bluuebunny/crossref_metadata_2025 huggingface dataset:
TtgV Bound to a Complex Operator Site Represses Transcription of the Promoter for the Multidrug and Solvent Extrusion TtgGHI Pump
Authors: Guazzaroni María-Eugenia , Terán Wilson , Zhang Xiaodong , Gallegos María-Trinidad , Ramos Juan L.
Published: May 2004

The TtgGHI efflux pump of
Pseudomonas putida
extrudes a variety of antibiotics and solvents. We show that the
ttgGHI
operon is transcribed in vitro and in vivo from a single promoter and not from two overlapping promoters as previously proposed. The expression of this promoter is controlled by the TtgV repressor, whose operator expands through four helical turns that overlap the −10 region of the promoter. We also show that TtgV is released from its operator on binding of effectors such as aliphatic alcohols. Mutational analysis of the
ttgGHI
promoter revealed that substitutions at −13, −12, and −8 yielded promoters that were unable to drive transcription whereas certain mutations at −9, −11, and −6 to −3 increased expression in vivo. The cause of the increased expression was either a decrease in the affinity of the TtgV protein for its operator or an increase in the affinity of RNA polymerase for the mutant promoters.
Mutations in
Haemophilus influenzae
Mismatch Repair Genes Increase Mutation Rates of Dinucleotide Repeat Tracts but Not Dinucleotide Repeat-Driven Pilin Phase Variation Rates
Authors: Bayliss Christopher D. , Sweetman Wendy A. , Moxon E. Richard
Published: May 2004

High-frequency, reversible switches in expression of surface antigens, referred to as phase variation (PV), are characteristic of
Haemophilus influenzae
. PV enables this bacterial species, an obligate commensal and pathogen of the human upper respiratory tract, to adapt to changes in the host environment. Phase-variable hemagglutinating pili are expressed by many
H. influenzae
isolates. PV involves alterations in the number of 5′ TA repeats located between the −10 and −35 promoter elements of the overlapping, divergently orientated promoters of
hifA
and
hifBCDE
, whose products mediate biosynthesis and assembly of pili. Dinucleotide repeat tracts are destabilized by mismatch repair (MMR) mutations in
Escherichia coli
. The influence of mutations in MMR genes of
H. influenzae
strain Rd on dinucleotide repeat-mediated PV rates was investigated by using reporter constructs containing 20 5′ AT repeats. Mutations in
mutS
,
mutL
, and
mutH
elevated rates approximately 30-fold, while rates in
dam
and
uvrD
mutants were increased 14- and 3-fold, respectively. PV rates of constructs containing 10 to 12 5′ AT repeats were significantly elevated in
mutS
mutants of
H. influenzae
strains Rd and Eagan. An intact
hif
locus was found in 14 and 12% of representative nontypeable
H. influenzae
isolates associated with either otitis media or carriage, respectively. Nine or more tandem 5′ TA repeats were present in the promoter region. Surprisingly, inactivation of
mutS
in two serotype b
H. influenzae
strains did not alter pilin PV rates. Thus, although functionally analogous to the
E. coli
MMR pathway and active on dinucleotide repeat tracts, defects in
H. influenzae
MMR do not affect 5′ TA-mediated pilin PV.
Positive Control of Swarming, Rhamnolipid Synthesis, and Lipase Production by the Posttranscriptional RsmA/RsmZ System inPseudomonas aeruginosaPAO1
Authors: Heurlier Karin , Williams Faye , Heeb Stephan , Dormond Corinne , Pessi Gabriella , Singer Dustin , Cámara Miguel , Williams Paul , Haas Dieter
Published: May 2004

InPseudomonas aeruginosa, the small RNA-binding, regulatory protein RsmA is a negative control element in the formation of several extracellular products (e.g., pyocyanin, hydrogen cyanide, PA-IL lectin) as well as in the production ofN-acylhomoserine lactone quorum-sensing signal molecules. RsmA was found to control positively the ability to swarm and to produce extracellular rhamnolipids and lipase, i.e., functions contributing to niche colonization byP. aeruginosa. AnrsmAnull mutant was entirely devoid of swarming but produced detectable amounts of rhamnolipids, suggesting that factors in addition to rhamnolipids influence the swarming ability ofP. aeruginosa. A small regulatory RNA,rsmZ, which antagonized the effects of RsmA, was identified inP. aeruginosa. Expression of thersmZgene was dependent on both the global regulator GacA and RsmA, increased with cell density, and was subject to negative autoregulation. Overexpression ofrsmZand a null mutation inrsmAresulted in quantitatively similar, negative or positive effects on target genes, in agreement with a model that postulates titration of RsmA protein by RsmZ RNA.
Dual Control ofHelicobacter pyloriHeat Shock Gene Transcription by HspR and HrcA
Authors: Spohn Gunther , Danielli Alberto , Roncarati Davide , Delany Isabel , Rappuoli Rino , Scarlato Vincenzo
Published: May 2004

The HspR repressor regulates transcription of thegroESL,hrcA-grpE-dnaK, andcbpA-hspR-orfoperons ofHelicobacter pylori. Here we show that two of the HspR-regulated operons, namely, thegroESLanddnaKoperons, encoding the major cellular chaperone machineries are also regulated by theH. pylorihomologue of the HrcA repressor. Similarly to thehspRmutation, deletion of thehrcAgene also leads to complete derepression of the Pgroand Phrcpromoters. The presence of both HspR and HrcA is therefore necessary for regulated transcription from these promoters. HrcA binds directly to Pgroand Phrc, likely contacting two inverted repeats with similarity to the CIRCE motif, which are present on both promoters. HrcA regulation is, however, shown to depend on binding of the HspR protein, since deletion of the HspR-binding site of the Pgropromoter leads to loss of heat inducibility of this promoter. In contrast, transcription from the Pcbppromoter is regulated solely by HspR. HspR is also shown to form oligomers in vivo through a stretch of hydrophobic repeats between amino acid positions 66 and 97. The implications of these findings for the elucidation of the networks regulating heat shock gene expression inH. pyloriare discussed.
Effects of a
gerF
(
lgt
) Mutation on the Germination of Spores of
Bacillus subtilis
Authors: Igarashi Takao , Setlow Barbara , Paidhungat Madan , Setlow Peter
Published: May 2004

One of the proteins of the membrane-bound receptors that recognize individual nutrients that trigger germination of spores of
Bacillus subtilis
contains the recognition sequence for diacylglycerol addition to a cysteine residue near the protein's N terminus.
B. subtilis
spores lacking the
gerF
(
lgt
) gene that codes for prelipoprotein diacylglycerol transferase exhibited significantly slowed germination in response to nutrient germinants as found previously, but germination of
gerF
spores with a mixture of Ca
2+
and dipicolinic acid or with dodecylamine was normal, as was the spontaneous germination of
gerF
spores lacking all nutrient germinant receptors. The deleterious effects of the
gerF
mutation on nutrient germination were highest on germination triggered by the GerA nutrient receptor and were less so (but still significant) on germination triggered by the GerB nutrient receptor. However, there was little, if any, effect on GerK nutrient receptor-mediated spore germination. As predicted from the latter results, replacement by alanine of the cysteine residue to which diacylglycerol is thought to be added to these nutrient receptors had a large effect on GerA receptor function, less effect on GerB receptor function, and little, if any, effect on GerK receptor function.
Drastic Differences in Crh and HPr Synthesis Levels Reflect Their Different Impacts on Catabolite Repression in
Bacillus subtilis
Authors: Görke Boris , Fraysse Laetitia , Galinier Anne
Published: May 2004

In
Bacillus subtilis
, carbon catabolite repression (CCR) of catabolic genes is mediated by ATP-dependent phosphorylation of HPr and Crh. Here we show that the different efficiencies with which these two proteins contribute to CCR may be due to the drastic differences in their synthesis rates under conditions that cause CCR.
PhaQ, a New Class of Poly-β-Hydroxybutyrate (PHB)-Responsive Repressor, Regulates
phaQ
and
phaP
(Phasin) Expression in
Bacillus megaterium
through Interaction with PHB
Authors: Lee Tian-Ren , Lin Jer-Sheng , Wang Shih-Shin , Shaw Gwo-Chyuan
Published: May 2004

Bacillus megaterium
can produce poly-β-hydroxybutyrate (PHB) as carbon and energy storage materials. We now report that the
phaQ
gene, which is located upstream of the phasin-encoding
phaP
gene, codes for a new class of transcriptional regulator that negatively controls expression of both
phaQ
and
phaP
. A PhaQ binding site that plays a role in this control has been identified by gel mobility shift assays and DNase I footprinting analysis. We have also provided evidence that PhaQ could sense the presence of PHB in vivo and that artificial PHB granules could inhibit the formation of PhaQ-DNA complex in vitro by binding to PhaQ directly. These suggest that PhaQ is a PHB-responsive repressor.
Agrobacterium rhizogenes
GALLS Protein Substitutes for
Agrobacterium tumefaciens
Single-Stranded DNA-Binding Protein VirE2
Authors: Hodges Larry D. , Cuperus Josh , Ream Walt
Published: May 2004

Agrobacterium tumefaciens
and
Agrobacterium rhizogenes
transfer plasmid-encoded genes and virulence (Vir) proteins into plant cells. The transferred DNA (T-DNA) is stably inherited and expressed in plant cells, causing crown gall or hairy root disease. DNA transfer from
A. tumefaciens
into plant cells resembles plasmid conjugation; single-stranded DNA (ssDNA) is exported from the bacteria via a type IV secretion system comprised of VirB1 through VirB11 and VirD4. Bacteria also secrete certain Vir proteins into plant cells via this pore. One of these, VirE2, is an ssDNA-binding protein crucial for efficient T-DNA transfer and integration. VirE2 binds incoming ssT-DNA and helps target it into the nucleus. Some strains of
A. rhizogenes
lack VirE2, but they still transfer T-DNA efficiently. We isolated a novel gene from
A. rhizogenes
that restored pathogenicity to
virE2
mutant
A. tumefaciens
. The GALLS gene was essential for pathogenicity of
A. rhizogenes
. Unlike VirE2, GALLS contains a nucleoside triphosphate binding motif similar to one in TraA, a strand transferase conjugation protein. Despite their lack of similarity, GALLS substituted for VirE2.
Two Separate Quorum-Sensing Systems Upregulate Transcription of the Same ABC Transporter inStreptococcus pneumoniae
Authors: Knutsen Eivind , Ween Ola , Håvarstein Leiv Sigve
Published: May 2004

Streptococcus pneumoniaesecretes two different peptide pheromones used for intercellular communication. These peptides, which have completely unrelated primary structures, activate two separate signal transduction pathways, ComABCDE and BlpABCSRH, which regulate natural genetic transformation and bacteriocin production, respectively. Each signal transduction pathway contains a response regulator (ComE and BlpR, respectively) that activates transcription of target genes by binding to similar, but not identical, imperfect direct repeat motifs. In general the direct repeat binding sites are specific for one or the other of the two response regulators, ensuring that competence development and bacteriocin production are regulated separately. However, in the present study we show that the rate of transcription of an operon, encoding an ABC transporter of unknown function, can be stimulated by both peptide pheromones. We also show that this cross-induction is due to a hybrid direct repeat motif that can respond to both ComE and BlpR. To our knowledge this kind of convergent gene regulation by two separate two-component regulatory systems has not been described before in bacteria.
Precise Excision of the Large Pathogenicity Island, SPI7, inSalmonella entericaSerovar Typhi
Authors: Bueno Susan M. , Santiviago Carlos A. , Murillo Alejandro A. , Fuentes Juan A. , Trombert A. Nicole , Rodas Paula I. , Youderian Philip , Mora Guido C.
Published: May 2004

The large pathogenicity island (SPI7) ofSalmonella entericaserovar Typhi is a 133,477-bp segment of DNA flanked by two 52-bp direct repeats overlapping thepheU(phenylalanyl-tRNA) gene, contains 151 potential open reading frames, and includes theviaBoperon involved in the synthesis of Vi antigen. Some clinical isolates ofS. entericaserovar Typhi are missing the entire SPI7, due to its precise excision; these strains have lost the ability to produce Vi antigen, are resistant to phage Vi-II, and invade a human epithelial cell line more rapidly. Excision of SPI7 occurs spontaneously in a clinical isolate ofS. entericaserovar Typhi when it is grown in the laboratory, leaves an intact copy of thepheUgene at its novel join point, and results in the same three phenotypic consequences. SPI7 is an unstable genetic element, probably an intermediate in the pathway of lateral transfer of such pathogenicity islands among enteric gram-negative bacteria.
Nitrite-Responsive Activation of the Nitrate Assimilation Operon in Cyanobacteria Plays an Essential Role in Up-Regulation of Nitrate Assimilation Activities under Nitrate-Limited Growth Conditions
Authors: Aichi Makiko , Maeda Shin-Ichi , Ichikawa Kazuhiro , Omata Tatsuo
Published: May 2004

NtcB of the cyanobacterium
Synechococcus elongatus
strain PCC 7942 is a LysR family protein that enhances expression of the nitrate assimilation operon (
nirA
operon) in response to the presence of nitrite, an intermediate of assimilatory nitrate reduction. Inactivation of
ntcB
in this cyanobacterium specifically abolishes the nitrite responsiveness of
nirA
operon expression, but under nitrate-replete conditions (wherein negative feedback by intracellularly generated ammonium prevails over the positive effect of nitrite) activity levels of the nitrate assimilation enzymes are marginally higher in the wild-type cells than in the mutant cells, raising the issue of whether the nitrite-promoted regulation has physiological importance. On the other hand, the strains carrying
ntcB
expressed much higher nitrate assimilation enzyme activities under nitrate-limited growth conditions than under nitrate-replete conditions whereas the
ntcB
-deficient strains showed levels of the enzyme activities lower than those seen under the nitrate-replete conditions. Although the
ntcB
mutant maintained a constant cell population in a nitrate-limited chemostat when grown as a single culture, it was diluted at a rate expected for nondividing cells when mixed with the wild-type cells and subjected to nitrate limitation in the chemostat culture system. These results demonstrated that the nitrite-promoted activation of the nitrate assimilation operon is essential for up-regulation of the nitrate assimilation activities under the conditions of nitrate limitation and for competitive utilization of nitrate.
Horizontal Transfer of CS1 Pilin Genes of EnterotoxigenicEscherichia coli
Authors: Froehlich Barbara , Holtzapple Erik , Read Timothy D. , Scott June R.
Published: May 2004

CS1 is one of a limited number of serologically distinct pili found in enterotoxigenicEscherichia coli(ETEC) strains associated with disease in people. The genes for the CS1 pilus are on a large plasmid, pCoo. We show that pCoo is not self-transmissible, although our sequence determination for part of pCoo shows regions almost identical to those in the conjugative drug resistance plasmid R64. When we introduced R64 into a strain containing pCoo, we found that pCoo was transferred to a recipient strain in mating. Most of the transconjugant pCoo plasmids result from recombination with R64, leading to acquisition of functional copies of all of the R64 transfer genes. Temporary coresidence of the drug resistance plasmid R64 with pCoo leads to a permanent change in pCoo so that it is now self-transmissible. We conclude that when R64-like plasmids are transmitted to an ETEC strain containing pCoo, their recombination may allow for spread of the pCoo plasmid to other enteric bacteria.
ClgR, a Novel Regulator of
clp
and
lon
Expression in
Streptomyces
Authors: Bellier Audrey , Mazodier Philippe
Published: May 2004

The
clp
genes encoding the Clp proteolytic complex are widespread among living organisms. Five
clpP
genes are present in
Streptomyces.
Among them, the
clpP1 clpP2
operon has been shown to be involved in the
Streptomyces
growth cycle, as a mutation blocked differentiation at the substrate mycelium step. Four Clp ATPases have been identified in
Streptomyces coelicolor
(ClpX and three ClpC proteins) which are potential partners of ClpP1 ClpP2. The
clpC1
gene appears to be essential, since no mutant has yet been obtained.
clpP1 clpP2
and
clpC1
are important for
Streptomyces
growth, and a study of their regulation is reported here. The
clpP3 clpP4
operon, which has been studied in
Streptomyces lividans
, is induced in a
clpP1
mutant strain, and regulation of its expression is mediated via PopR, a transcriptional regulator. We report here studies of
clgR
, a paralogue of
popR
, in
S. lividans.
Gel mobility shift assays and DNase I footprinting indicate that ClgR binds not only to the
clpP1
and
clpC1
promoters, but also to the promoter of the Lon ATP-dependent protease gene and the
clgR
promoter itself. ClgR recognizes the motif GTTCGC-5N-GCG. In vivo, ClgR acts as an activator of
clpC1
gene and
clpP1
operon expression. Similarly to PopR, ClgR degradation might be ClpP dependent and could be mediated via recognition of the two carboxy-terminal alanine residues.
Contribution of the RpoA C-Terminal Domain to Stimulation of the
Salmonella enterica hilA
Promoter by HilC and HilD
Authors: Olekhnovich Igor N. , Kadner Robert J.
Published: May 2004

Expression of invasion genes in
Salmonella
pathogenicity island 1 (SPI-1) is mainly driven by the transcriptional activator HilA. Transcription of
hilA
is subject to complex control and is stimulated by the SPI-1-encoded HilC and HilD proteins. The C-terminal domain of RpoA contributes to
hilA
activation by HilC/D under certain inducing conditions.
Lipid II-Mediated Pore Formation by the Peptide Antibiotic Nisin: a Black Lipid Membrane Study
Authors: Wiedemann Imke , Benz Roland , Sahl Hans-Georg
Published: May 2004

The antibiotic peptide nisin is the first known lantibiotic that uses a docking molecule within the bacterial cytoplasmic membrane for pore formation. Through specific interaction with the cell wall precursor lipid II, nisin forms defined pores which are stable for seconds and have pore diameters of 2 to 2.5 nm.
The Nucleotide Transporter of
Caedibacter caryophilus
Exhibits an Extended Substrate Spectrum Compared to the Analogous ATP/ADP Translocase of
Rickettsia prowazekii
Authors: Daugherty Robin M. , Linka Nicole , Audia Jonathon P. , Urbany Claude , Neuhaus H. Ekkehard , Winkler Herbert H.
Published: May 2004

The two obligate intracellular alphaproteobacteria
Rickettsia prowazekii
and
Caedibacter caryophilus
, a human pathogen and a paramecium endosymbiont, respectively, possess transport systems to facilitate ATP uptake from the host cell cytosol. These transport proteins, which have 65% identity at the amino acid level, were heterologously expressed in
Escherichia coli
, and their properties were compared. The results presented here demonstrate that the caedibacter transporter had a broader substrate than the more selective rickettsial transporter. ATP analogs with modified sugar moieties, dATP and ddATP, inhibited the transport of ATP by the caedibacter transporter but not by the rickettsial transporter. Both transporters were specific for di- and trinucleotides with an adenine base in that adenosine tetraphosphate, AMP, UTP, CTP, and GTP were not competitive inhibitors. Furthermore, the antiporter nature of both transport systems was shown by the dependence of the efflux of [α-
32
P]ATP on the influx of substrate (ATP but not dATP for rickettsiae, ATP or dATP for caedibacter).
Characterization of a Nucleotide-Binding Domain Associated with Neisserial Iron Transport
Authors: Lau Gloria H. Y. , MacGillivray Ross T. A. , Murphy Michael E. P.
Published: May 2004

The
fbpABC
operon in
Neisseria gonorrhoeae
encodes an ATP-binding cassette transporter required for iron uptake from the host ferric binding proteins. The gene for the nucleotide-binding domain (
fbpC
) expressed in
Escherichia coli
has intrinsic ATPase activity (0.5 mmol/min/mg) uncoupled from the iron transport process. The FbpC E164D mutant is found to have a 10-fold reduction in specific activity. FbpC is covalently modified by 8-azido-[γ
32
P]ATP, indicating that FbpC is a functional ATPase that likely combines with FbpB to form a ferric iron transporter.
A Phage Protein Confers Resistance to the Lactococcal Abortive Infection Mechanism AbiP
Authors: Domingues Susana , Chopin Alain , Ehrlich S. Dusko , Chopin Marie-Christine
Published: May 2004

Phage bIL66M1 is sensitive to the lactococcal abortive infection mechanism AbiP. No spontaneous AbiP-resistant variant could be obtained at a frequency of <10
−10
. However, AbiP-resistant variants were readily obtained during infection with both bIL66M1 and the highly homologous AbiP-resistant phage bIL170. Gain of AbiP resistance was due to the acquisition of the
e6
gene from bIL170.
A neighborhood analysis of canopy tree competition: effects of shading versus crowding
Authors: Canham Charles D , LePage Philip T , Coates K Dave
Published: May 2004

We have developed extensions of traditional distance-dependent, spatial competition analyses that estimate the magnitude of the competitive effects of neighboring trees on target tree growth as a function of the species, size, and distance to neighboring trees. Our analyses also estimate inter- and intra-specific competition coefficients and explicitly partition the competitive effects of neighbors into the effects of shading versus crowding. We tested the method using data from forests of northern, interior British Columbia dominated by western hemlock (Tsuga heterophylla (Raf.) Sarg.) and western redcedar (Thuja plicata Donn ex D. Don). For both species, the most parsimonious regression models included terms for the effects of tree size, crowding, and shading and separate competitive effects of four different groups of competing species. The models explained 33%59% of the variation in radial growth of the two species. For both species, growth declined more steeply as a function of crowding than shading. There was striking asymmetry in the strength of interspecific competition between hemlock and redcedar, with crowding by hemlock having a strong per capita effect on redcedar, while crowding by redcedar had relatively little effect on the radial growth of hemlock.
A model to estimate light interception by tree crowns, applied to black spruce
Authors: Groot Arthur
Published: May 2004

CORONA is a spatially explicit model designed to efficiently estimate the quantity of shortwave radiation intercepted by individual tree crowns. Radiation interception is determined from intersections of light rays with tree crowns for rays originating throughout the sky hemisphere. CORONA comprises a flexible, asymmetric description of crowns, a computationally efficient ray-tracing procedure, numerical solution of ray × crown intersections, and several alternative within-crown light interception functions. The interception functions were calibrated and evaluated in two plots located in black spruce (Picea mariana (Mill.) BSP) stands, where tree positions and crowns were mapped. An interception function using only the number of intercepting crowns (i.e., a hits function) generally resulted in better agreement between modelled and observed light levels than an interception function using the total path length through crowns. There was some evidence that transmission was greater in parts of crowns within low-light-level environments. This effect can be incorporated into an interception function for more realistic modelling of interception. Errors in crown description are likely the main cause of discrepancies between modelled and observed light levels on a half-hourly basis. The agreement between modelled and observed light levels on a daily basis indicates that CORONA can provide useful estimates of light interception by tree crowns.
Effects of fertilization on resin canal defences and incidence of Pissodes strobi attack in interior spruce
Authors: vanAkker Lara , Alfaro René I , Brockley Robert
Published: May 2004

The effects of six fertilization treatments on tree height and incidence of attack by the white pine weevil, Pissodes strobi (Peck), on interior spruce (a hybrid, Picea glauca (Moench) Voss × Picea engelmannii Parry ex Engelm.) were explored in a field study. In a corresponding laboratory study, changes in constitutive and traumatic resin canal defences in response to fertilization were measured. Incidence of weevil attack increased with fertilization intensity. This trend was explained by increased resources available for weevil feeding (adults and larvae) as a result of increased leader size and bark thickness, as well as by an observed weakening in the tree's constitutive resin canal defences. The ability of interior spruce to produce a traumatic resin response was not influenced by fertilization. Although incidence of weevil attack was greatest in trees from the most intense fertilization treatments, height losses due to weevil attack were not as great as height gains due to fertilization treatment. Therefore, we concluded that fertilization is a feasible option for increasing productivity of interior spruce plantations, particularly if other weevil control alternatives are implemented.
Potential pollen contamination effects on progeny from an off-site Douglas-fir seed orchard: 9-year field results
Authors: Stoehr M U , Webber J E , Hollefreund C CA , Painter R A
Published: May 2004

To evaluate the potential effects of seed orchard pollen contamination from surrounding background sources, we made control pollinations with outside orchard pollen and inside orchard pollen on trees of a Douglas-fir (Pseudo tsuga menziesii (Mirb.) Franco) coastalinterior transition zone seed orchard. The resulting progeny were tested on a transition zone and a coastal site. After nine growing seasons, survival was above 90% on both sites for both pollen sources, and the trees height differences due to pollen source were statistically nonsignificant. Wildstand operational seedlots, used as controls, were 17% shorter than the "contaminated" seedlings. Orchard management implications of these results are discussed.
Postdispersal seed predation of white spruce in cutblocks in the boreal mixedwoods: a short-term experimental study
Authors: Peters Susan H , Macdonald S Ellen , Boutin Stan , Moses Richard A
Published: May 2004

We conducted a 1-year study to examine the influence of postdispersal seed predation by small mammals and other vertebrate predators on seedling recruitment rates (percentage of seeds surviving to seedling stage) and seed loss of white spruce (Picea glauca (Moench) Voss) in recently logged areas in the boreal mixedwood forest in north-central Alberta. Experimental exclosures showed that predators reduced recruitment rates, on average, by 46% for seeds exposed to predation for 6 weeks in the summer and by 79% for seeds exposed to predation between autumn (seed dispersal) and the following summer (germination). We were unable to detect an influence of initial seed density on recruitment rates. A seed tray experiment suggested that predators can detect and consume 80%94% of white spruce seeds available in cutblocks within 1 month of sowing and that seed predation rates do not vary predictably with distance from the cutblockforest edge. Our results suggest that vertebrate seed predators, especially small mammals, have the potential to severely affect recruitment rates of white spruce in recent cutblocks, although long-term work is needed to understand how predators might affect recruitment under natural conditions with predator and seed densities that vary in space and time.
Finite element modeling of guyed back spars in cable logging
Authors: Saravi Albert , Lyons C Kevin
Published: May 2004

In this study a finite element model of a back spar system was developed with three guylines opposing the skyline strap tension. In this paper the allowable skyline strap tension is the tension in the skyline strap that results in the maximum normal stress on a transverse cross section of the tree being equal to an assumed allowable stress. An iterative routine was developed to find the allowable skyline strap tension, and this routine was found to converge rapidly from initial values that were below and above the allowable skyline strap tension. Two algorithms were developed for finding the maximum normal stress on a transverse cross section of a tree, method 1 and method 2. If the plane that the tree displaced in was known a priori, then method 2 could be used, and it was found to be less sensitive to mesh coarseness. If the plane that the tree displaced in was not known a priori, then method 1 had to be used with a less coarse mesh. It was found that the stress concentrations due to simplified cable connections were not significant for rigging configurations that allowed a larger rigging point displacement. The rigging configurations that allowed larger rigging point displacements have stress fields that are dominated by bending, while for rigging configurations that allow only small rigging point displacements, the stress fields are dominated by axial compression.
The impact of tree and stand characteristics on spruce beetle (Coleoptera: Scolytidae) induced mortality of white spruce in the Copper River Basin, Alaska
Authors: Doak Patricia
Published: May 2004

I examined the relationships between individual and stand-level characteristics of white spruce, Picea glauca (Moench) Voss, and the incidence of spruce beetle, Dendroctonus rufipennis Kirby, induced mortality. The study region, in the Kennicott Valley of the Copper River Basin, Alaska, has contained an active spruce beetle epidemic since 1989. I investigated the relationship among the individual traits of host age, size (diameter at breast height, DBH), and growth rate (basal area increment, BAI) and mortality from the spruce beetle. I also examined the effects of stand density, mean DBH, and mean BAI on percent mortality within plots. Survival was higher for younger, smaller, and faster-growing trees. However, the effect of age is not significant when included in a logistic regression model examining the effect of individual host traits on host survival. Mortality increased with increasing DBH and decreasing BAI, and there was a significant interaction between DBH and BAI. While the proportion of individuals killed by the spruce beetle significantly differed between stands, I found no significant relationships between stand-level characteristics and mortality rate. This research suggests that the individual traits of host size and growth rate, as well as their interaction are the best predictors of susceptibility to spruce beetle-induced mortality in this system.
Optimal stand density: a solution
Authors: Zeide Boris
Published: May 2004

The search for a stand density that maximizes total volume growth has continued since the beginning of forestry without producing a definite answer. One of the reasons is that the effect of density on growth is not always separated from those of tree size and age. Such a separation is not easy when the relationship between density and growth is expressed as a graph (Langsaeter's curve). This study develops a simple model that accounts for each main growth predictor individually. It allows one to calculate the density that maximizes volume growth at any given moment (current annual increment of volume). Just as the maximum Reineke's index, this density optimum does not change with age. Fitting the model to long-term data confirms the obvious: because a complete crown closure intercepts more light than a broken canopy, the densest stands produce maximum volume growth. Thus, the current optimal density is equal to maximum density. What is less obvious is that maximum current stand volume growth does not sum up to maximum stand volume. In addition to density, stand volume depends on average tree size, which is larger in less dense stands. The high current density that maximizes volume growth also minimizes diameter increment, which eventually reduces average diameter and stand volume. When density is kept at a stationary (over time) level by thinning, maximum volume is produced by stands with substantially lower density than the current optimum. even higher volume can probably be obtained when density changes with age. The challenge is to find this optimum path of density.
Estimating time since death of Picea glauca × P. engelmannii and Abies lasiocarpa in wet cool sub-boreal spruce forest in east-central British Columbia
Authors: Newberry J E , Lewis K J , Walters M B
Published: May 2004

A new method for studying stand disturbance regimes, which could be used alone or combined with other approaches (e.g., age class analysis, tree ring analysis, direct gap measurements), is presented. The method is a set of multiple regression models that estimate the year of death of trees on the basis of external characteristics (e.g., bark presence) and tree position (standing or down). The models were calibrated for Picea glauca (Moench) Voss × P. engelmannii Parry ex Engelm. and Abies lasiocarpa (Hook.) Nutt. trees with known dates of death determined from permanent sample plot data obtained from the Aleza Lake Research Forest, in east-central British Columbia, in the wet cool foothills of the Rocky Mountains. The P. glauca × P. engelmannii model explained 95.3% and 79.3%, and the A. lasiocarpa model explained 81.2% and 78.2%, of the variation in years since death for standing and down trees, respectively. The models were validated by an independent sample of dead trees, where the model estimate was compared with year of release determined from tree ring cores in subordinate understory trees. The two estimates were related (R2 = 61.3%, for both species), indicating that the model provides acceptable estimates for year of death in the two species. This approach may be particularly useful for determining year of death for trees that do not have subordinate individuals that release following overstory mortality.
Foliar nutrients and induced susceptibility: genetic mechanisms of Douglas-fir resistance to western spruce budworm defoliation
Authors: Clancy Karen M , Chen Zhong , Kolb Thomas E
Published: May 2004

We conducted greenhouse defoliation experiments with clones of interior Douglas-fir (Pseudotsuga menziesii var. glauca (Beissn.) Franco) over 3 years to assess the role of foliar nutrients as a resistance mechanism to western spruce budworm (Choristoneura occidentalis Freeman) defoliation. The grafted clones were derived from mature trees (i.e., ortets) that showed resistance or susceptibility to budworm defoliation in the forest. Current-year foliage was analyzed for concentrations of nitrogen (N), sugars (sucrose + fructose + glucose), phosphorus (P), potassium (K), magnesium (Mg), calcium (Ca), manganese (Mn), copper (Cu), iron (Fe), and zinc (Zn). We computed rank correlations between foliar nutrient levels in the ortets and their corresponding clones to test the null hypothesis that foliar chemistry does not have a genetic basis (H01). Foliar concentrations of sugars and P were under genetic control to some degree, but concentrations of other nutrients were not. We used analysis of variance to test the null hypotheses that foliar chemistry does not change in response to budworm defoliation (H02) and that it is not different between resistant and susceptible clones (H03). We rejected H02 for sugars, P, K, Mn, and Zn; defoliation by the budworm changed levels of these nutrients and had divergent effects on concentrations of P, K, and Zn in resistant clones. We concluded that induced susceptibility, whereby defoliation alters foliar nutrients to make trees more favorable for insect feeding, appears to be an important determinant of Douglas-fir resistance to the western spruce budworm. Failure to reject H03 implies that previously reported differences between the foliar nutrient levels in resistant Douglas-firs and those in susceptible Douglas-firs in the forest are probably caused by induced susceptibility.
Accuracy of partially visually assessed stand characteristics: a case study of Finnish forest inventory by compartments
Authors: Kangas Annika , Heikkinen Elina , Maltamo Matti
Published: May 2004

In Finland, forest management planning is based on standwise assessment of forest variables. The data is traditionally gathered partly by (subjective) sampling and partly by visual assessment, which makes the accuracy assessments difficult. This study consists of an experiment where the visual assessments of field technicians were compared with the accurately measured values. The data consists of assessments from 18 sample plots made by 19 technicians. Each technician assessed four forest characteristics from each stand, for each tree species and each tree class. Basal area was observed in all cases; the other three variables varied according to 18 different measurement strategies. From these observations, mixed models were estimated to analyze to what extent the assessment errors depend on forest characteristics. Variation among both sample plots and field technicians was also considered. The results show that some of the variables could be interpreted as Berkson cases. The assessment errors were also often highly hetero sce dastic. Therefore, variance was explicitly modeled, and the final error models were estimated with weighted mixed regression using the variance estimates as weights. The results show clear variation among technicians, especially in characteristics that include personal judgment. The effect of training could be detected from variation between the technician groups. Furthermore, the broad-leaved tree classes were generally more difficult to assess than conifers.
Examining the reciprocal property of base-age invariant site index models
Authors: Wang Yonghe
Published: May 2004

The reciprocal property of published base-age invariant site index models was examined through simulation. Various tree heights and ages were combined as input and were alternatively assigned to (H1, t1) and (H2, t2) in the models to predict heights. Numerical methods were required because some of the models did not have an inverse function. The difference between the two predicted heights with the same input assigned to (H1, t1) and (H2, t2), respectively, was computed to reflect reciprocity; as such predicted heights would be identical if the models were reciprocal. Examination of the differences through graphs and summary statistics indicated that some models possessed numerical reciprocity, although they were analytically nonreciprocal, whereas the others did not. An understanding of the reciprocal property of the models would improve their application in growth and yield studies.
Stand dynamics of mixed red alder  conifer forests of southeast Alaska
Authors: Deal Robert L , Hennon Paul E , Orlikowska Ewa H , D'Amore David V
Published: May 2004

Stand structure and dynamics were evaluated in mixed red alder (Alnus rubra Bong.)  conifer forests of southeast Alaska. We assessed stand development, tree density, total basal area, diameter distribution of live and dead trees, height distribution of live trees, and mean diameter of all and largest conifers in 40-year-old red alder  conifer stands that developed following logging. Forty-five plots were established in nine stands sampled across a com po si tional range of 0%86% alder. Alder height growth was initially rapid then slowed considerably, whereas conifer height growth was initially slow then rapidly increased with conifers now being 49 m taller than associated alders. Most alder diameters were 2030 cm and conifer diameters were more variable with numerous small (310 cm) and a few large (>25 cm) trees. Total stand basal area significantly decreased (p = 0.013) with increasing proportions of alder, but density of live and dead trees was not closely associated with alder composition. More than 60% of all dead trees died standing regardless of size or species. Overall, these mixed red alder  conifer stands provided more heterogeneous structures than pure conifer stands, with more even diameter distributions, multiple canopy layers, and similar numbers of large diameter conifers.
Effect of chronically elevated CO2 on CA1 neuronal excitability
Authors: Gu Xiang Q. , Xue Jin , Haddad Gabriel G.
Published: May 2004

To study the effect of chronically elevated CO2 on the excitability and function of neurons, we exposed mice to 7.5–8% CO2 for ∼2 wk (starting at 2 days of age) and examined the properties of freshly dissociated hippocampal neurons. Neurons from control mice (CON) and from mice exposed to chronically elevated CO2 had similar resting membrane potentials and input resistances. CO2-exposed neurons, however, had a lower rheobase and a higher Na+ current density (580 ± 73 pA/pF; n = 27 neurons studied) than did CON neurons (280 ± 51 pA/pF, n = 34; P < 0.01). In addition, the conductance-voltage curve was shifted in a more negative direction in CO2-exposed than in CON neurons (midpoint of the curve was −46 ± 3 mV for CO2 exposed and −34 ± 3 mV for CON, P < 0.01), while the steady-state inactivation curve was shifted in a more positive direction in CO2-exposed than in CON neurons (midpoint of the curve was −59 ± 2 mV for CO2 exposed and −68 ± 3 mV for CON, P < 0.01). The time constant for deactivation at −100 mV was much smaller in CO2-exposed than in CON neurons (0.8 ± 0.1 ms for CO2 exposed and 1.9 ± 0.3 ms for CON, P < 0.01). Immunoblotting for Na+ channel proteins (subtypes I, II, and III) was performed on the hippocampus. Our data indicate that Na+ channel subtype I, rather than subtype II or III, was significantly increased (43%, n = 4; P < 0.05) in the hippocampi of CO2-exposed mice. We conclude that in mice exposed to elevated CO2, 1) increased neuronal excitability is due to alterations in Na+ current and Na+ channel characteristics, and 2) the upregulation of Na+ channel subtype I contributes, at least in part, to the increase in Na+ current density.
Selective regulation by δ-PKC and PI 3-kinase in the assembly of the antiapoptotic TNFR-1 signaling complex in neutrophils
Authors: Kilpatrick Laurie E. , Sun Shuang , Korchak Helen M.
Published: May 2004

TNF is implicated in the attenuation of neutrophil constitutive apoptosis during sepsis. Antiapoptotic signaling is mediated principally through the TNF receptor-1 (TNFR-1). In adherent neutrophils, when β-integrin signaling is activated, TNF phosphorylates TNFR-1 and activates prosurvival and antiapoptotic signaling. Previously, we identified the δ-PKC isotype and phosphatidylinositol (PI) 3-kinase as critical regulators of TNF signaling in adherent neutrophils. Both kinases associate with TNFR-1 in response to TNF and are required for TNFR-1 serine phosphorylation, NF-κB activation, and inhibition of apoptosis. The purpose of this study was to examine the role of δ-PKC and PI 3-kinase in the assembly of TNFR-1 signaling complex that regulates NF-κB activation and antiapoptotic signaling. Coimmunoprecipitation studies established that PI 3-kinase, δ-PKC, and TNFR-1 formed a signal complex in response to TNF. δ-PKC recruitment required both δ-PKC and PI 3-kinase activity, whereas PI 3-kinase recruitment was δ-PKC independent, suggesting that PI 3-kinase acts upstream of δ-PKC. An important regulatory step in control of antiapoptotic signaling is the assembly of the TNFR-1-TNFR-1-associated death domain protein (TRADD)-TNFR-associated factor 2 (TRAF2)-receptor interacting protein (RIP) complex that controls NF-κB activation. Inhibition of either δ-PKC or PI 3-kinase decreased TNF-mediated recruitment of RIP and TRAF2 to TNFR-1. In contrast, TRADD recruitment was enhanced. Thus δ-PKC and PI 3-kinase are positive regulators of TNF-mediated association of TRAF2 and RIP with TNFR-1. Conversely, these kinases are negative regulators of TRADD association. These results suggest that δ-PKC and PI 3-kinase regulate TNF antiapoptotic signaling at the level of the TNFR-1 through control of assembly of a TNFR-1-TRADD-RIP-TRAF2 complex.
Longitudinal changes in energy expenditure and body composition in obese women with normal and impaired glucose tolerance
Authors: Okereke Ndubueze C. , Huston-Presley Larraine , Amini Saeid B. , Kalhan Satish , Catalano Patrick M.
Published: May 2004

Our primary objective was to evaluate changes in energy expenditure and body composition in women with normal glucose tolerance (NGT) and gestational diabetes mellitus (GDM). A secondary objective was to examine the relationship between maternal leptin and nutrient metabolism. Fifteen obese women, eight with NGT and seven with GDM, were evaluated before conception (P), at 12–14 wk (E), and at 34–36 wk (L). Energy expenditure and glucose and fat metabolism were measured using indirect calorimetry. Basal hepatic glucose production was measured using [6,6-2H2]glucose and insulin sensitivity by euglycemic clamp. There was a significant increase (6.6 kg, P = 0.0001) in fat mass from P to L. There was a 30% ( P = 0.0001) increase in basal O2 consumprion (V̇o2, ml/min). There were no significant changes in carbohydrate oxidation during fasting or storage from P to L. There was, however, a significant ( P = 0.0001) 150% increase in basal fat oxidation (mg/min) from P to L. Under hyperinsulinemic conditions, there were similar 25% increases in V̇o2 ( P = 0.0001) from P to L in both groups. Because of the significant increases in insulin resistance from P to L, there was a significant ( P = 0.0001) decrease in carbohydrate oxidation and storage. There was a net change from lipogenesis to lipolysis, i.e., fat oxidation (30–40 mg/min, P = 0.0001) from P to L. Serum leptin concentrations had a significant positive correlation with fat oxidation at E ( r = 0.76, P = 0.005) and L ( r = 0.72, P = 0.009). Pregnancy in obese women is associated with significant increases in fat mass and basal metabolic rate and an increased reliance on lipids both in the basal state and during the clamp. These modifications are similar in women with NGT and GDM. The increased reliance on fat metabolism is accompanied by a concomitant decrease in carbohydrate metabolism during hyperinsulinemia. The increase in fat oxidation may be related to increased maternal serum leptin.
Muscularis inflammation and the loss of interstitial cells of Cajal in the endothelin ETB receptor null rat
Authors: Suzuki Toshihiko , Won Kyung-Jong , Horiguchi Kazuhide , Kinoshita Kazuya , Hori Masatoshi , Torihashi Shigeko , Momotani Eiichi , Itoh Kikuji , Hirayama Kazuhiro , Ward Sean M. , Sanders Kenton M. , Ozaki Hiroshi
Published: May 2004

Endothelin receptor null rats [ETB(−/−)] are a model for long-segment Hirschsprung’s disease. These animals have significant intestinal distension (megaileum) proximal to a constricted region of the gastrointestinal tract lacking enteric ganglia. Experiments were performed to determine the pathophysiological changes that occur in these animals and to examine the tunica muscularis as a unique, immunologically active compartment. We observed abnormal intestinal flora in ETB(−/−) rats, which included a marked increase in gram-negative aerobes ( Enterobacteriaceae) and anaerobes ( Bacteroidaceae) in the distended region of the small intestine. Histochemical observations showed that neutrophilic infiltration was rarely or not observed, but the number of ED2 positive macrophages was increased in the tunica muscularis. Expression of IL-1β and IL-6 mRNA was also significantly increased, and the level of CD14 (LPS receptors) were increased significantly in the tunica muscularis. Spontaneous phasic contractions were irregular in the distended intestinal regions of ETB(−/−) rats, and this was associated with an increased number of macrophages and damage to interstitial cells of Cajal (ICC) as revealed by using Kit-like immunoreactivity and electron microscopy. These results suggest that ED2-positive resident macrophages may play an important role in the inflammation of tunica muscularis in ETB(−/−) rats. Increased numbers and activation of macrophages may result in damage to ICC networks leading to disordered intestinal rhythmicity in regions of the gut in which myenteric ganglia are intact.