolog
ylaG
and the σ
L
-dependent transcriptional activator homolog
yplP
, have been examined by construction and analysis of deletion mutants.
Radiocaesium in forests  A review on most recent research
Authors: Riesen T K
Published: October 2002

This review presents the most recent findings on radiocaesium cycling in temperate forest ecosystems, which are specified with selected examples. Based on a matrix method it was concluded that key processes occur at the soilplant interface, the rhizosphere, and that the three most important compartments are fungal structures, plant roots, and clay minerals. The complexity of forest ecosystems led to the development of several sub-models, which then are combined in one package. Research needs to be directed towards more standardized and comparable data sets, which then can be used for modelling and can be integrated in geographical information systems. key words: radioecology, forest, soil, caesium, fluxes.
Terrestrial net primary productivity  A brief history and a new worldwide database
Authors: Scurlock J MO , Olson R J
Published: October 2002

Consistent data on terrestrial net primary productivity (NPP) are urgently needed to constrain model estimates of carbon fluxes and hence to refine our understanding of ecosystem responses to climate change. The NPP data have been collected in a coordinated manner for the past 30 years, but comprehensive summaries are rare. We report on the development and availability of a global NPP database that is suitable for modeling of the terrestrial carbon cycle at global and regional scales, for validation of remote sensing data, and for other applications. These data were obtained from the literature on ecophysiological field work and from detailed consultation with the scientific community. Data on NPP, biomass, and associated environmental variables are now publicly available for 53 detailed study sites, of which more than half have data for belowground biomass or biomass dynamics. Aboveground NPP ranges from 35 to 2320 g m2a1 (dry matter) and total NPP from 182 to 3538 g m2a1. Well-known but previously unobtainable compilations of data, such as the "Osnabrück Data Set" and the International Biological Program (IBP) Woodlands Data Set, are also incorporated in this database. Preliminary exploration of relationships between NPP and mean annual precipitation and temperature suggests that the new 53-site data collection, as well as the Osnabrück and IBP data, are all consistent with the historic "Miami" statistical model. These data are available from the Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC) for biogeochemical dynamics (see http://www.daac.ornl.gov/NPP/).Key words: net primary productivity, grasslands, forests, biogeochemical dynamics, global carbon cycle, model validation.
Carbon cycling in peatlands  A review of processes and controls
Authors: Blodau C
Published: October 2002

Covering only 3% of the land area, northern peatlands store about 30% of the global soil carbon and account for 5 to 10% of the global methane burden to the atmosphere. A review of the literature on net ecosystem exchange, net primary productivity, carbon mineralization, methane emissions, and dissolved organic carbon dynamics indicates that peatlands can be both C sources and sinks. The temporal and spatial variability of fluxes is large, but a substantial portion of this variation can be explained by environmental and ecological variables. Uncertainty in predictions about carbon dynamics under changing environmental conditions arises from a number of knowledge gaps: (i) the understanding of how organic matter is mineralized and partitioned into carbon dioxide, methane, and dissolved organic carbon is insufficient; (ii) little is known about the consequences of long-term and short-term disturbances, such as elevated carbon dioxide concentrations, nitrogen and sulfur deposition, fire, and droughts, on the individual components of the carbon cycle; (iii) models that capture the dynamic interaction of the processes and their controls have not been developed yet, with the notable exception of methane dynamics. Key words: peatlands, carbon cycle, organic matter, carbon dioxide, methane, climate change.
Effects of domestication on growth physiology and endocrinology of Atlantic salmon (Salmo salar)
Authors: Fleming Ian A , Agustsson Thorleifur , Finstad Bengt , Johnsson Jörgen I , Björnsson Björn Thrandur
Published: October 2002

Selection programs for fish frequently target growth rate as a breeding goal, yet surprisingly little is known about which mechanisms underlying the growth process are being targeted. The aim of this study was thus to examine whether the process of artificial selection of Atlantic salmon (Salmo salar) that has resulted in higher growth rate resulted in underlying changes in the growth hormone (GH)  insulin-like growth factor I (IGF-I) axis of endocrine growth regulation. This was tested by comparing similarly reared seventh-generation farm salmon with wild salmon from the principal founder population of the farm strain at three life stages. Not unexpectedly, the domesticated fish outgrew their wild counterparts; this was most evident in salt water, where they averaged three times the weight by the end. Pituitary GH content was positively correlated with growth rate and correspondingly was significantly higher in the faster growing domesticated fish than in the wild fish. Plasma GH levels were also significantly higher in the domesticated fish, whereas IGF-I levels did not differ. These findings provide some of the first direct evidence indicating a link between domestication selection for growth and its endocrine regulation, whereby individuals with more active endocrine growth regulatory components are targeted.
Marine carbon and nitrogen in southeastern Alaska stream food webs: evidence from artificial and natural streams
Authors: Chaloner Dominic T , Martin Kristine M , Wipfli Mark S , Ostrom Peggy H , Lamberti Gary A
Published: October 2002

Incorporation of marine-derived nutrients (MDN) into freshwater food webs of southeastern Alaska was studied by measuring the natural abundance of nitrogen and carbon stable isotopes in biota from artificial and natural streams. Biofilm, aquatic macroinvertebrates (detritivores, shredders, and predators), and fish (coho salmon, Oncorhynchus kisutch, and cutthroat trout, Oncorhynchus clarki) were sampled from streams in which Pacific salmon (Oncorhynchus spp.) carcasses had been artificially placed or were present naturally. In the presence of carcasses, all trophic levels incorporated marine-derived nitrogen (range, 2273% of total N) and carbon (range, 752% of total C). In general, chironomid midges assimilated more marine-derived nitrogen and carbon than did other consumers. The assimilation of MDN by aquatic organisms and subsequent isotopic enrichment (56 for 15N, 34 for 13C) were similar in experimentally and naturally carcass-enriched streams. For specific taxa, however, percent assimilation for marine nitrogen and carbon were often dissimilar, possibly because of fractionation or transfer inefficiencies. These results suggest that pathways of MDN incorporation into stream food webs include both consumption of salmon material by macroinvertebrates and fish and uptake of mineralized MDN by biofilm. Incorporation of MDN into multiple trophic levels demonstrates the ecological significance of annual returns of anadromous fishes for sustaining the productivity of freshwater food webs.
Water transparency and nutrients as controls on phytoplankton along a flood-frequency gradient among lakes of the Mackenzie Delta, western Canadian Arctic
Authors: Squires Margaret M , Lesack Lance F.W
Published: October 2002

Relatively low phytoplankton production among lakes of the Mackenzie Delta has been attributed to light limitation in frequently flooded lakes and to nutrient limitation among infrequently flooded lakes; productivity peaks have been attributed to optimal lightnutrient conditions at intermediate flood frequency. We found that the distribution and abundance of phytoplankton among a large number of lakes was explained by optimal lightnutrient conditions but not by nutrient or light limitation. For a subset of lakes, seasonal dynamics of biomass were consistent with light limitation and optimal lightnutrient conditions but not nutrient limitation; photosynthetic rates were consistent with optimal lightnutrient conditions and nutrient limitation but not light limitation. Results of dilutiondeletion experiments across a lightnutrient gradient indicated transition from light limitation to optimal lightnutrient conditions to nutrient limitation. Surprisingly, adding river water to lake water did not increase photosynthetic rates; this result and experimental incubations in situ during river inflow and lake outflow suggested that continuous supply of river water may be necessary to increase phytoplankton growth rates. Among infrequently flooded lakes, phytoplankton response to nutrient additions showed that phosphorus (P) limitation was no more likely than nitrogen (N) limitation, co-limitation, or no limitation by N or P.
Risk and information use in two competing fleets: Russian and Cuban exploitation of silver hake (Merluccius bilinearis)
Authors: Gillis D M , Showell M A
Published: October 2002

Information exchange should influence the ability of individual vessels to exploit fish aggregations, ultimately influencing fishing efficiency. We examined this hypothesis using data from Cuban and Russian vessels pursuing silver hake (Merluccius bilinearis) on the Scotian Shelf from 1989 to 1993. Cuban fleet size and organization were similar among the years, while the Russian fleet decreased in size and became profit driven during this time. Changing fish abundances prevent direct comparisons of fishing success between years, but the relative performance of the nations provided a basis for interannual comparison of fishing success. The risk of gear damage during a trawl differed between the nations in the years studied. From 1989 to 1992, vessel performance improved after a move of over 20 nautical miles, but this trend was absent from the 1993 data. When movements were separated into potential tactics, moving to an area where other ships were fishing was most common, suggesting the use of public information. Russian vessels were significantly less mobile than Cubans immediately following the dissolution of the Soviet Union and their seasonal catch rates were typically lower. In the following year, Russians were more mobile than Cubans and their seasonal performance was comparable.
Critical loads of acidity for surface waters in south-central Ontario, Canada: regional application of the Steady-State Water Chemistry (SSWC) model
Authors: Henriksen A , Dillon P J , Aherne J
Published: October 2002

Critical loads of acidity and the amount by which these critical loads are exceeded by atmospheric deposition (termed "exceedances") were estimated for 1469 lakes from five regions in south-central Ontario, Canada, using single lake chemistry measurements and sulphur deposition data for the period 19761999. Based on the Steady-State Water Chemistry (SSWC) model, four of the five regions had low critical loads, which is consistent with the underlying geology (silicate bedrock) and the thin glacial soils in these regions. Sulphur deposition in the study area showed a clear downward trend over the time period, with a decrease of approximately 50% to current levels of approximately 44 meq·m2·year1. As a result of the declining deposition, the portion of lakes with critical load exceedances has dropped substantially, from 7482% in the four sensitive regions in 1976 to 1126% in 1999. The pentile critical load is typically used as a regional target to account for uncertainties, but also to ensure that a sufficient percentage of lakes are protected (95%). This suggests that further reductions in emissions are required to reduce depositions to approximately 34 meq·m2·year1 (11 kg S·ha1·year1) to prevent critical load exceedance.
A survival model of the effects of bottom-water hypoxia on the population density of an estuarine clam (Macoma balthica)
Authors: Borsuk Mark E , Powers Sean P , Peterson Charles H
Published: October 2002

The effect of bottom-water hypoxia on the population density of the clam Macoma balthica is estimated using a survival-based approach. We used Bayesian parameter estimation to fit a survival model to times-to-death corresponding to multiple dissolved oxygen (DO) concentrations assessed from scientific experts. We describe guidelines for ensuring the accuracy of such assessments and claim that elicitation of quantities that pertain to measurable variables of interest, rather than unobservable parameters, should improve the use of judgment-based information in Bayesian analyses. When directly relevant data are lacking, predictions based on subjective assessments can serve as the basis for preliminary management decisions and additional data collection efforts. To inform pending water quality controls for the Neuse River estuary, North Carolina, we combined the survival model with a model describing the time dependence of DO. For current conditions, the mean summer survival rate is predicted to be only 11%. However, if sediment oxygen demand (SOD) is reduced as a result of nutrient management, summer survival rates will increase, reaching 23% with a 25% reduction in SOD and 46% with a 50% SOD reduction. Full model predictions are expressed as probabilities to provide a quantitative basis for risk-based decision-making and experimental design.
Estimating route-specific passage and survival probabilities at a hydroelectric project from smolt radiotelemetry studies
Authors: Skalski John R , Townsend Richard , Lady James , Giorgi Albert E , Stevenson John R , McDonald Robert D
Published: October 2002

A tagrelease study is illustrated using radio-tagged chinook (Oncorhynchus tshawytscha) smolts to concurrently estimate passage rates and survival probabilities through the spillway and turbines of a hydroelectric project. The radio antennas at the forebays of the dam were arranged in double arrays allowing the estimation of route-specific detection probabilities and converting smolt detections to estimates of absolute passage. A maximum likelihood model is presented using the downstream detection histories to jointly estimate the route-specific passage and survival probabilities. In turn, these estimates were combined to estimate smolt survival through the dam, pool, and the entire hydroelectric project. The detailed migration information derived by these techniques can be used to evaluate mitigation programs focused on improving downstream passage of migrating salmonid smolts. At a mid-Columbia River hydroproject, the average spillbay survival calculated across replicate releases of hatchery and run-of-river yearling chinook salmon smolts was 1.000 ( estimated standard error, [Formula: see text] = 0.0144). Average survivals through the two different powerhouses at the hydroproject were estimated to be 0.9409 ([Formula: see text] = 0.0294) and 0.9841 ([Formula: see text] = 0.0119). Project survival after combining the route-specific survival and passage probabilities was estimated across stocks to be 0.9461 ([Formula: see text] = 0.0016).
Effects of environmental metal contamination on the condition, swimming performance, and tissue metabolic capacities of wild yellow perch (Perca flavescens)
Authors: Rajotte James W , Couture Patrice
Published: October 2002

In this study, the general condition, swimming capacities, and tissue metabolic capacities and metal concentrations in wild yellow perch (Perca flavescens) were examined from a range of metal-contaminated lakes near Sudbury, Ontario. Fish exposed to elevated environmental cadmium and copper concentrations showed higher liver concentrations of these metals and lower condition indices. Because growth rate appeared lower in the most metal-contaminated fish, the high tissue activities of nucleoside diphosphate kinase, an indicator of biosynthesis, in these fish indicated an increased rate of protein turnover and suggested a bioenergetic cost of metal exposure. Yellow perch from the most metal-contaminated lakes exhibited lower aerobic capacities, as indicated by citrate synthase and β-hydroxyacyl coenzyme A dehydrogenase activities, two mitochondrial enzymes involved in aerobic adenosine triphosphate production, and by critical swimming speed. There was no evidence from our data that environmental metal exposure affected anaerobic capacities of tissues as measured by lactate dehydrogenase activities or anaerobic fast-start swimming performance. Overall, these data show that metal exposure leads to measurable effects on metabolic capacities in wild yellow perch.
A comparison of the functional ecology of visual vs. nonvisual foraging in two planktivorous marine fishes
Authors: Ryer Clifford H , Lawton Angela , Lopez Ricardo J , Olla Bori L
Published: October 2002

Some visually foraging planktivorous fish will facultatively engage in nonvisual foraging when opportunities arise or necessity dictates. Yet, little is known about the ecology of nonvisual foraging. We examined the roles of prey size, fish size, and prey density on the nonvisual foraging of walleye pollock, Theragra chalcogramma (40100 mm total length), and sablefish, Anoplopoma fimbria (6689 mm), in the laboratory. Both species were size selective, disproportionately consuming large prey just as they do during visual foraging. Large prey were encountered more often, presumably because they were more easily detected by the fish's lateral-line system. When foraging visually, larger fish consumed more prey, but during nonvisual foraging, there was no foraging advantage to greater fish size. Unlike visual detection distances, lateral-line detection distances may not increase appreciably with fish size. Lastly, prey density influenced nonvisual prey consumption. Walleye pollock were characterized by a type I functional response, whereas sablefish were characterized by a type II functional response. Models of planktivore foraging typically assume negligible foraging by particulate feeders below their visual foraging thresholds. On the basis of this study and field data, we suggest that foraging models for particulate feeders, such as juvenile walleye pollock and sablefish, should account for nonvisual size-selective foraging.
Population structure of copper rockfish (Sebastes caurinus) reflects postglacial colonization and contemporary patterns of larval dispersal
Authors: Buonaccorsi Vincent P , Kimbrell Carol A , Lynn Eric A , Vetter Russell D
Published: October 2002

The copper rockfish (Sebastes caurinus) is a benthic, nonmigratory, rocky reef species with pelagic larval and juvenile stages lasting several months. Adults are commonly distributed in temperate coastal waters of the Pacific Ocean from British Columbia to southern California, including the inland waterways of Puget Sound, Washington, a semi-enclosed fjord system of known postglacial origin. Here, we report the distribution of genetic variation at six microsatellite DNA loci from six locations throughout the species' range. Among four coastal samples, significant population subdivision was detected (FST = 0.007), and a significant correlation between genetic and geographic distance was observed. Divergence was large and significant between Puget Sound proper and coastal samples (FST = 0.087). A sample taken only 100 km north of Puget Sound (the Canadian Gulf Islands) was also highly divergent from Puget Sound and coastal samples and was genetically intermediate between the two. The Puget Sound sample also displayed significantly lower allelic diversity and a more substantial presence of private alleles. The patterns of genetic divergence and diversity are most consistent with a historical colonization followed by limited oceanographic exchange among geographically proximate locations.
A simulation study to evaluate impacts of uncertainty on the assessment of American lobster fishery in the Gulf of Maine
Authors: Chen Yong , Wilson Carl
Published: October 2002

The status of the American lobster (Homarus americanus) in the Gulf of Maine (GOM) has been assessed for the last two decades by comparing an estimated current fishing mortality rate for females (Fcur) with a deterministically estimated biological reference point, F10%. The most recent assessment determined that GOM had exceeded the F10% for every year calculated, although in this time landings and abundance have doubled. The current policy does not consider uncertainty in the assessment. This study evaluates the impacts of uncertainty in F10% and Fcur on the status assessment of lobster fishery. Using a Monte Carlo simulation approach, we found that the status assessment would be influenced by uncertainties in estimating F10% and Fcur, and by the choice of decision confidence level reflecting the level of risk managers would like to take. A large uncertainty in Fcur and F10% and a high decision confidence level reduce the likelihood of defining the stock as overfished, and vice versa. Our results suggest that the probability of lobster overfishing may be less than previously thought, and that uncertainty in Fcur and F10% should be quantified and considered in determining the status of the GOM lobster stock.