bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of refining on the fibre structure of kraft pulps as revealed by FE-SEM and TEM: Influence of alkaline degradation
Authors: Molin U. , Daniel G.
Published: September 2004

The aim of the study was to evaluate the effect of refining
on the ultrastructure of spruce pulp fibres. Pulps with different
molar masses of cellulose (estimated as intrinsic
viscosity) were studied after PFI-refining. The molar
masses of the polymers were decreased by increases in
alkali concentration during pulping. Fibre surface structures
were examined using Field Emission Scanning
Electron Microscopy (FE-SEM) and Transmission Electron
Microscopy (TEM) was used to observe changes in
the internal structure of the fibres. Pulps with lower (125
and 329 ml g−1) intrinsic viscosity showed more damaged
during refining than pulps with higher (620 and
1120 ml g−1) intrinsic viscosity. Observations showed
pulps with lower intrinsic viscosity to have large decreases
in fibre length after refining. Fibres with low intrinsic
viscosity (i.e., 125 ml g−1) had less primary wall and S1
layer remaining and the external fibrillation and damage
of the S2 layer had increased. The S2 wall of fibres with
high intrinsic viscosity showed characteristic delamination.
Similar delamination was not visible for fibres with
low intrinsic viscosity.
Changes in the fiber wall during refining of bleached pine kraft pulp
Authors: Laine C. , Wang X. , Tenkanen M. , Varhimo A.
Published: September 2004

The effect of refining on the fiber wall was studied for
bleached kraft pulp fractions from pine first thinnings and
pine sawmill chips. Hydrocyclone fractionation of both
pulps produced fractions enriched in earlywood and latewood
fibers. Some external fibrillation but no changes in
fiber wall thickness were observed for the thin-walled
earlywood fibers during refining. Refining the thick-walled
latewood fibers led to extensive external fibrillation and
a decrease in fiber wall thickness. The pore structure of
the fiber wall opened up during refining for all pulp fractions.
Earlywood fibers were more porous than latewood
fibers, and fibers from first thinnings more porous than
those from sawmill chips. The earlywood fibers from first
thinnings had more large pores than the other fiber fractions.
In the region of the smaller pores, the pore volume
did not change significantly with refining, whereas in the
region of the larger pores it increased markedly. In all the
fractions investigated, specific hydrolytic enzymes
hydrolyzed cellulose more easily after refining. This is an
indication of an increase in cellulose surface area and/or
disordering of cellulose as a result of refining, probably
due to local disorder of the cellulose in the fibril aggregates.
Bonding developed most strongly for the earlywood
fiber fraction from first thinnings. This is concluded
to be due to a combination of fiber dimensions and fiber
wall porosity.
An unusual formation of tension wood in a natural forest Acacia sp.
Authors: Hillis W.E. , Evans R. , Washusen R.
Published: September 2004

The determination of microfibril angle (MFA), cellulose
crystallite width and microdensity by SilviScan-2 at CSIRO
confirmed that several dark bands in the heartwood
of an Acacia species were associated with tension wood
(TW) fibres. The straight log was taken from a tree of
about 30 years of age that had been apparently growing
vertically as there were no signs of the usual stimuli for
TW formation. The continuous dark bands of about 5 mm
width extended radially from the inner heartwood in a
spiral pattern and were separated by continuous normal
wood bands of similar width. The TW bands continued
in the sapwood from the heartwood boundary to the
cambium but were not coloured. The dark colour of the
TW was probably caused by extractives being polymerised
at the heartwood boundary by enzymes in the TW
fibres in the sapwood. The MFA and cellulose crystallite
width indicated the TW in a band was of similar intensity
throughout its length, indicating similar microstructural
characteristics at different cambial ages. The initiation of
spiral grain formation occurs before that of tension wood
in the Acacia samples studied.
Changes in the surface properties of wood due to sanding
Authors: Sinn G. , Gindl M. , Reiterer A. , Stanzl-Tschegg S.
Published: September 2004

Spruce and beech wood specimens were sanded with
four different grain sizes. Surface morphological and
chemical changes were determined by roughness measurement,
surface free energy determination according to
acid-base theory and X-ray photoelectron spectroscopy.
An analysis model was proposed to describe chemical
changes due to sanding and the data were analysed
according to it. It could be shown that spruce and beech
behave similarly over a wide range and that chemical
changes are non-linear functions of grain size and thus
surface roughness. A maximum of surface free energy
and a maximum of carbon C1s sub-peak ratio (ratio of
carbon bonded to a single non-carbonyl oxygen to carbon
bonded only to hydrogen or other carbon atoms)
was found for middle grain size.
The creep of wood destabilized by change in moisture content. Part 1: The creep behaviors of wood during and immediately after drying
Authors: Takahashi C. , Ishimaru Y. , Iida I. , Furuta Y.
Published: September 2004

To better understand mechano-sorptive creep, creep
behaviors were compared in wood samples during the
drying process, immediately after drying, and after a long
conditioning under constant humidity and temperature.
Creep was greater in the sample tested immediately after
drying than in the sample conditioned for a long time
under relative humidity equal to that after drying, despite
the fact that these samples had almost the same moisture
content (MC). While the wood that has been moisture-conditioned for a long time is in a stable state, the
wood tested immediately after the drying is presumed to
be in an unstable state. Moreover, creep of the sample
tested during the drying process was greater than that
of the sample tested immediately after the drying. It has
also been found that the instability decreased with time,
indicating that stabilization and destabilization occur
simultaneously during the drying process. In recent studies,
a decrease in the elastic modulus and an increase in
the fluidity of wood immediately after a change in MC or
temperature have been reported. These findings are
attributed to the instability caused by changes in MC or
temperature. Based on the results of the present study
and recent studies, we consider the increase in the fluidity
of wood as the MC changes to be attributable to
instability.
Moisture adsorption thermodynamics of wood from fractal-geometry approach
Authors: Cao J. , Kamdem D.P.
Published: September 2004

The fractal-geometry approach was used to calculate the
thermodynamic properties of moisture sorption by wood
from the adsorption isotherms in this study. The results
were compared with those from an isosteric approach
and a calorimetric approach. The adsorption isotherms
of Southern yellow pine (Pinus spp.) were measured at
4, 15, 30, and 40°C to provide source data for the calculation
of both fractal-geometry and isosteric approaches.
The results show that the fractal dimensions of the
internal surfaces of wood vary between 2.4 and 2.5. The
curves of the differential heat of adsorption −∆H against
moisture content from the fractal-geometry approach are
similar to those from calorimetric measurements in previous
research. The −∆H values from the isosteric
approach increased with moisture content within a moisture
content range up to 3%. And, at moisture contents
higher than 3%, the −∆H values from this method are
much higher than those from the fractal-geometry
approach and calorimetric approach. As a result, the
fractal-geometry approach is applicable to calculate the
differential thermodynamic properties of moisture sorption
by wood in future research.
Ionic liquids in wood preservation
Authors: Pernak J. , Zabielska-Matejuk J. , Kropacz A. , Foksowicz-Flaczyk J.
Published: September 2004

In this study ionic liquids (3-alkoxymethyl-1-methylimidazolium
tetrafluoroborates and hexafluoro-phosphates)
are successfully used for wood preservation. These liquids
are new biocides as well as new solvents which
penetrate wood well. The prepared ionic liquids with an
alkoxymethyl substituent, which consisted of 7, 8 or 9
carbon atoms, exhibited fungicidal activity against Coniophora
puteana (Schum.: Fr.) Karst., Trametes versicolor
(L.: Fr.) Pilát and Sclerophoma pityophila (Corda) v.
Höhn. The effective and lethal doses were measured by
the agar-plate method. In their activity against wood
degrading fungi, ionic liquids such as 1-methyl-3-octyloxy-methylimidazolium
and 1-methyl-3-nonyloxymethylimidazolium
tetrafluoroborates were comparable with
commercially available benzalkonium chloride and didecyldimethylammonium
chloride. Ionic liquids both with
and without DDAC penetrated into Scots pine wood very
well.
New bis-quaternary ammonium and bis-imidazolium chloride wood preservatives
Authors: Zabielska-Matejuk J. , Urbanik E. , Pernak J.
Published: September 2004

Bis-quaternary ammonium and bis-imidazolium chlorides,
the compounds containing in their structure two
symmetrical quaternary nitrogen atoms, were prepared
and tested on wood destroying and sapstaining fungi.
The effect of the position of quaternary nitrogen atoms
upon fungicidal and surface properties was analysed.
The antifungal activity of new bis-quaternary ammonium
and bis-imidazolium chlorides against Coniophora
puteana (Schum.:Fr.)Kr., Trametes versicolor (L.:Fr.)Pilát
and Aspergillus niger van Tieghem was much more pronounced
than that of quaternary ammonium chlorides.
The results confirm the correlation between surface
activity and fungicidal activity. The adsorption of bisimidazolium
chloride onto pine wood was influenced by
pH of applied solutions and the initial solution concentration.
With increasing pH of ammonium solution, the
adsorption was much greater than in neutral or acidic
solutions. Cation structure of the quaternary ammonium
chloride exerted a strong influence on quantity of wood-adsorbed
chemicals and resistance to water leaching.
Fungal decay resistance of wood reacted with phosphorus pentoxide-amine system
Authors: Lee H.-L. , Chen G.C. , Rowell R.M.
Published: September 2004

Resistance of wood reacted in situ with phosphorus
pentoxide-amine to the brown-rot fungus Gloeophyllum
trabeum and white-rot fungus Trametes versicolor was
examined. Wood reacted with either octyl, tribromo, or
nitro derivatives were more resistant to both fungi.
Threshold retention values of phosphoramide-reacted
wood to white-rot fungus T. versicolor ranged from 2.9
to 13.3 mmol, while these for brown-rot fungus G. trabeum
ranged from 8.1 to 19.2 mmol. Wood reacted with
phosphoramide tested to be more resistant to white-rot
than brown-rot attack.
Bioactive phenolic substances in industrially important tree species. Part 1: Knots and stemwood of different spruce species
Authors: Willför S. , Nisula L. , Hemming J. , Reunanen M. , Holmbom B.
Published: September 2004

Knots (i.e., branch bases inside tree stems) in spruce
trees contained remarkably higher concentrations of lignans
and oligolignans than the adjacent stemwood. The
amount of lignans in some knots exceeded 10% (w w−1)
and some knots contained hundreds of times more lignans
than the heartwood in the same tree. However,
there were large variations between different species and
even between different knots in the same tree. 7-Hydroxymatairesinol was the predominant lignan in knots
of Picea abies, P. glauca, P. koraiensis, P. mariana, and
P. omorika, while liovil and secoisolariciresinol dominated
in P. sitchensis and P. pungens. The lignans occur in free
form in knots and are easily extracted with polar solvents.
In addition to the true lignans, especially the knots contained
large amounts of lignan-related oligomeric aromatic
substances, here called oligolignans, consisting of
three or four phenylpropane units.

7-Hydroxymatairesinol, but also other lignans, could
be extracted in large scale from spruce knots at pulp and
paper mills. Other potentially important lignans could be
produced from 7-hydroxymatairesinol by semisynthesis.
The ready availability of large amounts of lignans and oligolignans
now enables research to assess their bioactivity
and provide the basis for applications in medicine and
nutrition or as natural antioxidants and antimicrobial
agents in a variety of technical products.
Delignification mechanism during high-boiling solvent pulping. Part 6: Changes in lignin structure analyzed by 1H-13C correlation 2-D NMR spectroscopy
Authors: Kishimoto T. , Ueki A. , Takamori H. , Uraki Y. , Ubukata M.
Published: September 2004

In order to investigate the delignification mechanism during
high-boiling solvent (HBS) pulping, softwood HBS lignin
samples from todo fir (Abies sachalinensis) were
analyzed by 1H–13C correlation NMR spectroscopy
(HMQC). Nine lignin model compounds that may represent
the substructures in HBS lignin were prepared. The
1H and 13C NMR spectral data were compared with HBS
lignin samples. The HMQC spectra of HBS lignin samples
showed the disappearance of β-O-4 structures.
Introduction of a pulping solvent into lignin was plainly
observed with new signals in aliphatic regions. Only the
erythro β-1 structure was detected in softwood milled
wood lignin from todo fir by HMQC spectra. The β-1
structure was very reactive and probably produced the
stilbene structure. The β-β and β-5 structures remained
in HBS lignin. The 4-O-5 structure was successfully
detected by HMQC spectra, and it was found to be stable
under the conditions used.
Ozonation of conventional kraft and SuperBatch residual lignins in methanol/water and water
Authors: Widsten P. , Hortling B. , Poppius-Levlin K.
Published: September 2004

The chemistry of ozone bleaching of chemical pulps was
explored by ozonating residual lignins isolated from conventional
kraft and SuperBatch pulps in methanol/water
medium to detect possible differences in the reactivity of
the two types of lignin. SuperBatch lignin was ozonated
also in water to study the effect of ozonation medium on
the lignin reactivity. The residual lignins were found to
display similar reactivities in methanol/water, implying
that ozonation should result in equal delignification rates
for both conventional kraft and SuperBatch pulps unless
the rates of reagent diffusion in the pulps are different.
The lignins were partly oxidized to volatile and nonvolatile
low-molecular weight oxidation products by the so-called
“peeling mechanism”, according to which oxidation
products go into solution and insoluble reaction products
resemble the starting lignins. The reaction products
obtained upon ozonation of SuperBatch lignin in neutral
water resembled those formed in methanol/water, but
their yield was much lower. This is probably due to the
better solubility of lignin in methanol/water than in water
and/or higher degradability of lignin by ozone than by
radicals formed as ozone decomposition products.
Relationship between dissolution of fiber materials and development of pulp strength in alkaline peroxide bleaching of mechanical pulp
Authors: Pan G.X.
Published: September 2004

This study elucidates the relationship between the dissolution
of pulp components and the development of
fiber bonding properties in alkaline peroxide bleaching of
aspen mechanical pulp. In general, bleaching reactions
cause the removal of pulp substances from the fibers,
which in turn improves pulp strength properties. Nonetheless,
alkaline hydrolysis is particularly important to the
development of strength because this reaction mechanism
plays a key role in imparting additional carboxylic
acid groups onto the fibers. The strong correlation
between fiber carboxylic acid group concentration and
the amount of anionic dissolved substances makes it
possible for us to predict the strength properties of
bleached pulps by estimating the anionicity of bleaching
filtrates using analytical methods such as cationic
demand. The paper also provides insights into the importance
of the alkalinity in peroxide bleaching to the dissolution
of pulp materials and the strength development.
Nondestructive estimation of tracheid length from sections of radial wood strips by near infrared spectroscopy
Authors: Schimleck L.R. , Jones P.D. , Peter G.F. , Daniels R.F. , ClarkIII A.
Published: September 2004

The use of calibrated near infrared (NIR) spectroscopy for
predicting tracheid length of Pinus taeda L. (loblolly pine)
wood samples is described. Ten-mm sections of 14 P. taeda radial strips were selected and NIR spectra
obtained from the radial longitudinal face of each section.
The fibers in these sections were characterized in terms
of arithmetic and length-weighted mean tracheid length
using a fiber quality analyzer, and calibrations with NIR
spectra were developed for both measures of tracheid
length. Relationships were good, with coefficients of
determination (R
2) of 0.88 for arithmetic tracheid length
and 0.96 for length-weighted tracheid length. The accuracy
of NIR predicted length-weighted tracheid length
was sufficient for ranking purposes.
Heat transfer model for estimating pinene emissions from hot-pressing softwood flakeboard
Authors: Radhakrishnan J.S. , Banerjee S.
Published: September 2004

A heat transfer model for estimating pinene emissions
from hot-pressing strand for the manufacture of flake-board
has been constructed from first principles and validated.
The model predicts α-pinene emissions of 0.4 kg/1000 kg from a 0.95-cm board, which is within the
0.3–0.6 kg/1000 kg range reported for commercial operations.
Most of the emissions originate from the hot
1-mm layer of wood adjoining the platen surface. As a
result, residual pinene in the board is depleted at the surface
for both commercial and laboratory-prepared
boards. Emissions are drastically reduced when the mat
is surfaced with a layer of aspen, which prevents the hot
platen from directly contacting softwood.
Monitoring creep-rupture in oriented strandboard using acoustic emission: Effects of moisture content
Authors: Vun R.Y. , Beall F.C.
Published: September 2004

Creep-rupture studies of large specimens of commercial
oriented strandboard (OSB) were conducted using a fourpoint
flexural test in combination with an acoustic emission
(AE) monitoring system. Four equilibrium moisture
content (EMC) conditioning and testing regimens were
used: ambient room conditions, constantly moderate
EMC (12/12), dynamic rising EMC (12/24), and constant
high EMC (24/24). Compared with deflection, the cumulative
event AE parameter was found to be more sensitive
and representative to detect cumulative damage to final
failure. Under 80% ultimate stress, the 24/24 specimens
had the highest creep rate (1.43 mm h−1) as compared
with 0.27 and 0.04 mm h−1 for 12/24 and 12/12 specimens,
respectively. However, for the 12/24 specimens, a
step-like deflection occurred, accelerating the rupture
process and attaining the greatest creep factor of 2.28—a recommended safety factor for prolonged exposure to
humid service conditions. The total recovered deflection
under ambient conditions was 85% recoverable elastic,
5% recoverable viscoelastic, and 10% permanent irreversible
creep. Correspondingly, the total recovered stiffness
was 70% recoverable elastic, 10% recoverable
viscoelastic, and 20% permanent irreversible creep. The
observed creep-rupture limit of the OSB was 24 days to
failure.
Adhesives made from isocyanates and pyrolysis oils for wood composites
Authors: Gagnon M. , Roy C. , Riedl B.
Published: September 2004

Wood adhesives derived from softwood bark pyrolysis
oils (PO) and isocyanates (pMDI) have been developed
for particleboards with a non-conventional blending system.
The PO produced by the vacuum pyrolysis Pyrocycling™ process was used to replace between 30 and
40% by weight of the pMDI in a 4% adhesive-containing
particleboard. Results showed that mechanical properties
(IB, MOE and MOR) and thickness swelling of homogeneous
boards exceeded the minimum requirements
set by ANSI A208.1-1993 and ASTM 1037-96a standards.
The study showed that pyrolysis oils can be mixed
at ratios as high as 40% with pMDI and give acceptable
interior grade particleboard properties. It was also shown
that PO reduces panel to metal adhesion by 86%, in
comparison to the control.
Effect of wood acidity and catalyst on UF resin gel time
Authors: Xing C. , Zhang S.Y. , Deng J.
Published: September 2004

Knowledge of pH and buffering capacity of raw fiber
materials is important for understanding the effects of
raw material on the curing rate of urea formaldehyde (UF)
resin, used for panel manufacturing, especially with some
less-desirable wood materials such as bark, top, and
commercial thinnings.

The effects of pH and buffering capacity as well as
catalyst content on the gel time of UF resin were investigated.
The results obtained from this study indicate that
bark has a lower pH value as well as higher acid and
alkaline buffering capacities than wood of the same species
due to their extractives. The pH values of the raw
fiber materials studied decrease with increased absolute
and relative acid buffering capacity due to the increased
absolute acidity mass in the solution.

At lower levels of added catalyst, the effect of raw
material pH on UF resin gel time is significant, while it is
insignificant at higher catalyst contents. This may be due
to the acidity of wood, which is the main acid catalyst
source of the mixture at lower levels of added catalyst,
while at higher levels, catalyst is the main source. With
higher catalyst contents, all studied raw materials mixed
with UF resin result in a longer gel time than does UF
resin alone.
Exploratory evaluation of oscillation drying for thick hemlock timbers
Authors: Sackey E. K. , Avramidis S. , Oliveira L.C.
Published: September 2004

The study explores the effect of dry-bulb (Tdb
) and wet-bulb
(Twb
) temperature oscillation in a conventional kiln
on the drying characteristics of 105-mm-square Pacific
coast hemlock. Five kiln-charges were dried using four
oscillating drying schedules and a control. The base drying
temperatures for the control were Twb
=53°C,
Tdb
=60°C for the first drying phase and increased to
Twb
=65°C, Tdb
=80°C in the second phase. These temperatures
were oscillated at two amplitude and frequency
combinations, namely, 3°C for 4 h (low) and 6°C for 8 h
(high). The results indicated that the total impact of oscillating
schedules on the drying rate was more pronounced
at the early stages of the drying process.
Oscillating Tdb
at higher amplitudes increased drying rate
by 12%, whereas the low amplitude counterpart reduced
kiln residence time by 10–14%. The final moisture content
variability decreased in both Twb
oscillated schedules.
Core and shell moisture content variation also
slightly decreased in the low amplitude Twb
oscillated
schedules. High amplitude oscillated Tdb
also showed
5% less casehardening than the control, whilst its low
amplitude counterpart increased. The low amplitude Twb

oscillated schedule had the least surface checks and
splits.
A biopulping mechanism: Creation of acid groups on fiber
Authors: Hunt C. , Kenealy W. , Horn E. , Houtman C.
Published: September 2004

We investigated how biopulping modifies chemical and
physical properties of wood and how these changes
affect the properties of the resulting fiber. Mechanical and
chemical testing revealed wood cell changes during
2 weeks of colonization by Ceriporiopsis subvermispora.
Typical mechanical properties, such as modulus of elasticity
and maximum load, tracked reductions in energy
needed for mechanical refining to pulp. The data indicate
the fiber saturation point of spruce increased from 29%
to 42% during biopulping. At the same time, titratable
acid groups increased up to 62%. Chemical analysis
showed that oxalic acid esters were produced in the
wood during biopulping in sufficient amounts to account
for the increase in acid groups. The benefits of biopulping—energy savings and increased handsheet strength—as
well as other physical property changes are consistent
with the mechanism we propose: biopulping increases
the acid group content of wood.
Enzymatically polymerized phenolic compounds as wood preservatives
Authors: Rättö M. , Ritschkoff A.-C. , Viikari L.
Published: September 2004

Phenolic compounds were studied as natural preservatives
against wood decaying fungi. Vanillin and tannin
decreased the growth of the test organisms Coniophora puteana and Coriolus versicolor and decreased the
weight losses caused by these organisms in wood
blocks. Both compounds were, however, leached in standard
washing tests, and higher weight losses were
observed in leached samples. Enzymatic polymerization
with laccase was used as a means of binding the phenolic
preservatives into the wood. Using an optimized
laccase dosage, wood impregnation with enzymatically
polymerized vanillin reduced the weight loss by C. puteana from 25% to 5%.
The Probability and Chromosomal Extent of trans-specific Polymorphism
Authors: Wiuf Carsten , Zhao Keyan , Innan Hideki , Nordborg Magnus
Published: September 2004

Balancing selection may result in trans-specific polymorphism: the maintenance of allelic classes that transcend species boundaries by virtue of being more ancient than the species themselves. At the selected site, gene genealogies are expected not to reflect the species tree. Because of linkage, the same will be true for part of the surrounding chromosomal region. Here we obtain various approximations for the distribution of the length of this region and discuss the practical implications of our results. Our main finding is that the trans-specific region surrounding a single-locus balanced polymorphism is expected to be quite short, probably too short to be readily detectable. Thus lack of obvious trans-specific polymorphism should not be taken as evidence against balancing selection. When trans-specific polymorphism is obvious, on the other hand, it may be reasonable to argue that selection must be acting on multiple sites or that recombination is suppressed in the surrounding region.
Tree Scanning
Authors: Templeton Alan R , Maxwell Taylor , Posada David , Stengård Jari H , Boerwinkle Eric , Sing Charles F
Published: September 2004

We use evolutionary trees of haplotypes to study phenotypic associations by exhaustively examining all possible biallelic partitions of the tree, a technique we call tree scanning. If the first scan detects significant associations, additional rounds of tree scanning are used to partition the tree into three or more allelic classes. Two worked examples are presented. The first is a reanalysis of associations between haplotypes at the Alcohol Dehydrogenase locus in Drosophila melanogaster that was previously analyzed using a nested clade analysis, a more complicated technique for using haplotype trees to detect phenotypic associations. Tree scanning and the nested clade analysis yield the same inferences when permutation testing is used with both approaches. The second example is an analysis of associations between variation in various lipid traits and genetic variation at the Apolipoprotein E (APOE) gene in three human populations. Tree scanning successfully identified phenotypic associations expected from previous analyses. Tree scanning for the most part detected more associations and provided a better biological interpretative framework than single SNP analyses. We also show how prior information can be incorporated into the tree scan by starting with the traditional three electrophoretic alleles at APOE. Tree scanning detected genetically determined phenotypic heterogeneity within all three electrophoretic allelic classes. Overall, tree scanning is a simple, powerful, and flexible method for using haplotype trees to detect phenotype/genotype associations at candidate loci.
Reconstituting the Frequency Spectrum of Ascertained Single-Nucleotide Polymorphism Data
Authors: Nielsen Rasmus , Hubisz Melissa J , Clark Andrew G
Published: September 2004

Most of the available SNP data have eluded valid population genetic analysis because most population genetical methods do not correctly accommodate the special discovery process used to identify SNPs. Most of the available SNP data have allele frequency distributions that are biased by the ascertainment protocol. We here show how this problem can be corrected by obtaining maximum-likelihood estimates of the true allele frequency distribution. In simple cases, the ML estimate of the true allele frequency distribution can be obtained analytically, but in other cases computational methods based on numerical optimization or the EM algorithm must be used. We illustrate the new correction method by analyzing some previously published SNP data from the SNP Consortium. Appropriate treatment of SNP ascertainment is vital to our ability to make correct inferences from the data of the International HapMap Project.
Molecular Cytogenetic Characterization of the Antirrhinum majus GenomeSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under the accession nos. AY630561 (for BAC 5E10) and AY6305612 (for BAC 36D21).
Authors: Zhang Dongfen , Yang Qiuying , Bao Weidong , Zhang Yu , Han Bin , Xue Yongbiao , Cheng Zhukuan
Published: September 2004

As a model system in classical plant genetics, the genus Antirrhinum has been well studied, especially in gametophytic self-incompatibility, flower development biology, and transposon-induced mutation. In contrast to the advances in genetic and molecular studies, little is known about Antirrhinum cytogenetics. In this study, we isolated two tandem repetitive sequences, CentA1 and CentA2, from the centromeric regions of Antirrhinum chromosomes. A standard karyotype has been established by anchoring these centromeric repeats on meiotic pachytene chromosome using FISH. An ideogram based on the DAPI-staining pattern of pachytene chromosomes was developed to depict the distribution of heterochromatin in the Antirrhinum majus genome. To integrate the genetic and chromosomal maps, we selected one or two molecular markers from each linkage group to screen an Antirrhinum transformation-competent artificial chromosome (TAC) library. These genetically anchored TAC clones were labeled as FISH probes to hybridize to pachytene chromosomes of A. majus. As a result, the relationship between chromosomes and the linkage groups (LGs) in Antirrhinum has been established.
Mapping Quantitative Trait Loci for Anxiety in Chromosome Substitution Strains of Mice
Authors: Singer Jonathan B , Hill Annie E , Nadeau Joseph H , Lander Eric S
Published: September 2004

Anxious behavior in the mouse is a complex quantitative phenotype that varies widely among inbred mouse strains. We examined a panel of chromosome substitution strains bearing individual A/J chromosomes in an otherwise C57BL/6J background in open-field and light-dark transition tests. Our results confirmed previous reports of quantitative trait loci (QTL) on chromosomes 1, 4, and 15 and identified novel loci on chromosomes 6 and 17. The studies were replicated in two separate laboratories. Systematic differences in the overall activity level were found between the two facilities, but the presence of the QTL was confirmed in both laboratories. We also identified specific effects on open-field defecation and center avoidance and distinguished them from overall open-field activity.
Quantifying the Relationship Between Gene Expressions and Trait Values in General Pedigrees
Authors: Lu Yan , Liu Peng-Yuan , Liu Yong-Jun , Xu Fu-Hua , Deng Hong-Wen
Published: September 2004

Treating mRNA transcript abundances as quantitative traits and examining their relationships with clinical traits have been pursued by using an analytical approach of quantitative genetics. Recently, Kraft et al. presented a family expression association test (FEXAT) for correlation between gene expressions and trait values with a family-based (sibships) design. This statistic did not account for biological relationships of related subjects, which may inflate type I error rate and/or decrease power of statistical tests. In this article, we propose two new test statistics based on a variance-components approach for analyses of microarray data obtained from general pedigrees. Our methods accommodate covariance between relatives for unmeasured genetic effects and directly model covariates of clinical importance. The efficacy and validity of our methods are investigated by using simulated data under different sample sizes, family sizes, and family structures. The proposed LR method has correct type I error rate with moderate to large sample sizes regardless of family structure and family sizes. It has higher power with complex pedigrees and similar power to the FEXAT with sibships. The other proposed FEXAT(R) method is favorable with large family sizes, regardless of sample sizes and family structure. Our methods, robust to population stratification, are complementary to the FEXAT in expression-trait association studies.
The Caenorhabditis elegans Ror RTK CAM-1 Inhibits EGL-20/Wnt Signaling in Cell Migration
Authors: Forrester Wayne C , Kim Changsung , Garriga Gian
Published: September 2004

During Caenorhabditis elegans development, the HSN neurons and the right Q neuroblast and its descendants undergo long-range anteriorly directed migrations. Both of these migrations require EGL-20, a C. elegans Wnt homolog. Through a canonical Wnt signaling pathway, EGL-20/Wnt transcriptionally activates the Hox gene mab-5 in the left Q neuroblast and its descendants, causing the cells to migrate posteriorly. In this report, we show that CAM-1, a Ror receptor tyrosine kinase (RTK) family member, inhibits EGL-20 signaling. Excess EGL-20, like loss of cam-1, caused the HSNs to migrate too far anteriorly. Excess CAM-1, like loss of egl-20, shifted the final positions of the HSNs posteriorly and caused the left Q neuroblast descendants to migrate anteriorly. The reversal in the migration of the left Q neuroblast and its descendants resulted from a failure to express mab-5, an egl-20 mutant phenotype. Our data suggest that CAM-1 negatively regulates EGL-20.
Non-Mendelian Inheritance Induced by Gene Amplification in the Germ Nucleus of Paramecium tetraurelia
Authors: Matsuda Atsushi , Takahashi Mihoko
Published: September 2004

A genetic investigation of strain d4-95, which carries a recessive mutant allele (pwB95) of pawn-B, one of the controlling elements of voltage-dependent calcium channels in Paramecium tetraurelia, revealed a non-Mendelian feature. Progeny of the cross between d4-95 and wild type often expressed a clonally stable mutant phenotype, even when they had a wild-type gene. The mutant phenotype was also expressed after self-fertilization of theoretical wild-type homozygotes recovered from the cross. Our molecular analysis demonstrated that the copy number of the mutant pwB gene in the micro- and macronucleus of d4-95 was much greater than that of the wild type. Most of the amplified, extra pwB gene copies in d4-95 were heritable independently from the original pwB locus. Repeated backcrossing of d4-95 with the wild type to dilute extra pwB genes in the strain produced segregants with a completely normal Mendelian trait in testcrosses. These results strongly suggest that a non-Mendelian inheritance of d4-95 was induced by gene amplification in the micronucleus.
Role of the Unfolded Protein Response Pathway in Secretory Stress and Regulation of INO1 Expression in Saccharomyces cerevisiae
Authors: Chang Hak J , Jesch Stephen A , Gaspar Maria L , Henry Susan A
Published: September 2004

The unfolded protein response pathway (UPR) enables the cell to cope with the buildup of unfolded proteins in the endoplasmic reticulum (ER). UPR loss-of-function mutants, hac1Δ and ire1Δ, are also inositol auxotrophs, a phenotype associated with defects in expression of INO1, the most highly regulated of a set of genes encoding enzymes of phospholipid metabolism. We now demonstrate that the UPR plays a functional role in membrane trafficking under conditions of secretory stress in yeast. Mutations conferring a wide range of membrane trafficking defects exhibited negative genetic interaction when combined with ire1Δ and hac1Δ. At semipermissive temperatures, carboxypeptidase Y transit time to the vacuole was slower in Sec− cells containing an ire1Δ or hac1Δ mutation than in Sec− cells with an intact UPR. The UPR was induced in Sec− cells defective in subcellular membrane trafficking events ranging from ER vesicle trafficking to distal secretion and in erg6Δ cells challenged with brefeldin A. However, the high levels of UPR induction observed under these conditions were not correlated with elevated INO1 expression. Indeed, many of the Sec− mutants that had elevated UPR expression at semipermissive growth temperatures failed to achieve wild-type levels of INO1 expression under these same conditions.
Core Promoter Sequences Contribute to ovo-B Regulation in the Drosophila melanogaster Germline
Authors: Bielinska Beata , Lü Jining , Sturgill David , Oliver Brian
Published: September 2004

Utilization of tightly linked ovo-A vs. ovo-B germline promoters results in the expression of OVO-A and OVO-B, C2H2 transcription factors with different N –termini, and different effects on target gene transcription and on female germline development. We show that two sex-determination signals, the X chromosome number within the germ cells and a female soma, differentially regulate ovo-B and ovo-A. We have previously shown that OVO regulates ovarian tumor transcription by binding the transcription start site. We have explored the regulation of the ovo-B promoter using an extensive series of transgenic reporter gene constructs to delimit cis-regulatory sequences as assayed in wild-type and sex-transformed flies and flies with altered ovo dose. Minimum regulated expression of ovo-B requires a short region flanking the transcription start site, suggesting that the ovo-B core promoter bears regulatory information in addition to a “basal” activity. In support of this idea, the core promoter region binds distinct factors in ovary and testis extracts, but not in soma extracts, suggesting that regulatory complexes form at the start site. This idea is further supported by the evolutionarily conserved organization of OVO binding sites at or near the start sites of ovo loci in other flies.
Reversible Histone Acetylation and Deacetylation Mediate Genome-Wide, Promoter-Dependent and Locus-Specific Changes in Gene Expression During Plant Development
Authors: Tian Lu , Fong M Paulus , Wang Jiyuan J , Wei Ning E , Jiang Hongmei , Doerge R W , Chen Z Jeffrey
Published: September 2004

Histone acetylation and deacetylation activate or repress transcription, yet the physiological relevance of reversible changes in chromatin structure and gene expression is poorly understood. We have shown that disrupting the expression of AtHD1 that encodes a putative Arabidopsis thaliana histone deacetylase induces a variety of developmental abnormalities. However, causal effects of the AtHD1 disruption on chromatin structure and gene expression are unknown. Using Arabidopsis spotted oligo-gene microarray analysis, here we report that >7% of the transcriptome was up- or downregulated in A. thaliana plants containing a T-DNA insertion in AtHD1 (athd1-t1), indicating that AtHD1 provides positive and negative control of transcriptional regulation. Remarkably, genes involved in ionic homeostasis and protein synthesis were ectopically expressed, whereas genes in ionic homeostasis, protein transport, and plant hormonal regulation were repressed in athd1-t1 leaves or flowers, suggesting a role of AtHD1 in developmental and environmental regulation of gene expression. Moreover, defective AtHD1 induced site-specific and reversible acetylation changes in H3-Lys9, H4-Lys12, and H4 tetra-lysines (residues 5, 8, 12, and 16) in homozygous recessive and heterozygous plants. Transcriptional activation was locus specific and often associated with specific acetylation sites in the vicinity of promoters, whereas gene repression did not correlate with changes in histone acetylation or correlated directly with H3-Lys9 methylation but not with DNA methylation. The data suggest that histone acetylation and deacetylation are promoter dependent, locus specific, and genetically reversible, which provides a general mechanism for reversible gene regulation responsive to developmental and environmental changes.
Characterization of the grappa Gene, the Drosophila Histone H3 Lysine 79 Methyltransferase
Authors: Shanower Gregory A , Muller Martin , Blanton Jason L , Honti Viktor , Gyurkovics Henrik , Schedl Paul
Published: September 2004

We have identified a novel gene named grappa (gpp) that is the Drosophila ortholog of the Saccharomyces cerevisiae gene Dot1, a histone methyltransferase that modifies the lysine (K)79 residue of histone H3. gpp is an essential gene identified in a genetic screen for dominant suppressors of pairing-dependent silencing, a Polycomb-group (Pc-G)-mediated silencing mechanism necessary for the maintenance phase of Bithorax complex (BX-C) expression. Surprisingly, gpp mutants not only exhibit Pc-G phenotypes, but also display phenotypes characteristic of trithorax-group mutants. Mutations in gpp also disrupt telomeric silencing but do not affect centric heterochromatin. These apparent contradictory phenotypes may result from loss of gpp activity in mutants at sites of both active and inactive chromatin domains. Unlike the early histone H3 K4 and K9 methylation patterns, the appearance of methylated K79 during embryogenesis coincides with the maintenance phase of BX-C expression, suggesting that there is a unique role for this chromatin modification in development.
Haploidy, Diploidy and Evolution of Antifungal Drug Resistance in Saccharomyces cerevisiae
Authors: Anderson James B , Sirjusingh Caroline , Ricker Nicole
Published: September 2004

We tested the hypothesis that the time course of the evolution of antifungal drug resistance depends on the ploidy of the fungus. The experiments were designed to measure the initial response to the selection imposed by the antifungal drug fluconazole up to and including the fixation of the first resistance mutation in populations of Saccharomyces cerevisiae. Under conditions of low drug concentration, mutations in the genes PDR1 and PDR3, which regulate the ABC transporters implicated in resistance to fluconazole, are favored. In this environment, diploid populations of defined size consistently became fixed for a resistance mutation sooner than haploid populations. Experiments manipulating population sizes showed that this advantage of diploids was due to increased mutation availability relative to that of haploids; in effect, diploids have twice the number of mutational targets as haploids and hence have a reduced waiting time for mutations to occur. Under conditions of high drug concentration, recessive mutations in ERG3, which result in resistance through altered sterol synthesis, are favored. In this environment, haploids consistently achieved resistance much sooner than diploids. When 29 haploid and 29 diploid populations were evolved for 100 generations in low drug concentration, the mutations fixed in diploid populations were all dominant, while the mutations fixed in haploid populations were either recessive (16 populations) or dominant (13 populations). Further, the spectrum of the 53 nonsynonymous mutations identified at the sequence level was different between haploids and diploids. These results fit existing theory on the relative abilities of haploids and diploids to adapt and suggest that the ploidy of the fungal pathogen has a strong impact on the evolution of fluconazole resistance.
Organ-Specific Silencing of Duplicated Genes in a Newly Synthesized Cotton Allotetraploid
Authors: Adams Keith L , Percifield Ryan , Wendel Jonathan F
Published: September 2004

Most eukaryotes have undergone genome doubling at least once during their evolutionary history. Hybridization followed by genome doubling (allopolyploidization) is a prominent mode of speciation in plants, leading to phenotypic novelty and changes in genome structure and gene expression. Molecular events that take place immediately after polyploid formation can be studied using newly synthesized allopolyploids. Here we studied the extent of gene silencing in a newly created and genomically stable allotetraploid cotton, of genotype AAGG, using an AFLP-cDNA display screen. Over 2000 transcripts were screened and ∼5% of the duplicated genes in the allotetraploid were inferred to have been silenced or downregulated. Sequencing of 24 AFLP-cDNA fragments revealed genes with a variety of functions. Analysis by RT-PCR showed silencing or a strong expression bias toward one copy for 9 of 13 genes examined. Comparisons of expression patterns among eight organs in the allopolyploid showed that silencing and preferential expression are organ specific. Examination of silencing patterns in two other synthetic polyploids, of genotype AADD, showed that the same gene can be silenced independently in different genotypes. These results provide a detailed portrayal of gene silencing events that can occur following allopolyploidization and suggest epigenetic causal factors.
Transmissible and Nontransmissible Mutations Induced by Irradiating Arabidopsis thaliana Pollen With γ-Rays and Carbon IonsThis article is dedicated to Toshiya Takano, who passed away in December 2003.
Authors: Naito Ken , Kusaba Makoto , Shikazono Naoya , Takano Toshiya , Tanaka Atsushi , Tanisaka Takatoshi , Nishimura Minoru
Published: September 2004

An early genetic study showed that most radiation-induced mutations are not transmitted to progeny. In recent molecular studies in plants, mainly M2 plants or their progeny, which contain only transmissible mutations, have been analyzed, but the early results imply that these studies are insufficient as comprehensive descriptions of radiation-induced mutations. To study radiation-induced mutations caused by low-LET γ-rays and high-LET carbon ions at the molecular level, we used the pollen-irradiation method and the plant Arabidopsis thaliana to study various mutations, including nontransmissible mutations. This analysis revealed that most mutants induced with irradiation with γ-rays (150–600 Gy) or carbon ions (40–150 Gy) carried extremely large deletions of up to >6 Mbp, the majority of which were not transmitted to progeny. Mutations containing 1- or 4-bp deletions, which were transmitted normally, were also found. Comparison of the deleted regions in the mutants showing various manners of transmission suggests that the nontransmissibility of the large deletions may be due to the deletion of a particular region that contains a gene or genes required for gamete development or viability.
Initiators, Cationic
Authors: Faust Rudolf
Published: September 2004

Cationic initiation in general and the cation donor (initiator)/Friedel‐Crafts acid (coinitiator) initiating system in particular are reviewed. The efficiency of a particular initiating system depends on the reactivity of the initiating cation relative to that of the propagating center. The strength of the Friedel‐Crafts acid and the nucleophilicity of the formed counteranion also affect the rates of initiation and propagation as well as the influence of solvent polarity. Controlled initiation in the absence of chain transfer, the inifer technique, and living cationic polymerization systems are reviewed. These systems have resulted in head group control, molecular weight, and end group control, and in the synthesis of well‐defined materials with controlled architecture, molecular weight, molecular weight distributions, and end functionalities.