bluuebunny/crossref_metadata_2025 huggingface dataset:
Heterocyst-Specific Excision of the
Anabaena
sp. Strain PCC 7120
hupL
Element Requires
xisC
Authors: Carrasco Claudio D. , Holliday Scott D. , Hansel Alfred , Lindblad Peter , Golden James W.
Published: August 2005

In nitrogen-limiting conditions, approximately 10% of the vegetative cells in filaments of the cyanobacterium
Anabaena
(
Nostoc
) sp. strain PCC 7120 differentiate into nitrogen-fixing heterocysts. During the late stages of heterocyst differentiation, three DNA elements, each embedded within an open reading frame, are programmed to excise from the chromosome by site-specific recombination. The DNA elements are named after the genes that they interrupt:
nifD
,
fdxN
, and
hupL
. The
nifD
and
fdxN
elements each contain a gene,
xisA
or
xisF
, respectively, that encodes the site-specific recombinase required for programmed excision of the element. Here, we show that the
xisC
gene (alr0677), which is present at one end of the 9,435-bp
hupL
element, is required for excision of the
hupL
element. A strain in which the
xisC
gene was inactivated showed no detectable excision of the
hupL
element.
hupL
encodes the large subunit of uptake hydrogenase. The
xisC
mutant forms heterocysts and grows diazotrophically, but unlike the wild type, it evolved hydrogen gas under nitrogen-fixing conditions. Overexpression of
xisC
from a plasmid in a wild-type background caused a low level of
hupL
rearrangement even in nitrogen-replete conditions. Expression of
xisC
in
Escherichia coli
was sufficient to produce rearrangement of an artificial substrate plasmid bearing the
hupL
element recombination sites. Sequence analysis indicated that XisC is a divergent member of the phage integrase family of recombinases. Site-directed mutagenesis of
xisC
showed that the XisC recombinase has functional similarity to the phage integrase family.
Phosphoenolpyruvate Carboxykinase Is an Acid-Induced, Chromosomally Encoded Virulence Factor in
Agrobacterium tumefaciens
Authors: Liu Pu , Wood Derek , Nester Eugene W.
Published: August 2005

The
pckA
gene, encoding phosphoenolpyruvate carboxykinase, catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to form phosphoenolpyruvate. Located on the circular chromosome of
Agrobacterium
, this locus is adjacent to the loci
chvG
and
chvI
, encoding a two-component regulatory system that has been shown to be important in virulence. Using a reporter gene fusion, studies showed that the
pckA
gene is induced by acidic pH but not by acetosyringone. This acid induction is regulated by the
chvG-chvI
regulatory system, which controls acid-inducible genes. A
pckA
mutant had no demonstrable PckA enzyme activity and grew on AB minimal medium with glucose but did not grow on the same medium with succinate as the sole carbon source and was more inhibited in its growth than the wild-type strain by an acidic environment. A
pckA
mutant was highly attenuated in tumor-inducing ability on tobacco leaf disks and was severely attenuated in
vir
gene expression. Although
vir
gene induction was completely restored when a constitutive
virG
gene was introduced into the mutant strain, virulence was only partially restored. These results suggest that avirulence may be due to a combination of the inhibition of this mutant in the acidic plant wound environment and the poor induction of the
vir
genes.
PtrB of
Pseudomonas aeruginosa
Suppresses the Type III Secretion System under the Stress of DNA Damage
Authors: Wu Weihui , Jin Shouguang
Published: August 2005

In a search for regulatory genes of the type III secretion system (TTSS) in
Pseudomonas aeruginosa
, transposon (Tn
5
) insertional mutants of the
prtR
gene were found defective in the TTSS. PrtR is an inhibitor of
prtN
, which encodes a transcriptional activator for pyocin synthesis genes. In
P. aeruginosa
, pyocin synthesis is activated when PrtR is degraded during the SOS response. Treatment of a wild-type
P. aeruginosa
strain with mitomycin C, a DNA-damaging agent, resulted in the inhibition of TTSS activation. A
prtR
/
prtN
double mutant had the same TTSS defect as the
prtR
mutant, and complementation by a
prtR
gene but not by a
prtN
gene restored the TTSS function. Also, overexpression of the
prtN
gene in wild-type PAK had no effect on the TTSS; thus, PrtN is not involved in the repression of the TTSS. To identify the PrtR-regulated TTSS repressor, another round of Tn mutagenesis was carried out in the background of a
prtR
/
prtN
double mutant. Insertion in a small gene, designated
ptrB
, restored the normal TTSS activity. Expression of
ptrB
is specifically repressed by PrtR, and mitomycin C-mediated suppression of the TTSS is also abolished in a
ptrB
mutant strain. Therefore, PtrB is a new TTSS repressor that coordinates TTSS repression and pyocin synthesis under the stress of DNA damage.
MtdC, a Novel Class of Methylene Tetrahydromethanopterin Dehydrogenases
Authors: Vorholt Julia A. , Kalyuzhnaya Marina G. , Hagemeier Christoph H. , Lidstrom Mary E. , Chistoserdova Ludmila
Published: August 2005

Novel methylene tetrahydromethanopterin (H
4
MPT) dehydrogenase enzymes, named MtdC, were purified after expressing in
Escherichia coli
genes from, respectively,
Gemmata
sp. strain Wa1-1 and environmental DNA originating from unidentified microbial species. The MtdC enzymes were shown to possess high affinities for methylene-H
4
MPT and NADP but low affinities for methylene tetrahydrofolate or NAD. The substrate range and the kinetic properties revealed by MtdC enzymes distinguish them from the previously characterized bacterial methylene-H
4
MPT dehydrogenases, MtdA and MtdB. While revealing higher sequence similarity to MtdA enzymes, MtdC enzymes appear to fulfill a function homologous to the function of MtdB, as part of the H
4
MPT-linked pathway for formaldehyde oxidation/detoxification.
An Amino-Terminal Secretion Signal Is Required for YplA Export by the Ysa, Ysc, and Flagellar Type III Secretion Systems ofYersinia enterocoliticaBiovar 1B
Authors: Warren Sasha M. , Young Glenn M.
Published: August 2005

Yersinia enterocoliticabiovar 1B maintains three distinct type III secretion (TTS) systems, which independently operate to target proteins to extracellular sites. The Ysa and Ysc systems are prototypical contact-dependent TTS systems that translocate toxic effectors to the cytosols of targeted eukaryotic host cells during infection. The flagellar TTS system is utilized during the assembly of the flagellum and is required for secretion of the virulence-associated phospholipase YplA to the bacterial milieu. When ectopically produced, YplA is also a secretion substrate for the Ysa and Ysc TTS systems. In this study, we define elements that allow YplA recognition and export by the Ysa, Ysc, and flagellar TTS systems. Fusion of various amino-terminal regions of YplA toEscherichia colialkaline phosphatase (PhoA) lacking its native secretion signal demonstrated that the first 20 amino acids or corresponding mRNA codons of YplA were sufficient for export of YplA-PhoA chimeras by each TTS system. Export of native YplA by each of the three TTS systems was also found to depend on the integrity of its amino terminus. Introduction of a frameshift mutation or deletion ofyplAsequences encoding the amino-terminal 20 residues negatively impacted YplA secretion. Deletion of otheryplAregions was tolerated, including that resulting in the removal of amino acid residues 30 through 40 of the polypeptide and removal of the 5′ untranslated region of the mRNA. This work supports a model in which independent and distantly related TTS systems ofY. enterocoliticarecognize protein substrates by a similar mechanism.
Identification of theMycobacterium tuberculosisSUF Machinery as the Exclusive Mycobacterial System of [Fe-S] Cluster Assembly: Evidence for Its Implication in the Pathogen's Survival
Authors: Huet Gaëlle , Daffé Mamadou , Saves Isabelle
Published: August 2005

The worldwide recrudescence of tuberculosis and widespread antibiotic resistance have strengthened the need for the rapid development of new antituberculous drugs targeting essential functions of its etiologic agent,Mycobacterium tuberculosis. In our search for new targets, we found that theM. tuberculosis pps1gene, which contains an intein coding sequence, belongs to a conserved locus of seven open reading frames. In silico analyses indicated that the mature Pps1 protein is orthologous to the SufB protein of many organisms, a highly conserved component of the [Fe-S] cluster assembly and repair SUF (mobilization of sulfur) machinery. We showed that the mycobacterialpps1locus constitutes an operon which encodes Suf-like proteins. Interactions between these proteins were demonstrated, supporting the functionality of theM. tuberculosisSUF system. The noticeable absence of any alternative [Fe-S] cluster assembly systems in mycobacteria is in agreement with the apparent essentiality of thesufoperon inMycobacterium smegmatis. Altogether, these results establish that Pps1, as a central element of the SUF system, could play an essential function forM. tuberculosissurvival virtually through its implication in the bacterial resistance to iron limitation and oxidative stress. As such, Pps1 may represent an interesting molecular target for new antituberculous drugs.
Immobilization ofEscherichia coliRNA Polymerase and Location of Binding Sites by Use of Chromatin Immunoprecipitation and Microarrays
Authors: Herring Christopher D. , Raffaelle Marni , Allen Timothy E. , Kanin Elenita I. , Landick Robert , Ansari Aseem Z. , Palsson Bernhard Ø.
Published: August 2005

The genome-wide location of RNA polymerase binding sites was determined inEscherichia coliusing chromatin immunoprecipitation and microarrays (chIP-chip). Cross-linked chromatin was isolated in triplicate from rifampin-treated cells, and DNA bound to RNA polymerase was precipitated with an antibody specific for the β′ subunit. The DNA was amplified and hybridized to “tiled” oligonucleotide microarrays representing the whole genome at 25-bp resolution. A total of 1,139 binding sites were detected and evaluated by comparison to gene expression data from identical conditions and to 961 promoters previously identified by established methods. Of the detected binding sites, 418 were located within 1,000 bp of a known promoter, leaving 721 previously unknown RNA polymerase binding sites. Within 200 bp, we were able to detect 51% (189/368) of the known σ70-specific promoters occurring upstream of an expressed open reading frame and 74% (273/368) within 1,000 bp. Conversely, many known promoters were not detected by chIP-chip, leading to an estimated 26% negative-detection rate. Most of the detected binding sites could be associated with expressed transcription units, but 299 binding sites occurred near inactive transcription units. This map of RNA polymerase binding sites represents a foundation for studies of transcription factors inE. coliand an important evaluation of the chIP-chip technique.
Role of Disulfide Bridges in the Activity and Stability of a Cold-Active α-Amylase
Authors: Siddiqui Khawar Sohail , Poljak Anne , Guilhaus Michael , Feller Georges , D'Amico Salvino , Gerday Charles , Cavicchioli Ricardo
Published: August 2005

The cold-adapted α-amylase from
Pseudoalteromonas haloplanktis
unfolds reversibly and cooperatively according to a two-state mechanism at 30°C and unfolds reversibly and sequentially with two transitions at temperatures below 12°C. To examine the role of the four disulfide bridges in activity and conformational stability of the enzyme, the eight cysteine residues were reduced with β-mercaptoethanol or chemically modified using iodoacetamide or iodoacetic acid. Matrix-assisted laser desorption-time of flight mass spectrometry analysis confirmed that all of the cysteines were modified. The iodoacetamide-modified enzyme reversibly folded/unfolded and retained approximately one-third of its activity. Removal of all disulfide bonds resulted in stabilization of the least stable region of the enzyme (including the active site), with a concomitant decrease in activity (increase in activation enthalpy). Disulfide bond removal had a greater impact on enzyme activity than on stability (particularly the active-site region). The functional role of the disulfide bridges appears to be to prevent the active site from developing ionic interactions. Overall, the study demonstrated that none of the four disulfide bonds are important in stabilizing the native structure of enzyme, and instead, they appear to promote a localized destabilization to preserve activity.
Implications of Physiological Studies Based on Genomic Sequences:
Streptococcus pneumoniae
TIGR4 Synthesizes a Functional LytC Lysozyme
Authors: Moscoso Miriam , López Elena , García Ernesto , López Rubens
Published: August 2005

The
Streptococcus pneumoniae
LytC lysozyme is responsible for autolysis at 30°C (a temperature close to that of the upper respiratory tract), promotes DNA release in competent cultures, and participates in nasopharyngeal colonization. We show that the virulent pneumococcal TIGR4 strain encodes an active LytC enzyme, in contrast with genome-based predictions.
OpsX from
Haemophilus influenzae
Represents a Novel Type of Heptosyltransferase I in Lipopolysaccharide Biosynthesis
Authors: Gronow Sabine , Brabetz Werner , Lindner Buko , Brade Helmut
Published: August 2005

The inner core region of the lipopolysaccharide (LPS) of
Haemophilus influenzae
is characterized by the presence of a phosphorylated 3-deoxy-α-
d
-
manno
-octulosonic acid (Kdo). In this study, we show that the heptosyltransferase I adding the first
l
-
glycero
-
d
-
manno
-heptose residue to this acceptor is encoded by the gene
opsX
, which differs in substrate specificity from the other heptosyltransferase I, known as WaaC.
Effect of farming environment on sensitisation to allergens continues after childhood
Authors: Koskela H O , Happonen K K , Remes S T , Pekkanen J
Published: August 2005

Aims:The farming environment in childhood has been reported to decrease the risk of sensitisation to allergens. The purpose of the present study was to explore whether later exposure to a farming environment also could affect this sensitisation.

Methods:A population based sample of 202 women who did not live on a farm and 231 who did. The subjects filled in a questionnaire and underwent skin prick tests for several common and farming related allergens.

Results:The prevalence of sensitisation to any of the allergens was similar in the two groups (37.1v34.6% (p = NS). However, compared with women who did not live on a farm, the women who lived on a dairy farm showed a low prevalence of sensitisation to pollens (4.4v17.3%, p = 0.01) and cats (3.5v10.4%, p = 0.047). The risk of sensitisation to pollens and pets was lowest among women with both a childhood and adulthood farming environment and was dose dependently associated with current contact with farm animals. However, this contact increased the risk of sensitisation to bovine dander.

Conclusion:The farming environment may reduce sensitisation to common allergens also after early childhood. However, it may also increase sensitisation to farm allergens.
Sensitisation to mites in laboratory animal workers with rhinitis
Authors: Ruoppi P , Koistinen T , Pennanen S
Published: August 2005

Aims:To determine the frequency of sensitisation to mites among rhinitic laboratory animal workers and to clarify whether sensitisation could be occupational.

Methods:Skin prick tests (SPT) were performed in 40 subjects who were working with laboratory animals in Kuopio University research units and who had been referred to Kuopio University Hospital for work related rhinitis. The SPT panel consisted of three storage mites, two house dust mites, 11 other common environmental airborne allergens, latex, and 2–4 individually relevant laboratory animals. To determine signs of mites in animal facilities, guanine was determined in 22 dust samples taken from feedstuffs or bedding material used for laboratory animals and from rooms where these materials were stored and handled.

Results:Positive SPT results were found in 35 out of 40 workers: in 14 for storage mites, four for house dust mites, 25 for other common aeroallergens, as well as positive reactions to laboratory animals in 19 individuals. The guanine test was positive, indicating the presence of mite derived material in 21 out of 22 dust samples.

Conclusions:This study suggests that subjects who are occupationally exposed to laboratory animals are also exposed to mite derived allergens. Sensitisation to mites is common and may be work related.
Mould/dampness exposure at home is associated with respiratory disorders in Italian children and adolescents: the SIDRIA-2 Study
Authors: Simoni M , Lombardi E , Berti G , Rusconi F , La Grutta S , Piffer S , Petronio M G , Galassi C , Forastiere F , Viegi G
Published: August 2005

Aims:To report on the relation between home mould and/or dampness exposure and respiratory disorders in a large sample of children and adolescents in Italy, accounting for age at time of exposure.

Methods:20 016 children (mean age 7 years) and 13 266 adolescents (mean age 13 years) completed questionnaires on indoor exposures and respiratory symptoms/diseases. Statistical analyses were adjusted for sex, age, questionnaire’s compiler, area of residence, season of interview, parental educational status, family history of asthma, rhinitis, eczema, chronic obstructive pulmonary disease, presence of gas water heaters, passive smoking, pets, and active smoking (only for adolescents). Population attributable risk % (PAR) was also computed.

Results:Asthma was more strongly related to only early than to only current exposure, both in children (OR 1.80, 95% CI 1.41 to 2.30) and adolescents (OR 1.89, 95% CI 1.38 to 2.59). The same result was found for rhino-conjunctivitis (OR 1.46, 95% CI 1.17 to 1.82), in children, and for wheeze among adolescents (OR 1.56, 95% CI 1.15 to 2.11). In children, wheeze (OR 1.98, 95% CI 1.47 to 2.66) and eczema (OR 1.44, 95% CI 1.09 to 1.91) were more strongly related to mould/dampness when exposed both early and currently; the same occurred in adolescents for rhino-conjunctivitis (1.78, 95% CI 1.30 to 2.45). Although persistent cough/phlegm was significantly related to mould/dampness exposure in children, regardless of exposure timing, no significant association between mould/dampness exposure and eczema or cough/phlegm was found among adolescents. PAR estimates were higher for only early than only current exposures. Avoiding early only exposure would abate wheeze by 6%, asthma or cough/phlegm by 7%, rhino-conjunctivitis in children by 4%, and in adolescents, asthma by 6%, and wheeze by 4%.

Conclusions:Respiratory disorders such as wheeze and asthma can often be explained by exposure to home mould/dampness, especially early in life. The association seems more evident in children than in adolescents. These findings may suggest the need for environmental prevention strategies.
Darriwilian graptolites of the Hamburg succession (Dauphin Formation), Pennsylvania, and their geologic significance
Authors: Ganis G Robert
Published: August 2005

Graptolites from the Dauphin Formation in the allochthonous Hamburg succession of the Appalachians in Pennsylvania, USA, are late Darriwilian (Da) 3 to early Da 4 age (Middle Ordovician); this age range constrains the timing of the latest depositional episode before the terrane was tectonically mobilized. These rocks were emplaced into the Martinsburg foreland basin of Laurentia during the Taconic orogeny in the early Caradoc (Late Ordovician). Nineteen taxa are described defining a narrow biostratigraphic interval. Among the characteristic fauna collected from of the Da 4 Zone are Pterograptus elegans Holm, Cryptograptus schaeferi Lapworth, Hustedograptus teretiusculus (Hisinger) ?, Haddingograptus oliveri (Bouček), Glossograptus hincksii (Hopkinson), Pseudophyllograptus angustifolius s.l. (J. Hall), and Archiclimacograptus cf. riddellensis (Harris). Tetragraptus cf. erectus Mu et al. found with the above suggests a level low in the Da 4 Zone and a limited occurrence of Bergstromograptus crawfordi (Harris) may indicate some strata within the Da 3 Zone. Proposed new forms include Pseudotrigonograptus ? ricardo sp. nov., and at least two reteograptids. Four examples of Kalpinograptus and Kalpinograptus ? may be new.
Lithological analysis of the Lower Devonian vertebrate-bearing beds at the MOTH locality, N.W.T., Canada: insights to taphonomy and depositional setting
Authors: Zorn Marilyn E , Caldwell Michael W , Wilson Mark VH
Published: August 2005

Sedimentary and faunal characteristics of the Lower Devonian Man On The Hill (MOTH) vertebrate-bearing succession, Mackenzie Mountains, Northwest Territories, Canada provide insights to the paleoenvironmental conditions. Based on sedimentological and petrographic analyses of a 6-m vertical section of the vertebrate-bearing strata, three depositional scenarios for the MOTH locality are proposed, the favoured interpretation being that the vertebrate-bearing interval was deposited on the outer margin of a carbonate platform within an intra-shelf topographic low below storm-wave base. This interpretation is supported by the presence of fine, alternating laminae of light grey argillaceous limestone, or calcareous shale, and dark grey silt to sand-rich calcareous shale, as observed in thin section, and the characterization of the lithology for the vertebrate-bearing strata as an interlaminated argillaceous limestone and calcareous shale. An abundant, low-diversity association of cryptic trace fossils, previously unrecognized at MOTH, is described. These trace fossils and the presence of pyrite suggest that the intra-shelf topographic sag at MOTH had restricted circulation and was generally hypoxic. Based on the instability of such a restricted environment, a cause of death for the cyathaspids Dinaspidella and Nahanniaspis is unclear. However, turbidite deposition and seasonal turnover can be eliminated as possible causes of death, as vertebrates were not located frequently enough within light or dark grey layers and minimal signs of skeletal abrasion or fracturing were observed in Dinaspidella and Nahanniaspis. The high preservation potential of the fossils at MOTH likely was enhanced by the hypoxic nature of the bottom waters within the intra-shelf topographic low below storm-wave base.
SHRIMP UPb geochronology of detrital zircons from the Treasure Lake Group  new evidence for Paleoproterozoic collisional tectonics in the southern Hottah terrane, northwestern Canadian Shield
Authors: Gandhi S S , Breemen O van
Published: August 2005

The recently defined Treasure Lake Group is a platformal sedimentary sequence more than 3 km thick that was deformed and metamorphosed prior to formation of the Great Bear continental arc during 18751845 Ma. The group is exposed as remnants in the southern part of the arc. Its basement is not exposed, but is interpreted to comprise the Paleoproterozoic Hottah terrane, which is exposed at Hottah Lake in the northern part of the arc. Studies in that region show that the Hottah terrane collided with the Archean Slave craton to the east ca. 1883 Ma following reversal of subduction polarity from west to east. Continued eastward subduction under the collision zone formed the Great Bear arc. The present study was undertaken to determine the age and provenance of the Treasure Lake Group. Thirty-nine detrital zircon grains from a sample of a quartz arenite unit in the middle part of the Treasure Lake Group were analyzed by SHRIMP (sensitive high-resolution ion microprobe). They show an age range from ca. 2729 to ca. 1880 Ma, with main modes at ca. 1895, 1985, 2090, and 2330 Ma. These data confirm a mainly Paleoproterozoic provenance for the group. The youngest group of five zircon analyses places the maximum depositional age at 1886 ± 8 Ma. The Treasure Lake Group is close to the north-trending Wopmay medial zone formed during collision of the Hottah terrane and the Slave craton. Deformation and metamorphism of the group can now be attributed to the collisional event. The group may in part be coeval with the Bell Island Bay and Akaitcho groups of the northern Hottah terrane, the lower parts of which were deposited ca. 1900 Ma. The wide range of detrital zircons ages found in this study is interpreted to reflect a complex Paleoproterozoic evolution of the Hottah terrane.
Record of Late Mississippian tectonics in the new Percé Group (Viséan) of eastern Gaspésie, Quebec
Authors: Jutras Pierre , Prichonnet Gilbert
Published: August 2005

Viséan clastic units and structures at the northwest margin of the upper Paleozoic Maritimes Basin provide information on tectonic events that are only poorly recorded in more central parts of the basin. These continental units are time equivalent to marine sediments of the Windsor Group of Nova Scotia. They are herein assigned to the new Percé Group, which includes the La Coulée and Bonaventure formations, as well as a new unit, the Cap d'Espoir Formation. The latter unit unconformably underlies the Bonaventure Formation in a small but thick sub-basin of the Ristigouche Basin in eastern Quebec. It is characterized by a succession of sandstone and mudstone rhythmites that contrast with the coarse alluvial fan deposits of the overlying Bonaventure Formation. The Cap d'Espoir Formation was sourced from a broad area of subdued topography occupied by the Viséan La Coulée Formation and underlying units. Erosional remnants of the La Coulée Formation are unconformably overlain by the Bonaventure Formation in marginal parts of the Ristigouche Basin, whereas these units are separated by the Cap d'Espoir Formation in more central areas of the basin. The La Coulée and Cap d'Espoir formations underwent tilting and erosion during a normal faulting event that preceded deposition of the fault-controlled Bonaventure Formation. This series of events is interpreted to represent different steps in the reactivation of a pre-Carboniferous dextral strike-slip system in response to northwestsoutheast compression during the Viséan in Gaspésie.
Fish use of stage-specific fluvial habitats as refuge patches during a flood in a low-gradient Illinois stream
Authors: Schwartz John S , Herricks Edwin E
Published: August 2005

A stage-specific habitat classification scheme was developed emphasizing the ecological importance of habitat space as flow refugia for fish. Habitat units were based on planform and channel morphology and the resulting three-dimensional hydraulic patterns that form during floods. Fish were sampled in specific habitat patches using prepositioned areal electrofishing devices at two high-flow stages, near bankfull flow and one-half bankfull flow, during a flood. Fish were also sampled at baseflow immediately following the flood to compare changes in habitat use related to flow stage. During the bankfull stage, fish were found to use floodplain habitat units identified as vegetated point bars and concave-bank benches. During the one-half bank-full stage, fish density and biomass were greater in low-velocity habitat units identified as deflection eddies and expansion eddies than in the high-velocity habitat unit identified as the channel thalweg. Once flow returned to baseflow, fish density and biomass were greater in the main channel habitat units (pools, riffles, and glides) than in lateral habitat units identified as submerged point bars and lateral backwaters. This study provided a framework to quantify flow refugia in low-gradient streams, which is especially important in the restoration of anthropogenically disturbed watersheds that have lost habitat connectivity.
Population genetics of northern pike (Esox lucius) introduced into Lake Davis, California
Authors: Aguilar Andres , Banks James D , Levine Kenneth F , Wayne Robert K
Published: August 2005

We used molecular genetic techniques to identify the source population of northern pike (Esox lucius) illegally introduced into Lake Davis, California, and to study the dynamics of genetic change since the introduction. We typed 10 tetranucleotide microsatellite loci from 11 populations and used measures of population differentiation, phylogenetic analysis, and assignment tests to determine the origins of the pre- and post-rotenone-treatment populations. We found that levels of genetic differentiation were low between the pre- and both post-treatment Lake Davis samples and phylogenetic analysis revealed that they were all closely related. Assignment tests classified a high proportion of posttreatment individuals to the original Lake Davis population. Consequently, our results indicate that the fish population that reappeared in 1999 and a subsequent sample in 2002 were descendents or survivors of the initial population. We were unable to assign the pre- or post-treatment individuals consistently to any one population from a panel of potential source populations, indicating that the ultimate source of the Lake Davis population was likely not sampled. Genetic signatures of a recent population bottleneck are evident in the samples from Lake Davis and the effective population size over the sampling period was approximately 712 individuals.
A statistical model for in-season forecasts of sockeye salmon (Oncorhynchus nerka) returns to the Bristol Bay districts of Alaska
Authors: Hyun Saang-Yoon , Hilborn Ray , Anderson James J , Ernst Billy
Published: August 2005

We developed a model for in-season age-specific forecasts of salmon returns using preseason return forecasts, age composition of in-season returns, cumulative in-season returns by fishing district, and age composition and an index of abundance from an in-season test fishery. We apply this method to the sockeye salmon (Oncorhynchus nerka) fishery in the Bristol Bay districts of Alaska. The model generates point estimates and Bayesian probability distributions for return numbers by age and river, and it provides an integrated framework for including all of the major data sources currently used in in-season forecasting. We evaluated model performance using early-season data from 19992001 and compared the effects of four information sets on forecast accuracy. The four information sets were as follows: I, district-specific inshore return data; II, inshore return data and test fishery data; III, inshore return data and preseason forecasts; IV, inshore return data, test fishery data, and preseason forecasts. Forecasts from information sets II, III, and IV were less biased than those from information set I. However, in terms of the forecast interval, forecasts from information set II were best because the 95% highest posterior density regions of forecasts from information set II covered the actual returns most frequently.
Watershed-level sampling effort requirements for determining riverine fish species composition
Authors: Smith Katherine L , Jones Michael L
Published: August 2005

Accurate assessments of watershed-level species composition are necessary for comparative ecological studies, ecosystem health assessments, monitoring, and aquatic conservation prioritization. Several studies have addressed sampling effort requirements for characterizing fish species composition at a section of stream, but none have examined watershed-level requirements. In the spring and summer of 2002, we extensively sampled nine Great Lakes watersheds to assess sampling-effort requirements. Sampling requirements increased with the targeted percentage of estimated species richness. Sampling 15119 randomly selected reaches of stream, stratified by stream order, was on average sufficient to detect 80%100% of estimated species richness. Watershed size (km2) and estimated species richness each showed a weak, negative correlation with sampling-effort requirements in our study streams, with Pearson's correlation coefficients of 5.06 and 0.590, respectively. Because of among-watershed variability in sampling effort requirements, field crews should plot species accumulation curves onsite to determine adequate inventory completion. Based on the difficulty of detecting the last 10% of species, random sampling should be conducted in conjunction with targeted sampling of rare species.
Measurement of hyperfine structure and isotope shifts in Nd II
Authors: Rosner S D , Masterman D , Scholl T J , Holt R A
Published: August 2005

The high-resolution spectra of 110 transitions in Nd II over the range 418465 nm were observed using the collinear fast-ion-beam/laser method (FIBLAS). The lower states of these transitions include the ground state and 10 metastable even-parity states with energies up to 5986 cm1. The 64 odd-parity upper states have energies up to 29 434 cm1. For each transition isotope shifts were measured for all the stable isotopes (mass numbers 142, 143, 144, 145, 146, 148, and 150), as well as hyperfine parameters for the two odd-mass-number isotopes. These quantities are important in modeling profiles of absorption lines in stellar atmospheres to obtain abundances, and in the classification of atomic energy levels. PACS Nos.: 31.30.Gs, 32.10.Fn, 95.30.Ky
Relativistic many-body calculations of excitation energies, line strengths, transition rates, and oscillator strengths in Pd-like ions
Authors: Safronova U I , Cowan T E , Johnson W R
Published: August 2005

Excitation energies, line strengths, oscillator strengths, and transition probabilities are calculated for 4d14f, 4d15p, 4d15f, and 4d16p holeparticle states in Pd-like ions with nuclear charges Z ranging from 49 to 100. Relativistic many-body perturbation theory (MBPT), including the Breit interaction, is used to evaluate retarded E1 matrix elements in length and velocity forms. The calculations start from a [Kr] 4d10 closed-shell DiracHartreeFock (DHF) potential and include second- and third-order Coulomb corrections and second-order BreitCoulomb corrections. First-order perturbation theory is used to obtain intermediate-coupling coefficients and second-order MBPT is used to determine matrix elements. Contributions from negative-energy states are included in the second-order electric-dipole matrix elements. The resulting transition energies, line strengths, and transition rates are compared with experimental values and with other recent calculations. Trends of oscillator strengths as functions of nuclear charge Z are shown graphically for all transitions from the 4d14f, 4d15p, 4d15f, and 4d16p states to the ground state. PACS Nos.: 31.15.Ar, 31.15.Md, 32.70.Cs, 32.30.Rj, 31.25.Jf
Resistive-plate-chamber background particles simulation studies for the endcap region of a compact muon solenoid/large hadron collider using the geometry and tracking code
Authors: Rhee J T , Jamil M
Published: August 2005

We present a method to simulate the double-gap resistive plate chambers (RPC) background particles for the endcap region of a compact muon solenoid/large hadron collider using the geometry and tracking (GEANT) code. We demonstrate that the resistive plate chamber can be described using a realistic Monte Carlo simulation based on the GEANT code and analyzed with physics analysis work station (PAW) interfaces. Sensitivity calculations were performed for γ, e, e+, and such particles in the range 0.1100 MeV for their respective spectra. To evaluate the response of the detector in the large hadron collider (LHC) background environment, the γ, e, and e+ energy spectra expected in the compact muon solenoid (CMS) muon endcap region were taken into account whereas the RPC sensitivity was evaluated as a function of the detector size.PACS Nos.: 7.77.Ka, 7.85.Fv
Fundamental physical constants: looking from different angles
Authors: Karshenboim S G
Published: August 2005

We consider fundamental physical constants that are among a few of the most important pieces of information we have learned about Nature after intensive centuries-long study. We discuss their multifunctional role in modern physics including problems related to the art of measurement, natural and practical units, the origin of the constants, their possible calculability and variability, etc.PACS Nos.: 06.02.Jr, 06.02.Fn
Soil carbon stocks, mineralization rates, and CO2 effluxes under 10 tree species on contrasting soil types
Authors: Ladegaard-Pedersen Pernille , Elberling Bo , Vesterdal Lars
Published: August 2005

Afforestation can increase soil organic carbon (SOC) storage, but the selection of tree species may be critical. This study explored soil CO2 production and effluxes in relation to SOC contents in temperate forests. Sites included even-aged (38 years) first generation stands of eight coniferous and two deciduous species planted at three sites along a gradient in soil fertility. SOC stocks (forest floor + mineral soil 050 cm) differed significantly between tree species, but soil type influenced SOC stocks the most. SOC stocks were significantly higher for stands on low-fertility sandy soils (141 ± 31 Mg C·ha1) than stands on fertile loamy soils (62 ± 14 Mg C·ha1). Soil CO2 effluxes were measured on two occasions in 2002 and varied between 18.7 and 36.3 kg C·ha1·day1. Variability within temperature-adjusted fluxes was not clearly related to tree species or soil type. Potential CO2 production rates in a laboratory incubation experiment (reported as CO2 produced per unit soil C) were mainly affected by site and were two times higher for soils from the nutrient-rich site compared with the most nutrient-poor site. Thus, the combined effect of contrasting CO2 production rates and stocks of soil C may explain the similar CO2 effluxes measured in the field. Results suggest that selection of soil type and tree species are important for SOC sequestration in future afforestation projects.
Long-term effects of thinning and fertilization on growth of red fir in northeastern California
Authors: Zhang Jianwei , Oliver William W , Powers Robert F
Published: August 2005

To determine the impact of fertilization and thinning on growth and development of red fir (Abies magnifica A. Murr.) stands, we established an experiment in a 60-year-old stand using a 2 × 3 factorial design with nitrogen-fertilized and nonfertilized treatments and three stocking levels. Plots were established in 1976 and were measured every 5 years for 26 years. The periodic annual increment in basal area was 97%, 51%, 38%, and 33% greater in fertilized trees than in nonfertilized trees during the first, second, third, and fourth 5-year periods, respectively. After 20 years, annual basal area increment was greater in nonfertilized trees. The response of annual volume increment to fertilization was not statistically significant until the fourth period. Yet, volume increases of the fertilized plots were 25%92% greater than those of the nonfertilized plots from 1976 to 1996. Similarly, basal area increment was greater in lightly thinned plots than in unthinned plots from the second period on, until heavy mortality during 19962002. Basal area increment was greater in the heavily thinned plots from the fourth period on. Results indicate that red fir can respond to fertilization and thinning quickly and that both treatments speed stand development. In addition, fertilization increases the stand's carrying capacity. Therefore, forest managers can use these silvicultural practices to improve stand growth, to reduce fire fuels, and to accelerate stand development.
Predicting the future diameter of stems in Norway spruce stands subjected to different thinning regimes
Authors: Karlsson Kjell , Norell Lennart
Published: August 2005

The future diameter of stems in even-aged Norway spruce (Picea abies (L.) Karst.) stands subjected to different thinning regimes was modelled, using data from a thinning experiment established in 25 localities in southern Sweden. Separate models were developed for stands thinned from below, stands thinned from above, and unthinned stands. A bivariate approach was used to construct the models, based on DBH data from the initial stand and from the same trees at future points in time. The approach entails that the dependency between initial and future DBHs can be directly used to predict the future DBH. Also, the modelling used stand and site characteristics together with information about the stand density management regime. The initial stands were assumed to be unthinned, and the dominant height was assumed to be 1218 m. A logistic function was used to predict which individual trees would remain at future points in time. The mean and standard deviation of the differences between observed and predicted future diameters were used to validate the models. When the prediction period was approximately 33 years, the mean was typically underestimated by 4 mm, and the standard deviation was approximately 40 mm.
Incidence of main stem infections of lodgepole pine by western gall rust decreases with tree age
Authors: Blenis Peter V , Li Wuhan
Published: August 2005

Infection of lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia Engelm.) by western gall rust has been shown to decrease with tree height and age, but the effects of those two factors have not been separated. Five replicate artificial inoculations were done on a total of 327 trees of different ages in two height classes. Temperature and percentage of spore germination at the height of inoculation, shoot development (stem elongation at the time of inoculation as a proportion of final shoot elongation), main stem leader length at the time of inoculation, tree height, and tree age were measured. Modeled percentages of infected trees and the number of galls per 10 cm of shoot length decreased by 85% and 88%, respectively, as tree age increased between 2 and 10 years, indicating the undesirability of early, aggressive precommercial thinning of lodgepole pine stands in areas where western gall rust is common. By controlling and (or) statistically accounting for inoculum, microclimate, and phenological factors, it was possible to demonstrate that changes in susceptibility with tree age are sufficient to account for the reduction in infection with tree height.
Effects of partial cutting on the ectomycorrhizae ofPicea glaucaforests in northwestern Alberta
Authors: Lazaruk Lance W , Kernaghan Gavin , Macdonald S Ellen , Khasa Damase
Published: August 2005

This study assessed the impact of various harvesting practices (including those designed to emulate natural disturbances) on ectomycorrhizae (ECM) associated with white spruce (Picea glauca (Moench) Voss) in northwestern Alberta, Canada. Treatments included clearcuts, partial cuts (dispersed green-tree retention with 20%, 50%, and 75% residual live trees, and aggregated green-tree retention), unharvested control sites, and a burned stand. The percentage of active white spruce root tips and ECM richness and diversity, as observed in soil cores collected throughout the study site, all decreased with increasing disturbance intensity. Effects were particularly pronounced in clearcuts, machine corridors used for access by harvesting equipment in the dispersed green-tree retention stands, and in burned areas. Reductions in ECM biodiversity could be attributed to the sensitivity of late-stage ectomycorrhizae (e.g., Cortinarius spp., Lactarius spp., and Russula spp.) to soil disturbances and changes in microclimate associated with harvesting or burning. Areas of dispersed and aggregated green-tree retention were not dramatically different than unharvested forest in terms of root tip density and ECM richness, diversity, and composition. Harvesting practices that retain a percentage of residual live trees, either dispersed throughout the cutting unit or in aggregated patches, could be an effective means of maintaining ectomycorrhizal biodiversity at the stand level.
Succession of understory vegetation in managed and seminatural Scots pine forests in eastern Finland and Russian Karelia
Authors: Uotila Anneli , Hotanen Juha-Pekka , Kouki Jari
Published: August 2005

The aim of this study was to compare the understory vegetation in chronosequences representing seminatural and managed Scots pine (Pinus sylvestris L.) forests on dryish heaths of the Vaccinium type. The data represent the middle boreal vegetation zone and were collected in eastern Finland and the Dvina area of Karelia, on both sides of the border between Finland and the Russian Federation. Species diversity and the coverage of the various life-form groups (ground lichens, mosses, liverworts, grasses, herbs, dwarf shrubs, and tree seedlings) were used to analyse the properties of the ground vegetation over the succession from open forest land to closed forest communities. The clearest differences in diversity between the seminatural forests mainly influenced by fire and managed forests occurred in the early stages of succession. Forest management appeared to increase the species richness at the beginning of succession. The seminatural stands were rich in Cladonia lichens and dwarf shrubs up until tree canopy closure; however, the abundance of mosses was lower in the seminatural stands. Forest management favoured an abundance of grasses, notably Deschampsia flexuosa, which was common after clear-cutting. The use of prescribed burning in silviculture could result in more natural vegetation succession dynamics in managed stands.
Costs and regional impacts of restoration thinning programs on the national forests in eastern Oregon
Authors: Adams Darius M , Latta Gregory S
Published: August 2005

An intertemporal spatial equilibrium model of the eastern Oregon softwood log market was employed to estimate the market and economic welfare impacts of restoration thinning programs established on national forests in the region. Programs treated only lands with sawtimber thinning volume and varied by the extent of public subsidies for costs, the types of costs that could be subsidized, and the form of the subsidy payment. Impacts on private harvest timing, numbers of mills, and postprogram log prices in the region were found to vary markedly with the form of the program. Log consumers (lumber mills) consistently realized relatively large surplus gains, while private log producers' surplus showed smaller but consistent losses. For a comparable subsidy budget, programs that subsidized only hazard removal costs, on sites where net unsubsidized sawtimber returns promised to be less that these costs, led to a larger area treated than did programs with more flexible subsidy conditions. Across all programs, net agency receipts from sawtimber sales were estimated to be insufficient to cover the costs of all areas in need of thinning treatment (lands with and without sawtimber thinning volume).
Eleven-year response of foliar chemistry to chronic nitrogen and sulfur additions at the Bear Brook Watershed in Maine
Authors: Elvir Jose Alexander , Rustad Lindsey , Wiersma G Bruce , Fernandez Ivan , White Alan S , White Gregory J
Published: August 2005

The foliar chemistry of sugar maple (Acer saccharum Marsh.), American beech (Fagus grandifolia Ehrh.), and red spruce (Picea rubens Sarg.) was studied from 1993 to 2003 at the Bear Brook Watershed in Maine (BBWM). The BBWM is a paired-watershed forest ecosystem study, with one watershed treated bimonthly since 1989 with ammonium sulfate ((NH4)2SO4) at a rate of 25.2 kg N·ha1·year1. Foliar N concentrations were higher in all tree species within the treated watershed compared with trees within the reference watershed. Foliar Ca and Mg concentrations were lower in American beech and red spruce within the treated watershed. There were no significant differences in foliar K concentrations between watersheds. Foliar P and Mn concentration differences between watersheds were inconsistent among years. Differences in foliar N concentrations between watersheds declined over time in sugar maple but not in red spruce or American beech. Differences in foliar Ca and Mg concentrations between the treated and reference watersheds increased over time for American beech and red spruce, primarily because of a consistent decline in concentrations of these nutrients in trees within the treated watershed. No temporal trends in foliar Ca and Mg concentration differences between watersheds were observed for sugar maple.