bluuebunny/crossref_metadata_2025 huggingface dataset:
Disease Resistance and Abiotic Stress Tolerance in Rice Are Inversely Modulated by an Abscisic Acid–Inducible Mitogen-Activated Protein Kinase[W]
Authors: Xiong Lizhong , Yang Yinong
Published: March 2003

Mitogen-activated protein kinase (MAPK) cascades play an important role in mediating stress responses in eukaryotic organisms. However, little is known about the role of MAPKs in modulating the interaction of defense pathways activated by biotic and abiotic factors. In this study, we have isolated and functionally characterized a stress-responsive MAPK gene (OsMAPK5) from rice. OsMAPK5 is a single-copy gene but can generate at least two differentially spliced transcripts. The OsMAPK5 gene, its protein, and kinase activity were inducible by abscisic acid as well as various biotic (pathogen infection) and abiotic (wounding, drought, salt, and cold) stresses. To determine its biological function, we generated and analyzed transgenic rice plants with overexpression (using the 35S promoter of Cauliflower mosaic virus) or suppression (using double-stranded RNA interference [dsRNAi]) of OsMAPK5. Interestingly, suppression of OsMAPK5 expression and its kinase activity resulted in the constitutive expression of pathogenesis-related (PR) genes such as PR1 and PR10 in the dsRNAi transgenic plants and significantly enhanced resistance to fungal (Magnaporthe grisea) and bacterial (Burkholderia glumae) pathogens. However, these same dsRNAi lines had significant reductions in drought, salt, and cold tolerance. By contrast, overexpression lines exhibited increased OsMAPK5 kinase activity and increased tolerance to drought, salt, and cold stresses. These results strongly suggest that OsMAPK5 can positively regulate drought, salt, and cold tolerance and negatively modulate PR gene expression and broad-spectrum disease resistance.
The future of reference: an introduction
Authors: Tobin Carol M.
Published: March 2003

The Reference and User Services Association (RUSA) of the American Library Association held a program at the 2002 Annual ALA Meeting on “The future of reference services”. Five experts were asked to produce white papers on the topic and post them to the RUSA Web site (www.ala. org.rusa/forums/index.html) before the conference. At the program, the authors gave summaries of their major points and there was a general discussion of the topic. This forum was a part of a larger initiative by RUSA to help shape the future of reference. The papers and responses to them are presented here.
On the desirableness of personal relations between librarians and readers: the past and future of reference service
Authors: Tyckoson David
Published: March 2003

Presents a strong argument that the future of reference is part of an evolutionary process and that, by understanding the relationship of reference service to the library and of the library to its community, one can better understand how those relationships will evolve in the future. Notes that the four functions for reference librarians, as defined by Samuel Swett Green in 1876, remain the core of reference service today.
Reference futures: outsourcing, the Web, or knowledge counseling
Authors: Bell Whitlatch Jo
Published: March 2003

Three possible scenarios for the future of reference services are described: outsourcing, the Web, and knowledge counseling. The ability to design reference services that users will continue to value in libraries of the future is limited by current professional reference practices. These limits are related to the failure to incorporate total quality management (TQM) principles into the design and practice of present day reference services. The following TQM principles are utilized to discuss the contrasts between TQM principles and current reference practices: focus on the customer, quality work the first time, strategic holistic approach to improvement, continuous improvement as a way of life, and mutual respect and teamwork. Finally, the roles that library organizations must fulfill to change the current professional culture are described.
Using virtual reference transcripts for staff training
Authors: Ward David
Published: March 2003

The technology of virtual reference software has created new opportunities for libraries to examine the reference interview and consider its role in their institutions. The ability to capture transcripts of reference transactions (or "chats") allows for a routine analysis of the interview in ways only previously available through more time‐consuming and awkward means, such as obtrusive studies. This analysis leads to many new possibilities for alternative methods of staff training. This article examines one such method, in which graduate student workers at a university reference desk were asked to examine transcripts of actual virtual reference transactions, using the standard of the Reference and User Services Association’s Behavioral Guidelines for evaluation. The study sought to increase the students’ awareness of reference standards and expectations for reference desk behavior, as well as to help the group come to a consensus about how the reference interview should be conducted locally in the online and in‐person environments.
Uptake of
N
,
N
′-Diacetylchitobiose [(GlcNAc)
2
] via the Phosphotransferase System Is Essential for Chitinase Production by
Serratia marcescens
2170
Authors: Uchiyama Taku , Kaneko Ryousuke , Yamaguchi Junko , Inoue Akane , Yanagida Takahiro , Nikaidou Naoki , Regue Miguel , Watanabe Takeshi
Published: March 2003

The
chiR
gene of
Serratia marcescens
2170, encoding a LysR-type transcriptional activator, was identified previously as an essential factor for expression of chitinases and a chitin-binding protein, CBP21. To identify other genes that are essential for chitinase production, transposon mutagenesis with mini-Tn
5
Km1 was carried out, and 25 mutants that were unable to produce chitinases and CBP21 were obtained. Analysis of the mutated gene of one of the mutants, N22, revealed the presence of a
pts
operon in this bacterium, and a mutation was found in
ptsI
in the operon. In addition to its inability to produce chitinase, N22 did not grow well on
N
-acetyl-
d
-glucosamine (GlcNAc), (GlcNAc)
2
, and some other carbon sources, most of which were phosphotransferase system (PTS) sugars. Thus, the inability to produce chitinase was assumed to be caused by the defect in uptake of (GlcNAc)
2
via the PTS, considering that (GlcNAc)
2
is the minimal substrate for chitinase induction and the major product of chitin hydrolysis by chitinases of this bacterium. To confirm this assumption, the
chb
operon, encoding the (GlcNAc)
2
-specific enzyme II permease, was cloned by reference to its
Escherichia coli
counterpart, and the
Serratia chb
operon was shown to comprise
chbB
,
chbC
,
bglA
,
chbR
, and
chbG
. Disruption of
chbC
drastically reduced production of chitinases and CBP21 and impaired growth on colloidal chitin. These results indicate that uptake of (GlcNAc)
2
is mediated by the PTS and that the (GlcNAc)
2
-specific enzyme II permease constitutes its major pathway. Since (GlcNAc)
2
uptake is essential for induction of chitinases and CBP21 production, (GlcNAc)
2
appears to be the key molecule in recognition and utilization of chitin by
S. marcescens
.
The Activator of GntII Genes for Gluconate Metabolism, GntH, Exerts Negative Control of GntR-Regulated GntI Genes in
Escherichia coli
Authors: Tsunedomi Ryouichi , Izu Hanae , Kawai Takuya , Matsushita Kazunobu , Ferenci Thomas , Yamada Mamoru
Published: March 2003

Gluconate is one of the preferred carbon sources of
Escherichia coli
, and two sets of
gnt
genes (encoding the GntI and GntII systems) are involved in its transport and metabolism. GntR represses the GntI genes
gntKU
and
gntT
, whereas GntH was previously suggested to be an activator for the GntII genes
gntV
and
idnDO-gntWH.
The helix-turn-helix residues of the two regulators GntR and GntH exhibit extensive homologies. The similarity between the two regulators prompted analysis of the cross-regulation of the GntI genes by GntH. Repression of
gntKU
and
gntT
by GntH, as well as GntR, was indeed observed using transcriptional fusions and RNA analysis. High GntH expression, from cloned
gntH
or induced through 5-ketogluconate, was required to observe repression of GntI genes. Two GntR-binding elements were identified in the promoter-operator region of
gntKU
and were also shown to be the target sites of GntH by mutational analysis. However, the GntI genes were not induced by gluconate in the presence of enhanced amounts of GntH, whereas repression by GntR was relieved by gluconate. The repression of GntI genes by GntH is thus unusual in that it is not relieved by the availability of substrate. These results led us to propose that GntH activates GntII and represses the GntI genes in the presence of metabolites derived from gluconate, allowing the organism to switch from the GntI to the GntII system. This cross-regulation may explain the progressive changes in
gnt
gene expression along with phases of cell growth in the presence of gluconate.
Purification and In Vitro Characterization of the
Serratia marcescens
NucC Protein, a Zinc-Binding Transcription Factor Homologous to P2 Ogr
Authors: McAlister Victor , Zou Chao , Winslow Robert H. , Christie Gail E.
Published: March 2003

NucC is structurally and functionally homologous to a family of prokaryotic zinc finger transcription factors required for late gene expression in P2- and P4-related bacteriophages. Characterization of these proteins in vitro has been hampered by their relative insolubility and tendency to aggregate. We report here the successful purification of soluble, active, wild-type NucC protein. Purified NucC exhibits site-specific binding to a conserved DNA sequence that is located upstream of NucC-dependent
Serratia marcescens
promoters and the late promoters of P2-related phages. This sequence is sufficient for binding of NucC in vitro. NucC binding to the
S. marcescens
nuclease promoter P

nucA

and to the sequence upstream of the P2 late promoter P

F

is accompanied by DNA bending. NucC protects about 25 nucleotides of the P

F

upstream region from DNase I digestion, and RNA polymerase protects the promoter region only in the presence of NucC. Template DNA, RNA polymerase holoenzyme, and purified NucC are the only macromolecular components required for transcription from P

F

in vitro.
Analysis of Genome Plasticity in Pathogenic and Commensal
Escherichia coli
Isolates by Use of DNA Arrays
Authors: Dobrindt Ulrich , Agerer Franziska , Michaelis Kai , Janka Andreas , Buchrieser Carmen , Samuelson Martin , Svanborg Catharina , Gottschalk Gerhard , Karch Helge , Hacker Jörg
Published: March 2003

Genomes of prokaryotes differ significantly in size and DNA composition.
Escherichia coli
is considered a model organism to analyze the processes involved in bacterial genome evolution, as the species comprises numerous pathogenic and commensal variants. Pathogenic and nonpathogenic
E. coli
strains differ in the presence and absence of additional DNA elements contributing to specific virulence traits and also in the presence and absence of additional genetic information. To analyze the genetic diversity of pathogenic and commensal
E. coli
isolates, a whole-genome approach was applied. Using DNA arrays, the presence of all translatable open reading frames (ORFs) of nonpathogenic
E. coli
K-12 strain MG1655 was investigated in 26
E. coli
isolates, including various extraintestinal and intestinal pathogenic
E. coli
isolates, 3 pathogenicity island deletion mutants, and commensal and laboratory strains. Additionally, the presence of virulence-associated genes of
E. coli
was determined using a DNA “pathoarray” developed in our laboratory. The frequency and distributional pattern of genomic variations vary widely in different
E. coli
strains. Up to 10% of the
E. coli
K-12-specific ORFs were not detectable in the genomes of the different strains. DNA sequences described for extraintestinal or intestinal pathogenic
E. coli
are more frequently detectable in isolates of the same origin than in other pathotypes. Several genes coding for virulence or fitness factors are also present in commensal
E. coli
isolates. Based on these results, the conserved
E. coli
core genome is estimated to consist of at least 3,100 translatable ORFs. The absence of K-12-specific ORFs was detectable in all chromosomal regions. These data demonstrate the great genome heterogeneity and genetic diversity among
E. coli
strains and underline the fact that both the acquisition and deletion of DNA elements are important processes involved in the evolution of prokaryotes.
ARhizobium leguminosarumAcpXL Mutant Produces Lipopolysaccharide Lacking 27-Hydroxyoctacosanoic Acid
Authors: Vedam Vinata , Kannenberg Elmar L. , Haynes Janine G. , Sherrier D. Janine , Datta Anup , Carlson Russell W.
Published: March 2003

The structure of the lipid A fromRhizobium etliandRhizobium leguminosarumlipopolysaccharides (LPSs) lacks phosphate and contains a galacturonosyl residue at its 4′ position, an acylated 2-aminogluconate in place of the proximal glucosamine, and a very long chain ω-1 hydroxy fatty acid, 27-hydroxyoctacosanoic acid (27OHC28:0). The 27OHC28:0 moiety is common in lipid A's among members of theRhizobiaceaeand also among a number of the facultative intracellular pathogens that form chronic infections, e.g.,Brucella abortus,Bartonella henselae, andLegionella pneumophila. In this paper, a mutant ofR. leguminosarumwas created by placing a kanamycin resistance cassette withinacpXL, the gene which encodes the acyl carrier protein for 27OHC28:0. The result was an LPS containing a tetraacylated lipid A lacking 27OHC28:0. A small amount of the mutant lipid A may contain an added palmitic acid residue. The mutant is sensitive to changes in osmolarity and an increase in acidity, growth conditions that likely occur in the nodule microenvironment. In spite of the probably hostile microenvironment of the nodule, theacpXLmutant is still able to form nitrogen-fixing root nodules even though the appearance and development of nodules are delayed. Therefore, it is possible that theacpXLmutant has a host-inducible mechanism which enables it to adapt to these physiological changes.
Comprehensive Studies of Drug Resistance Mediated by Overexpression of Response Regulators of Two-Component Signal Transduction Systems in
Escherichia coli
Authors: Hirakawa Hidetada , Nishino Kunihiko , Hirata Takahiro , Yamaguchi Akihito
Published: March 2003

In
Escherichia coli
, there are 32 open reading frames (ORFs) that are assumed to be response regulator genes of two-component signal transduction systems on the basis of sequence similarities. We cloned all of these 32 ORFs into a multicopy expression vector and investigated whether or not they confer drug resistance via control of drug resistance determinants. Fifteen of these ORFs, i.e.,
baeR
,
citB
,
cpxR
,
evgA
,
fimZ
,
kdpE
,
narL
,
narP
,
ompR
,
rcsB
,
rstA
,
torR
,
yedW
,
yehT
, and
dcuR
, conferred increased single- or multidrug resistance. Two-thirds of them conferred deoxycholate resistance. Five of them, i.e.,
evgA
,
baeR
,
ompR, cpxR
, and
rcsB
, modulated the expression of several drug exporter genes. The drug resistance mediated by
evgA
,
baeR
, and
cpxR
could be assigned to drug exporters by using drug exporter gene knockout strains.
Interactions between the Outer Membrane Ferric Citrate Transporter FecA and TonB: Studies of the FecA TonB Box
Authors: Ogierman Monica , Braun Volkmar
Published: March 2003

Both induction of transcription of the ferric citrate transport genes and transport of ferric citrate by theEscherichia coliouter membrane receptor FecA require energy derived from the proton motive force (PMF) of the inner membrane. The energy is transduced to FecA by the inner membrane complex, TonB, ExbB, and ExbD. Region 160 of TonB and the conserved TonB box of other TonB-dependent receptors are implicated as sites of interaction. In the present study, the postulated TonB box (D80A81L82T83V84) of FecA was deleted in frame, with a subsequent loss of both FecA functions. DALTV of FecA could be functionally replaced with the core TonB boxes of FhuA (DTITV) and FepA (DTIVV). Each residue of the TonB box of FecA was sequentially replaced with cysteine residues, and only the D80C replacement showed a loss (reduction) of both FecA functions. A physical interaction between TonB and FecA was demonstrated using both in vivo site-specific disulfide bond cross-linking and nonspecific formaldehyde (FA) cross-linking. Pairwise combinations of FecA (DALTV)/Cys substitutions were cross-linked via disulfide bond formation with TonBQ160C, TonBQ162C, and TonBY163C. Unexpectedly, this cross-linking was not enhanced by substrate (ferric citrate). In contrast, the TonB-FecA interaction was enhanced by ferric citrate in the FA-cross-linking assay. Energy derived from the PMF was not required for the TonB-FecA interaction in either the disulfide- or FA-cross-linking assay. TonB/CysExbB/ExbD(D25N) was still able to cross-link with the FecA (DALTV)/Cys derivatives in atonB tolQbackground, even though ExbD25N renders the TonB/ExbBD complex nonfunctional (V. Braun, S. Gaisser, C. Herrmann, K. Kampfenkel, H. Killmann, and I. Traub, J. Bacteriol.178:2836-2845, 1996). TonB cross-linked to FecA via FA was not inhibited by either carbonylcyanide-m-chlorophenylhydrazone or 1 mM 2,4-dinitrophenol, which dissipate the electrochemical potential of the cytoplasmic membrane and disrupt both FecA functions. The studies shown here demonstrate the significance of the TonB box for FecA functions and are consistent with the view that it is the structure and not the sequence of the TonB box that is important for activity. Demonstrated here for the first time is the physical interaction of TonB and FecA, which is enhanced by ferric citrate.
Identification of Catabolite Repression as a Physiological Regulator of Biofilm Formation byBacillus subtilisby Use of DNA Microarrays
Authors: Stanley Nicola R. , Britton Robert A. , Grossman Alan D. , Lazazzera Beth A.
Published: March 2003

Biofilms are structured communities of cells that are encased in a self-produced polymeric matrix and are adherent to a surface. Many biofilms have a significant impact in medical and industrial settings. The model gram-positive bacteriumBacillus subtilishas recently been shown to form biofilms. To gain insight into the genes involved in biofilm formation by this bacterium, we used DNA microarrays representing >99% of the annotatedB. subtilisopen reading frames to follow the temporal changes in gene expression that occurred as cells transitioned from a planktonic to a biofilm state. We identified 519 genes that were differentially expressed at one or more time points as cells transitioned to a biofilm. Approximately 6% of the genes ofB. subtiliswere differentially expressed at a time when 98% of the cells in the population were in a biofilm. These genes were involved in motility, phage-related functions, and metabolism. By comparing the genes differentially expressed during biofilm formation with those identified in other genomewide transcriptional-profiling studies, we were able to identify several transcription factors whose activities appeared to be altered during the transition from a planktonic state to a biofilm. Two of these transcription factors were Spo0A and sigma-H, which had previously been shown to affect biofilm formation byB. subtilis. A third signal that appeared to be affecting gene expression during biofilm formation was glucose depletion. Through quantitative biofilm assays and confocal scanning laser microscopy, we observed that glucose inhibited biofilm formation through the catabolite control protein CcpA.
Global Characterization of Disulfide Stress inBacillus subtilis
Authors: Leichert Lars Ingo Ole , Scharf Christian , Hecker Michael
Published: March 2003

We used DNA macroarray and proteome analysis to analyze the regulatory networks inBacillus subtilisthat are affected by disulfide stress. To induce disulfide stress, we used the specific thiol oxidant diamide. After addition of 1 mM diamide to an exponentially growing culture, cell growth stopped until the medium was cleared of diamide. Global analysis of the mRNA expression pattern during growth arrest revealed 350 genes that were induced by disulfide stress by greater than threefold. Strongly induced genes included known oxidative stress genes that are under the control of the global repressor PerR and heat shock genes controlled by the global repressor CtsR. Other genes that were strongly induced encode putative regulators of gene expression and proteins protecting against toxic elements and heavy metals. Many genes were substantially repressed by disulfide stress, among them most of the genes belonging to the negative stringent response. Two-dimensional gels of radioactively labeled protein extracts allowed us to visualize and quantitate the massive changes in the protein expression pattern that occurred in response to disulfide stress. The observed dramatic alteration in the protein pattern reflected the changes found in the transcriptome experiments. The response to disulfide stress seems to be a complex combination of different regulatory networks, indicating that redox-sensing cysteines play a key role in different signaling pathways sensing oxidative stress, heat stress, toxic element stress, and growth inhibition.
Sequence of the 165-Kilobase Catabolic Plasmid pAO1 fromArthrobacter nicotinovoransand Identification of a pAO1-Dependent Nicotine Uptake System
Authors: Igloi Gabor L. , Brandsch Roderich
Published: March 2003

The 165-kb catabolic plasmid pAO1 enables the gram-positive soil bacteriumArthrobacter nicotinovoransto grow on the tobacco alkaloidl-nicotine. The 165,137-nucleotide sequence, with an overall G+C content of 59.7%, revealed, besides genes and open reading frames (ORFs) for nicotine degradation, a complete set of ORFs for enzymes essential for the biosynthesis of the molybdenum dinucleotide cofactor, as well as ORFs related to uptake and utilization of carbohydrates, sarcosine, and amino acids. Of the 165 ORFs, approximately 50% were related to metabolic functions. pAO1 conferred toA. nicotinovoransthe ability to take upl-[14C]nicotine from the medium, with anKmof 5.6 ± 2.2 μM. ORFs of putative nicotine transporters formed a cluster with the gene of thed-nicotine-specific 6-hydroxy-d-nicotine oxidase. ORFs related to replication, chromosome partitioning, and natural transformation functions (dprA) were identified on pAO1. Few ORFs showed similarity to known conjugation-promoting proteins, but pAO1 could be transferred by conjugation to a pAO1-negative strain at a rate of 10−2to 10−3per donor. ORFs with no known function represented approximately 35% of the pAO1 sequence. The positions of insertion sequence elements and composite transposons, corroborated by the G+C content of the pAO1 sequence, suggest a modular composition of the plasmid.
The Membrane Domain of SpoIIIE Is Required for Membrane Fusion during
Bacillus subtilis
Sporulation
Authors: Sharp Marc D. , Pogliano Kit
Published: March 2003

During
Bacillus subtilis
sporulation, SpoIIIE is required for both postseptational chromosome segregation and membrane fusion after engulfment. Here we demonstrate that SpoIIIE must be present in the mother cell to promote membrane fusion and that the N-terminal membrane-spanning segments constitute a minimal membrane fusion domain, as well as direct septal localization.
Identification and Functional Characterization of
Sphingomonas macrogolitabida
Strain TFA Genes Involved in the First Two Steps of the Tetralin Catabolic Pathway
Authors: Moreno-Ruiz Emilia , Hernáez María José , Martínez-Pérez Olga , Santero Eduardo
Published: March 2003

Five genes involved in the two initial steps of the tetralin biodegradation pathway of
Sphingomonas macrogolitabida
strain TFA have been characterized. ThnA1A2 and ThnA3A4, components of the ring-hydroxylating dioxygenase, were encoded in divergently transcribed operons. ThnA1, ThnA2, and ThnA3 were essential for tetralin ring-hydroxylating dioxygenase activity. ThnB was identified as a dehydrogenase required for tetralin biodegradation.
Measurement of Adhesive Forces between Individual
Staphylococcus aureus
MSCRAMMs and Protein-Coated Surfaces by Use of Optical Tweezers
Authors: Simpson Kathryn H. , Bowden Gabriela , Höök Magnus , Anvari Bahman
Published: March 2003

The force required to rupture bonds between individual
Staphylococcus aureus
MSCRAMMs and surfaces coated with extracellular matrix molecules has been quantified by using optical tweezers. The observed binding forces between fibrinogen or fibronectin and
S. aureus
MSCRAMMs occurred as an approximate integer multiple of 20 or 25 pN, respectively.
Excision and Integration of Cassettes by an Integron Integrase ofNitrosomonas europaea
Authors: Léon Grégory , Roy Paul H.
Published: March 2003

We found in the environmental strainNitrosomonas europaeaa chromosomal integron-like structure with an integrase gene,intINeu. We have tested the capacity of the IntINeu integrase to excise and integrate several resistance gene cassettes. The results allow us to consider IntINeu a new functional integron integrase.
Characterization of a Novel Fucose-Regulated Promoter (PfcsK) Suitable for Gene Essentiality and Antibacterial Mode-of-Action Studies inStreptococcus pneumoniae
Authors: Chan Pan F. , O'Dwyer Karen M. , Palmer Leslie M. , Ambrad Jennifer D. , Ingraham Karen A. , So Chi , Lonetto Michael A. , Biswas Sanjoy , Rosenberg Martin , Holmes David J. , Zalacain Magdalena
Published: March 2003

The promoter of theStreptococcus pneumoniaeputative fuculose kinase gene (fcsK), the first gene of a novel fucose utilization operon, is induced by fucose and repressed by glucose or sucrose. When the streptococcal polypeptide deformylase (PDF) gene (def1, encoding PDF) was placed under the control of PfcsK, fucose-dependent growth of theS. pneumoniae(PfcsK::def1) strain was observed, confirming the essential nature of PDF in this organism. The mode of antibacterial action of actinonin, a known PDF inhibitor, was also confirmed with this strain. The endogenous fuculose kinase promoter is a tightly regulated, titratable promoter which will be useful for target validation and for confirmation of the mode of action of novel antibacterial drugs inS. pneumoniae.
Which community indicators can measure the impact of fishing? A review and proposals
Authors: Rochet Marie-Joëlle , Trenkel Verena M
Published: March 2003

Population and community descriptors that might be used as indicators of the impact of fishing are reviewed. The criteria used for the evaluation of these indicators are meaning, expected effect of fishing, exclusiveness to fishing effects, and measurability. Population indicators such as total mortality rate, exploitation rate, or average length are the most operational indicators because their meaning is clear and the expected effect of fishing on them is well understood so that reference points can be set. On the other hand, indicators based on the composition of species assemblages such as diversity indices and ordination of species abundances are difficult to interpret, and the effect of fishing on them is not easily predicted. Robust indicators describing the community functions of interest (production and transfer of biomass to large fish), such as size spectra descriptors or the proportion of piscivorous fish in the community, are more promising but are not yet well developed. New candidate indicators are proposed: the change in fishing mortality required to reverse population growth rate, the proportion of noncommercial species in the community, and the average length and weight in the community.
The importance of dietary phosphorus and highly unsaturated fatty acids for sockeye (Oncorhynchus nerka) growth in Lake Washington  a bioenergetics approach
Authors: Ballantyne Ashley P , Brett Michael T , Schindler Daniel E
Published: March 2003

Juvenile sockeye salmon (Oncorhynchus nerka) in Lake Washington experience very high growth rates, but the mechanisms regulating their growth rates are poorly understood. The potential for food quality limitation of growth was tested using a coupled bioenergetics and mass balance model. Sockeye and zooplankton prey species were analyzed for their fatty acid composition. Ratios of phosphorus to carbon (P:C) for both sockeye and zooplankton were obtained from the literature. Based on sockeye stomach contents and zooplankton weights, diets of zooplankton biomass were calculated and monthly values of specific fatty acids and P:C ratios in the diet were derived. An increase in highly unsaturated fatty acids, especially in the liver, was observed with increased fork length up to smoltification size, with a subsequent decrease in smolts and kokanee. Measurements of docosahexaenoic (DHA) in daphnids were significantly lower than in cyclopoids. Model predictions suggest that sockeye are not limited by the availability of phosphorus or eicosapentaeinoic acid (EPA) in their diet but may experience limited growth because of DHA deficiencies. Thus, the ability and efficiency of sockeye at elongating 18:3 ω3, 18:4 ω3, and EPA to DHA may be of critical importance to lacustrine growth and production.
Changes in phytoplankton communities following logging in the drainage basins of three boreal forest lakes in northwestern Ontario (Canada), 19912000
Authors: Nicholls K H , Steedman R J , Carney E C
Published: March 2003

The phytoplankton communities of three small boreal forest lakes (L26, L39, and L42) on Ontario's Precambrian Shield (Canada) were investigated over 10 years for possible effects of forest harvesting (logging) within their drainage basins (5 years before logging vs. 5 years after logging). During the postlogging period, higher biovolumes of several taxa were recorded, consistent with previously reported changes in nutrients, chlorophyll, light penetration, and mixing depth. Among the most dramatic changes were increases of 100 and 266% in Cyanophyceae in L39 and L42, respectively, 167% in Dinophyceae in L26, 51 and 130% in Chlorophyceae in L26 and L42, respectively, 182% in Bacillariophyceae in L26, and 53 and 73% in total phytoplankton in L26 and L42, respectively. Other effects associated with logging in the watersheds of these lakes included an increase in the numbers of taxa (in accordance with the intermediate disturbance hypothesis) and a decrease in interannual variability in phytoplankton community structure (in accordance with the ecosystem diversitystability hypothesis). The less extensive logging of the L26 drainage basin and the maintenance of an unlogged shoreline buffer strip did not preclude apparent effects on phytoplankton comparable with some of those found in the other two lakes, where drainage basin logging was more extensive.
Modeling time-varying growth using a generalized von Bertalanffy model with application to bloater (Coregonus hoyi) growth dynamics in Lake Michigan
Authors: Szalai Emily B , Fleischer Guy W , Bence James R
Published: March 2003

A concurrent increase in lakewide abundance and decrease in size-at-age of bloater (Coregonus hoyi) in Lake Michigan have suggested density-dependent growth regulation. We investigated these temporal patterns by fitting a dynamic von Bertalanffy model and lengthweight relationship with time-varying parameters to mean length- and weight-at-ages (ages 17) from annual surveys (19651999). We modeled yearling length, asymptotic size (L[Formula: see text]), and the parameters of a power relationship between mean weight and mean length (α and β) as changing slowly over time using a random walk model. The Brody growth coefficient (k) was modeled as a linear function of L[Formula: see text] with year-specific random deviations. Our results support a positive relationship between L[Formula: see text] and k, indicating that under conditions supporting larger asymptotic lengths, individuals approach the asymptote more rapidly. We explored the relationship between year-specific growth parameters and indices of lakewide bloater abundance and found evidence of density-dependent growth. However, in the most recent years, L[Formula: see text] and yearling length have remained low in Lake Michigan despite low bloater abundances, suggesting the occurrence of a fundamental shift in the food web.
Aqueous nonelectrolyte solutions. Part XIX. Congruent dissociation melting point and the formula of structure II methane hydrate
Authors: Glew David N
Published: March 2003

Twenty-four equilibrium pressures, P(h2l1g), of structure II methane hydrate h2 with water l1 between 27.0 and 46.9°C are well represented by a four-parameter equation, which indicates a standard error (SE) of 1.95% on a single pressure measurement. Forty equilibrium constants Kp(h2[Formula: see text]l1g) for dissociation of structure II methane hydrate into water and methane between 27.0 and 47.7°C and at pressures up to 784 MPa at 45.0°C are best represented by a three-parameter thermodynamic equation, which indicates an SE 1.25% on a single Kp(h2[Formula: see text]l1g) determination. The congruent dissociation melting point C(h2l1gxm) of structure II methane hydrate is at 47.71°C with SE 0.03°C and at pressure 533 MPa with SE 5 MPa. The congruent Kp(h2[Formula: see text]l1g) is 102.9 with SE 0.3 MPa, ΔH°t(h2[Formula: see text]l1g) is 61 531 with SE 244 J mol1, and the congruent formula is CH4·5.670H2O with SE 0.061H2O. At congruent point ΔV(h2[Formula: see text]l1g) = 0 and its estimate is 1.0 with SE 1.6 cm3 mol1. Stability range of structure II methane hydrate with water extends from quadruple point Q(h1h2l1g) at 26.7°C and 55.5 MPa up to quadruple point Q(h2h3l1g) at 47.3°C and 620 MPa. The metastability range of structure I methane hydrate with water is discussed.Key words: methane hydrate, clathrate structure II, stability range, dissociation equilibrium constant, formula, congruent melting point, metastability of structure I hydrate.
Solvent-dependent rate constants of muonium atom reactions
Authors: Karolczak Stefan , Gillis Hugh A , Porter Gerald B , Walker David C
Published: March 2003

The rates of reaction of muonium atoms with solutes, ionic and organic, were studied in solvents of wildly differing polarities (water, methanol, and hexane) and their rate constants were compared, where possible. In these reactions  which are those of a highly reactive atom, an isotope of hydrogen  it transpires that the reaction rates are higher in solvents in which the solute is more soluble and muonium diffuses faster. This study leads to various kinetic-solvent-effect ratios and to the observation of the reaction of muonium with free radicals being among the fastest reactions recorded so far between two neutral species in solution.Key words: muonium atoms, kinetic isotope effects, solvent-dependent rates, non-aqueous solvents, muon spin rotation technique.
The relative stabilities of PhE(NH-t-Bu)2 and PhE(μ-N-t-Bu)2EPh (E = As, Sb, and Bi): X-ray structures of {Li2[PhAs(N-t-Bu)2]}2 and PhE(μ-N-t-Bu)2EPh (E = Sb, Bi)
Authors: Briand Glen G , Chivers Tristram , Parvez Masood
Published: March 2003

The reaction of PhECl2 with 2 equiv of LiHN-t-Bu has been studied for the series E = As, Sb, and Bi to determine the effect of the phenyl group on subsequent amine condensation processes. For PhAsCl2, the metathesis product PhAs(NH-t-Bu)2 4 was obtained as a colourless oil. Similar reactions involving PhECl2, where E = Sb or Bi, yielded the cyclodipnict(III)azanes PhE(μ-N-t-Bu)2EPh 5 (E = Sb) and 6 (E = Bi), respectively. Treatment of 4 with 2 equiv of n-BuLi produced the dilithium salt Li2[PhAs(N-t-Bu)2] 7a. Products 4, 5, 6, and 7a were characterized by 1H, 7Li (7a), and 13C NMR spectra, while 5, 6, and 7a were also structurally characterized by X-ray crystallography. Compound 7a is dimeric in the solid state via intermolecular Li···N and η6-Li···Ph interactions. The cyclodipnict(III)azanes 5 and 6 have similar structures, with the exocyclic phenyl groups in trans positions relative to the E2N2 ring. This synthetic approach provides a new route to the four-membered rings RE(μ-N-t-Bu)2ER (E = Sb, Bi) and the first example of a bis(organyl)cyclodibism(III)azane.Key words: arsenic, antimony, bismuth, amides, imides.
SYMMETRIES IN JUMP-DIFFUSION MODELS WITH APPLICATIONS IN OPTION PRICING AND CREDIT RISK
Authors: HOOGLAND J. K. , NEUMANN C. D. D. , VELLEKOOP M. H.
Published: March 2003

It is a well known fact that local scale invariance plays a fundamental role in the theory of derivative pricing. Specific applications of this principle have been used quite often under the name of "change of numeraire", but in recent work it was shown that when invoked as a fundamental first principle, it provides a powerful alternative method for the derivation of prices and hedges of derivative securities, when prices of the underlying tradables are driven by Wiener processes. In this article we extend this work to the pricing problem in markets driven not only by Wiener processes but also by Poisson processes, i.e. jump-diffusion models. It is shown that in this case too, the focus on symmetry aspects of the problem leads to important simplifications of, and a deeper insight into the problem. Among the applications of the theory we consider the pricing of stock options in the presence of jumps, and Lévy-processes. Next we show how the same theory, by restricting the number of jumps, can be used to model credit risk, leading to a "market model" of credit risk. Both the traditional Duffie-Singleton and Jarrow-Turnbull models can be described within this framework, but also more general models, which incorporate default correlation in a consistent way. As an application of this theory we look at the pricing of a credit default swap (CDS) and a first-to-default basket option.
UNCERTAINTY IN PRICING TRADABLE OPTIONS
Authors: SOBEHART JORGE R. , KEENAN SEAN C.
Published: March 2003

In this paper we introduce an options pricing model consistent with the level of uncertainty observed in the options market. By assuming that the price at which an option can be traded is intrinsically uncertain, either because of the inability to hedge continuously or because of errors in the estimation of the security's volatility and interest rates, random delays in the execution of orders or information deficiencies, we show that the Black-Scholes model produces a biased estimate of the expected value of tradable options. Information deficiencies lead to a call-put relationship that reduces to the standard call-put expression on average but shows random fluctuations consistent with the concept of market equilibrium. The same information deficiencies can contribute to the volatility skew that affects the Black-Scholes model.
Semisynthesis of Proteins by Expressed Protein Ligation
Authors: Muir Tom W.
Published: March 2003

▪ Abstract  Expressed protein ligation (EPL) is a protein engineering approach that allows recombinant and synthetic polypeptides to be chemoselectively and regioselectively joined together. The approach makes the primary structure of most proteins accessible to the tools of synthetic organic chemistry, enabling the covalent structure of proteins to be modified in an unprecedented fashion. The ability to incorporate noncoded amino acids, biophysical probes, and stable isotopes into specific locations within proteins provides research tools to peer into the inner workings of these molecules. In this review I discuss the development of this technology, its broad application to biological systems, and its possible role in the area of proteomics.
CELLMIGRATION IN THEFOREBRAIN
Authors: Marín Oscar , Rubenstein John L.R.
Published: March 2003

▪ Abstract  The forebrain comprises an intricate set of structures that are required for some of the most complex and evolved functions of the mammalian brain. As a reflection of its complexity, cell migration in the forebrain is extremely elaborated, with widespread dispersion of cells across multiple functionally distinct areas. Two general modes of migration are distinguished in the forebrain: radial migration, which establishes the general cytoarchitectonical framework of the different forebrain subdivisions; and tangential migration, which increases the cellular complexity of forebrain circuits by allowing the dispersion of multiple neuronal types. Here, we review the cellular and molecular mechanisms underlying each of these types of migrations and discuss how emerging concepts in neuronal migration are reshaping our understanding of forebrain development in normal and pathological situations.
BRAINREPRESENTATION OFOBJECT-CENTEREDSPACE INMONKEYS ANDHUMANS
Authors: Olson Carl R.
Published: March 2003

▪ Abstract  Visuospatial cognition requires taking into account where things are relative to each other and not just relative to the viewer. Consequently it would make sense for the brain to form an explicit representation of object-centered and not just of ego-centered space. Evidence bearing on the presence and nature of neural maps of object-centered space has come from two sources: single-neuron recording in behaving monkeys and assessment of the visual abilities of human patients with hemispatial neglect. Studies of the supplementary eye field of the monkey have revealed that it contains neurons with object-centered spatial selectivity. These neurons fire when the monkey has selected, as target for an eye movement or attention, a particular location defined relative to a reference object. Studies of neglect have revealed that in some patients the condition is expressed with respect to an object-centered and object-aligned reference frame. These patients neglect one side of an object, as defined relative to its intrinsic midline, regardless of its location and orientation relative to the viewer. The two sets of observations are complementary in the sense that the loss of neurons, such as observed in the monkey, could explain the spatial distribution of neglect in these patients.
CELL-CELL SIGNALING DURING SYNAPSE FORMATION IN THE CNS
Authors: Scheiffele Peter
Published: March 2003

▪ Abstract  Synapses join individual nerve cells into a functional network. Specific cell-cell signaling events regulate synapse formation during development and thereby generate a highly reproducible connectivity pattern. The accuracy of this process is fundamental for normal brain function, and aberrant connectivity leads to nervous system disorders. However, despite the overall precision with which neuronal circuits are formed, individual synapses and synaptic networks are also plastic and can readily adapt to external stimuli or perturbations. In recent studies, several trans-synaptic signaling systems have been identified that can mediate various aspects of synaptic differentiation in the central nervous system. It appears that these individual pathways functionally cooperate, thereby generating robustness and flexibility, which ensure normal nervous system function.
BIOLOGIC MECHANISMS OF THE PROTECTIVE ROLE OF LUTEIN AND ZEAXANTHIN IN THE EYE
Authors: Krinsky Norman I. , Landrum John T. , Bone Richard A.
Published: March 2003

▪ Abstract  The macular region of the primate retina is yellow in color due to the presence of the macular pigment, composed of two dietary xanthophylls, lutein and zeaxanthin, and another xanthophyll, meso-zeaxanthin. The latter is presumably formed from either lutein or zeaxanthin in the retina. By absorbing blue-light, the macular pigment protects the underlying photoreceptor cell layer from light damage, possibly initiated by the formation of reactive oxygen species during a photosensitized reaction. There is ample epidemiological evidence that the amount of macular pigment is inversely associated with the incidence of age-related macular degeneration, an irreversible process that is the major cause of blindness in the elderly. The macular pigment can be increased in primates by either increasing the intake of foods that are rich in lutein and zeaxanthin, such as dark-green leafy vegetables, or by supplementation with lutein or zeaxanthin. Although increasing the intake of lutein or zeaxanthin might prove to be protective against the development of age-related macular degeneration, a causative relationship has yet to be experimentally demonstrated.
NUTRITIONAL REGULATION OF MILK FAT SYNTHESIS
Authors: Bauman Dale E. , Griinari J. Mikko
Published: March 2003

▪ Abstract  Certain diets cause a marked reduction in milk fat production in ruminants. Commonly referred to as milk fat depression (MFD), the mechanism involves an interrelationship between rumen microbial processes and tissue metabolism. Numerous theories to explain this interrelationship have been proposed and investigations offer little support for theories that are based on a limitation in the supply of lipogenic precursors. Rather, the basis involves alterations in rumen biohydrogenation of dietary polyunsaturated fatty acids and a specific inhibition of mammary synthesis of milk fat. The biohydrogenation theory proposes that under certain dietary conditions, typical pathways of rumen biohydrogenation are altered to produce unique fatty acid intermediates that inhibit milk fat synthesis. Trans-10, cis-12 conjugated linoleic acid (CLA) has been identified as one example that is correlated with the reduction in milk fat. Investigations with pure isomers have shown that trans-10, cis-12 CLA is a potent inhibitor of milk fat synthesis, and similar to diet-induced MFD, the mechanism involves a coordinated reduction in mRNA abundance for key enzymes involved in the biochemical pathways of fat synthesis. A more complete identification of these naturally produced inhibitors of fat synthesis and delineation of cellular mechanisms may offer broader opportunities for application and understanding of the regulation of lipid metabolism.
Homeodomain proteins MEIS1 and PBXs regulate the lineage-specific transcription of the platelet factor 4 gene
Authors: Okada Yoshiaki , Nagai Ryohei , Sato Takahiro , Matsuura Eri , Minami Takashi , Morita Ikuo , Doi Takefumi
Published: March 2003

Platelet factor 4 (PF4) is expressed during megakaryocytic differentiation. We previously reported that GATA-1 and ETS-1 regulate the rat PF4 promoter and transactivate the PF4 gene. For the present study, we investigated the regulatory elements and their transcription factors responsible for the lineage-specific expression of the PF4 gene. The promoter activities of deletion constructs were evaluated, and a novel regulatory element termed TME (tandem repeat of MEIS1 binding element) (–219 to –182) was defined. Binding proteins to TME were strongly detected in HEL nuclear extracts by electrophoresis mobility shift assay (EMSA), and they were purified by DNA affinity chromatography. By performing Western blottings and supershift assays, the binding proteins were identified as homeodomain proteins, MEIS1, PBX1B, and PBX2. These factors are expressed in megakaryocytes differentiated from CD34+ cells in human cord blood. MEIS1 and PBXs bind to the TME as MEIS1/PBX complexes and activate the PF4 promoter. In nonmegakaryocytic HepG2 cells, GATA-1 and ETS-1 activate the PF4 promoter approximately 10-fold. Surprisingly, we found that additional expression of both MEIS1 and PBX2 multiplied this major activation another 2-fold. This activation was not observed when MEIS1 binding sites in the TME were disrupted. Furthermore, inhibition of the binding of endogenous MEIS1/PBX complexes to the TME decreased the promoter activity by almost one half, in megakaryocytic HEL cells. Thus, these studies demonstrate that the homeodomain proteins, MEIS1, PBX1B, and PBX2, play an important role in megakaryocytic gene expression.