bluuebunny/crossref_metadata_2025 huggingface dataset:
Creating and testing a geometric soil-landscape model in dry steeplands using a very low sampling density
Authors: McIntosh P. D. , Lynn I. H. , Johnstone P. D.
Published: January 2006

The aim of this study was to determine whether a predictive geometric
soil-landscape model, potentially applicable to 400 000 ha of seasonally dry
greywacke steeplands in New Zealand, could be created for 29 soil properties,
using a very low soil sampling density. We postulated that in these deeply
dissected steeplands which have relatively uniform geology and slope form,
landscape geometry (through its effects on microclimate), rather than
vegetation, geology, or slope form will control the soil pattern. To create
and test the soil-landscape model we sampled the 26 000 ha Benmore Range,
South Canterbury, New Zealand, in a formally stratified way so that trends of
soil carbon, soil nutrients, and profile characteristics could be established
for predominant slopes, at various altitudes and aspects. We used a factorial
sampling system (3 land systems × 3 altitudes × 4 aspects ×
2 slope positions), giving 72 sampling sites in total, and a sampling density
of one site per 360 ha. Altitude and aspect had significant
(P < 0.05) effects on many topsoil characteristics,
particularly those likely to be related to soil moisture status, leaching, and
weathering (e.g. topsoil pH, carbon, nitrogen, and phosphate retention). For
most soil properties the effect of slope position was not significant
(P > 0.05).
The soil-landscape model was tested by comparing predicted and actual soil
properties at a further 22 sites. Soil properties that were
laboratory-determined were generally satisfactorily predicted by the model,
but properties based on several measurements (e.g. nutrient amounts in units
of kg/ha) were less satisfactorily predicted, presumably because they
incorporate more measurement error. Trends of soil properties that showed
strong altitude and aspect relationships were effectively illustrated using
360° ‘radar diagrams’. We conclude that for dry steeplands of
uniform geology, with simple and repeated landforms at the output scale being
used, a geometric soil-landscape model based on a very low sampling density
successfully predicts soil properties on dominant landscape units. The
methodology has application to national resource inventories.
Availability of nitrogen and phosphorus under recycled water irrigation
Authors: Sakadevan K. , Maheshwari B. L. , Bavor H. J.
Published: January 2006

Land application of recycled water is currently practised in many countries as
an alternative to discharge directly into inland and coastal waters. In this
field study, nitrogen (N) and phosphorus (P) availability in pasture plots
that received recycled water was compared with that of plots which received
single applications of superphosphate fertiliser (SSP). The treatments
included recycled water applied continuously, recycled water applied
alternately with fresh water, single application of SSP at the beginning of
the experiment, and a non-amended control. Results from the study showed that
the amount of N and P removed by pasture was significantly
(P < 0.01) greater in plots that received both
recycled water treatments than in the SSP-treated plot and the control. The
amount of N (as nitrate and ammonium) leached below 1.0 m soil depth was
significantly greater (P < 0.01) for the continuous
recycled water treatment than the other treatments or the control. Nitrate was
the dominant (>80%) form of N leached from all 4 treatments. In
contrast to the findings for N, a greater proportion of applied P
(47.9%) was leached below 1.0 m soil depth from the SSP-treated plots
than from plots that received recycled water continuously (26.0%),
alternately with fresh water (13.3%), and the control. Results from the
study may be useful for developing best management practices for recycled
water irrigation of pasture.
Changes in free living soil nematode and micro-arthropod communities under a canola - wheat - lupin rotation in Western Australia
Authors: Osler Graham H. R. , van Vliet Petra C. J. , Gauci Craig S. , Abbott Lynette K.
Published: January 2006

Diversification of the crops used in wheat production systems provides
alternative sources of income and can interrupt wheat pathogen lifecycles. Two
important alternative crops in Western Australia are canola and lupins, which
may both improve growth of following wheat. Improved growth of wheat following
canola may be the consequence of biofumigation or increased root penetration
by the wheat. Available nitrogen may be increased following lupins. We
examined free-living soil fauna in a canola–wheat–lupin rotation
near Moora, Western Australia, to determine the effects of these crops on the
soil fauna. Each crop in the rotation was sampled in June, August, and October
1998. Nematodes were sorted into functional groups and arthropods were sorted
to order level. Prostigmatid mites were the dominant arthropod group and they
were sorted to morphospecies. An active and abundant faunal community was
present under all crops, demonstrating that the canola variety in this study,
Pinnacle TT, did not eliminate the free-living fauna. The structure of the
mite communities changed throughout the year and the changes were different
under the 3 crops. The soil arthropod communities were distinctly different
under lupins compared with the other crops at the end of the growing season in
2 ways. First, 5 times more animals were present under the lupins than under
wheat or canola, primarily due to an increase in the numbers of a tydeid and a
tarsonemid mite species. Second, the tarsonemid species was always the second
most abundant species under lupins but was infrequently the second ranked
species under the other 2 crops. The soil arthropod communities were also
different at the start of the growing season when the prostigmatid community
under canola was dominated by a rhagidiid species, whilst under lupins and
wheat a caligonellid and eupodid species dominated. The canola followed a
lupin crop and therefore the difference in June may be attributed to the
preceding lupins. Mite data from the lupin plots were consistent with a
previously described succession from another environment. We hypothesise that
if net nutrient mineralisation rates are greatest at the start of a succession
then net mineralisation rates under lupins may be rapid at the end of the
lupin crop and slow when the next crop is planted in the remaining lupin
stubble. The difference between lupins and canola in their mite communities
would then imply that net mineralisation rates are a factor creating
differences between the effects of break crops on the following wheat crop.
Minimum threshold value of smectite for vertic properties
Authors: Shirsath S. K. , Bhattacharyya T. , Pal D. K.
Published: January 2006

From a significant positive correlation between linear extensibility (LE) and
the smectite content in the soil control section (SCS) of 8 soils (2 red
soils, Alfisols, and 6 black soils, Vertisols, and their intergrades), the
present study indicates an excellent compatibility between the marked
shrink–swell characteristics and the smectitic mineralogy. The
initiation of vertic properties at LE of 6 in shrink–swell soils
corresponded to a minimum threshold value of 20% smectite. In order to
highlight the inherent relationship between vertic properties and the swelling
minerals, the mineralogy class for shrink–swell soils in US Soil
Taxonomy should be only smectitic.
Sorption-desorption and column leaching of strychnine with soil
Authors: Ghadiri H. , Connell D. , Parker R.
Published: January 2006

Sorption–desorption of rodenticide strychnine by soil and its leaching
through soil columns were studied on 4 typical soils of south-east Queensland.
All 4 soils showed a high tendency to sorb strychnine, with the sorption rate
higher for clay soils. The sorption capacities of the 4 soils are in the order
Kingsthorpe > Warra > Oakey > Roma, which is also the order of
decline in their clay contents. The desorption process also closely followed
the clay content of the 4 soils. The 2 clay soils of Kingsthorpe and Warra not
only sorbed a higher proportion of the applied strychnine at any application
rate, they also showed a greater resistance to releasing their sorbed
strychnine compared with the 2 silty clay loam soils. The effects of pH and
organic matter content on the sorption–desorption of strychnine were
inconclusive due to the dominant influence of clay content and the narrow
range of these characteristics provided by the soils under investigation.
The 2 clay soils of Kingsthorpe and Warra required a significantly higher
number of pore volumes of leaching solution to pass through their respective
columns for the concentration of strychnine in the effluent to approach that
of the leaching solution, compared with the 2 silty clay soils of Oakey and
Roma. The pore volumes of the leaching solution necessary for this point to be
reached were not in the order of their clay contents, but when the cumulative
volume of solution was used instead of the pore volume, the trend followed the
clay content of the soils closely. Pore volume may not be an appropriate
characteristic for assessing the leachability of strychnine through soil
columns when the soil’s clay fraction is of an expanding type, as it is
the case for Kingsthorpe soil. No desorption or leaching of strychnine took
place in any of the 4 soils aged with a range of strychnine concentrations.
Predicting the probabilities of groundwater contamination by pesticides under variable recharge
Authors: Aylmore L. A. G. , Di H. J.
Published: January 2006

A major deficiency in many models used to assess the groundwater contamination
potential of organic pesticides used in agricultural and horticultural systems
has been the assumption of a constant average groundwater recharge rate. This
paper describes an enhanced version of a simple model designed to screen out
or identify those pesticides that have a high probability for causing
groundwater contamination in a region (e.g. a catchment, farm, or cropping
area), which enables the temporal variability of recharge to be taken into
account and illustrates the influence of a seasonal pattern of leaching and
variations in predicted mobilities and persistence from those associated with
averaging the recharge rate. The model is available as a user-friendly
software package (PESTSCRN 3).
The model was formulated based on the following assumptions: (1) linear,
equilibrium, and reversible sorption; (2) first-order breakdown or
degradation; (3) pesticide leaching by steady convective flow; and (4)
recharge rate varying with time. Random values of the input parameters
required by the calculations are generated from probability distributions as
specified by the means (m) and standard deviations (s), assuming normal
distributions. Outputs provide a statistical analysis of travel time and
fraction of pesticide remaining at different soil depths. Most distributions
for travel time are near normal with slight positive skewness and can be
approximated as normal distributions. The frequency distributions of residue
fractions for all the pesticides examined to date show significant positive
skewness (Beta distributions), with the peak frequency towards the lower bound
of 0. Simulations using metalaxyl as an example demonstrate that, depending on
recharge conditions, the use of daily data instead of mean recharge data can
result in important differences in the predicted values of both travel times
and residue percentages.
Crop rotation effects on soil carbon and physical fertility of two Australian soils
Authors: Blair Nelly , Crocker G. J.
Published: January 2006

The effect of using different crop rotations, including legumes and fallows,
on soil structural stability, unsaturated hydraulic conductivity, and the
concentration of different carbon fractions was examined in a long-term
rotation trial established in 1966 on a Black Earth (Pellic Vertisol) and a
Red Clay (Chromic Vertisol) soil. There was a large decrease in the
concentration of soil carbon fractions following cropping and cultivation on
both soils. The inclusion of some legume rotation crops resulted in an
increase in labile carbon concentrations compared with continuous wheat or a
long fallow treatment. Aggregate stability to wetting under both immersion and
tension wetting was reduced as a result of cropping and cultivation for both
soil types. However, there was an improvement in aggregate stability with
immersion wetting, on the Red Clay soil, for the lucerne
(Medicago sativa), clover
(Trifolium subterraneum), and continuous wheat
(Triticum aestivium) treatments compared with the long
fallow. Similar results were found for the Black Earth soil; however, on this
soil the medic (Medicago scutella) rotation also showed
an improvement in soil structure. On the Red Clay soil there was a decrease in
hydraulic conductivity (K) with cropping, at all tensions measured. K for the
Black Earth soil was higher at 30 and 40 mm tension on the cropped soil than
on the uncropped reference soil, but at 10 mm tension the reference soil had a
higher K value than all rotations except the lucerne. There was a significant
correlation between labile carbon and all determinations of aggregate
stability for the Red Clay soil. Farmers should be encouraged to eliminate
long fallowing and to adopt no-till techniques combined with the return of
residues from either the primary crop or rotation crops which have a slower
breakdown rate, as this management is likely to have a better potential for
increasing soil carbon content and improving soil structure. The investigation
of ways to better increase the quantity and quality of soil organic matter and
hence soil chemical and physical fertility is necessary if long-term
sustainable agriculture is to be possible.
Resistance to cropping pressure of two New Zealand soils with contrasting mineralogy
Authors: Sparling Graham P. , Schipper Louis A. , Hewitt Allan E. , Degens Bradley P.
Published: January 2006

Changes in soil properties in response to cropping pressure were measured in 2
mineralogically contrasting New Zealand topsoils. Waiareka clay (Vertic
Haplustoll) with >65% smectite clay was compared with Wakanui silt
loam (Aquic Haplustept), which contains about 20% mixed or illite
clays. Soil properties (0–10 cm) were assessed by changes in organic
carbon (C) and nitrogen (N), pH, cation exchange capacity, Olsen P, microbial
C, soil respiration, microbial functional evenness, mineralisable N, bulk
density, unsaturated hydraulic conductivity, readily available and total
available water, macro porosity and total porosity, particle density, and
particle size distribution. Additional samples of the Waiareka clay soil were
taken at 10–20 cm depth. Cropping pressure was estimated using a scale
based on the number of years in crop v. those in
pasture.
The organic and biological status of the Waiareka pasture soil (0–10 cm)
was greater than that of the Wakanui pasture, with contents of 5.1%
organic C, 0.43% total N, 1429 microbial C
(µg/cm3), and 123 mineralisable N
(µg/cm3), compared with values of 4.0%,
0.31%, 795 µg/cm3, and 89
µg/cm3, respectively. Total and macroporosity,
and total and readily available water, were also greater on the Waiareka
pasture soil compared with the Wakanui pasture soil. Under cropping pressure,
the Waiareka soil had marked declines in organic matter C and N, microbial C
and soil respiration, microbial functional evenness, macroporosity, and
available water. In contrast, the Wakanui silt loam showed little response to
cropping pressure; mineralisable N declined slightly and particle density
increased under cropping.
We concluded that the initial properties of a soil were not good predictors of
subsequent resistance to cropping pressure; and that soils with initially high
status have the potential for proportionally greater decline.
Comparison of single superphosphate and superphosphate coated with bauxite residue for subterranean clover production on phosphorus-leaching soils
Authors: Summers Robert , Clarke Martin , Pope Tim , O'Dea Tim
Published: January 2006

Bauxite residue from alumina refining was used to coat granules of single
superphosphate to reduce the leaching of phosphorus in coarse, sandy soils for
pastures in high rainfall areas of south-western Australia (>800 mm annual
average). The impact of coating the superphosphate on the leaching of
phosphorus was measured in a glasshouse experiment and the effectiveness of
the fertiliser using dry herbage yield of subterranean clover
(Trifolium subterraneum) was measured in a field
experiment. The glasshouse experiment measured the effect of coating the
superphosphate with bauxite residue at 0, 5, 10, 15, 20, 25, 30, 35, and
40% by weight. A coating of 25% (by weight) was chosen for the
field experiment.
In the glasshouse experiment, the coated granules were applied to columns of
soil, where subterranean clover was grown under leaching conditions. A coating
of 30%, by weight, reduced leaching of single superphosphate by about
half. Increasing the coating of bauxite residue also increased the phosphorus
uptake and increased the plant growth.
In the field trial, the effectiveness of single superphosphate with a bauxite
residue coating of 25% by weight was increased on average by
100% in Year 1, 303% in Year 2, and 158% in Year 3,
relative to freshly applied single superphosphate. The bauxite residue coating
also increased the phosphorus content of the herbage in a similar manner to
the increases in yield. Limited soil phosphorus tests showed only minor
increases in the residues of phosphorus where the superphosphate had been
coated with bauxite residue.
Hydrology of swelling soils: a review
Authors: Smiles D. E.
Published: January 2006

A generally accepted theory of liquid flow in rigid systems has been used in
soil science for more than 50 years. Liquid flow in systems that change volume
with liquid content is not so well described and remains a major challenge to
soil scientists, although its application in chemical and mining engineering
and soil mechanics is increasingly accepted. Theory of water flow in swelling
soils must satisfy material continuity. It must also account for changes in
the gravitational potential energy of the system during swelling and for
anisotropic stresses that constrain the soil laterally but permit vertical
movement. A macroscopic and phenomenological analysis based on material
balance and Darcy’s law is the most useful first approach to water flow
and volume change in such soils. Use of a material coordinate based on the
solid distribution results in a flow equation analogous to that L. A. Richards
enunciated for non-swelling soils. This framework is strain-independent and
solutions to the flow equation exist for a wide range of practically important
conditions. The approach has been well tested in clay suspensions and
saturated systems such as mine tailings and sediments. It is also applied in
soil mechanics. This paper reviews central elements in application of the
analysis to swelling soils. It argues that, as with use of the Richards’
equation in rigid soils, complexities are evident, but the approach remains
the most coherent and profitable to support current need and future research.
The use of material coordinates, to ensure material balance is assessed
correctly, is simple.
Geologically related variations in saturated hydraulic conductivity in the regolith of the western wheatbelt of Western Australia and its implications for the development of dryland salinity
Authors: Clarke C. J. , George R. J. , Bennett D. L. , Bell R. W.
Published: January 2006

This is the first systematic study of geology-related saturated hydraulic
conductivity differences in the regolith of the wheatbelt of Western
Australia. Except for 2 rock types studied, much lower permeability in the
pallid zone than in the underlying aquifer, is substantiated. Higher
permeability in major faults than in the surrounding granite is confirmed, and
this extends into the pallid zone. Mafic dykes have no significant differences
in permeability to granite in the saprolite aquifer but it is arguable that
the permeability of dykes in the pallid zone is greater than granite.
Permeability of the Tertiary valley filling sandstone aquifer is higher than
of the underlying granite and much higher than of the overlying claystone
aquiclude. The results presented in this paper provide a basis for groundwater
models to take into account differences in permeability between major faults
and granite and within Tertiary sediments, which is necessary in order to
improve predictions of salinity extent and treatment effectiveness.
Improved laboratory calibration of a single-probe surface gamma-neutron gauge
Authors: Cássaro F. A. M. , Tominaga T. T. , Bacchi O. O. S. , Reichardt K. , Oliveira J. C. M. , Timm L. C.
Published: January 2006

Surface gamma-neutron gauges are extensively used for the determination of
soil physical properties such as density. Substantial differences are
sometimes observed between density values provided by these gauges when using
factory-supplied calibrations and gravimetric density measurements. These
differences can be as high as 16%. In this paper it is shown that,
using homogeneous materials with different known densities covering a wider
range, it is possible to find a better calibration equation. This calibration
provides density values in agreement with gravimetric measurements.
Virtual fractionation of charcoal from soil organic matter using solid state 13C NMR spectral editing
Authors: Smernik R. J. , Skjemstad J. O. , Oades J. M.
Published: January 2006

The solid state 13C NMR spectral editing technique
proton spin relaxation editing (PSRE), which generates subspectra of
components that have different proton relaxation rates and are spatially
separated by at least 30–100 nm, was applied to hydrofluoric acid
treated <53 m soil fractions from 8 Australian surface soils. Most of the
aromatic signal was partitioned into the rapidly relaxing subspectrum,
especially for the soils known to have high charcoal contents. However, the
presence of other rapidly relaxing soil organic matter (SOM) components
prevented a clean separation of charcoal from non-charcoal components. PSRE
analysis was repeated after the samples had been treated with high energy
ultraviolet photo-oxidation, which brings about the mineralisation of most SOM
other than char. Excellent separation of the charcoal fraction by PSRE was
achieved after photo-oxidation for 5 of the samples with the highest charcoal
content. The rapidly relaxing subspectra for these samples also suggested that
the charcoal present in soil contains significant carbonyl functionality,
possibly as a result of in situ weathering.
A new PSRE methodology is described, designed to best suit SOM samples. Data
from inversion-recovery experiments were fitted to a model consisting of 2
components with different T1H relaxation rate constants,
thus providing an objective best fit to the inversion-recovery data and
avoiding the subjective judgements required in other PSRE methodologies.
Mobility of phosphorus through intact soil cores collected from the Adelaide Hills, South Australia
Authors: Cox J. W. , Kirkby C. A. , Chittleborough D. J. , Smythe L. J. , Fleming N. K.
Published: January 2006

Intact cores were collected from a variety of soils in the Adelaide Hills,
South Australia, and tested for phosphorus retention and mobility (P in
drainage) under various rainfall intensities (5, 25, and 50 mm/h).
Phosphorus mobility was high in soils with significant macropore structure.
However, all soils exhibited some degree of preferential flow of P, including
the heavy-textured soils with high P adsorption that were not P saturated. A
phosphorus adsorption index based only on the chemical properties of the soil
did not accurately predict the mobility of P through soils with macroporosity.
A phosphorus mobility index was developed encompassing both soil chemical and
physical parameters. Results showed the sandy soils, and the loams over clays
with high macroporosity that are located in the more elevated parts of the
Adelaide hills, are most susceptible to P leaching.
Management to reduce P loss to groundwater, streams, or surface water storages
must aim to increase the residence time of P within soils and thereby allow
mineral and organic fractions time to sorb P. Phosphorus loss through wet
soils was significantly less than P loss through dry soils with high
macroporosity. Application of P fertiliser to soils with high macroporosity
may need to be delayed until later in the growing season than is currently
practised.
Speciation and phytoavailability of cadmium in selected surface soils of South Australia
Authors: Krishnamurti G. S. R. , Naidu R.
Published: January 2006

A modified sequential extraction scheme was developed for partitioning the
particulate-bound cadmium (Cd) into 9 fractions: exchangeable,
carbonate-bound/specifically adsorbed, metal–fulvic
acid-complex-bound, metal–humic acid-complex-bound, easily reducible
metal oxide-bound, organic-bound, amorphous mineral colloid-bound, crystalline
Fe oxide-bound, and detrital (bound to mineral lattices). Results on 11
surface soils showed that Cd in these soils was predominantly present in
detrital form, bound to the mineral lattices, accounting for
15.8–61.9%, with an average of 33.4%, of the total Cd in
the soils. The average relative abundance of Cd bound to the different
particulate forms in the soils is in the order: detrital (0.077 mg/kg)
> specifically adsorbed/carbonate-bound (0.066 mg/kg) >
organic-bound (0.033 mg/kg) > metal–fulvic acid-complex-bound
(0.031 mg/kg) > easily reducible metal oxide-bound (0.019 mg/kg)
> exchangeable (0.013 mg/kg) > metal–humic acid-complex-bound
(0.011 mg/kg) > crystalline Fe oxide-bound (0.001 mg/kg)
=amorphous mineral colloid-bound (0.001 mg/kg).
The phytoavailable Cd content was determined as Cd concentration in the shoot
and leaf of durum wheat plants grown on the soils in a greenhouse study.
Statistical treatment of the data showed that the exchangeable Cd
(r = 0.735, P =
0.01) and the metal–fulvic acid-complex-bound Cd
(r = 0.824, P =
0.002) correlated significantly with the plant-available Cd, compared with
other species. The exchangeable and fulvic acid fraction of the
metal–organic-complex-bound Cd contents, together, could explain
91.5% of the variation in plant-available Cd, determined as Cd
concentration in leaf and stem of the durum wheat plants
(r = 0.956, P =
0.0001). The significance of metal–fulvic acid complexes on Cd
phytoavailability has not been reported so far and needs in-depth research in
explaining the toxicity and food chain contamination of Cd in the environment.
Bayesian classifiers for detecting HGT using fixed and variable order markov models of genomic signatures
Authors: Dalevi Daniel , Dubhashi Devdatt , Hermansson Malte
Published: January 2006

Motivation: Analyses of genomic signatures are gaining attention as they allow studies of species-specific relationships without involving alignments of homologous sequences. A naïve Bayesian classifier was built to discriminate between different bacterial compositions of short oligomers, also known as DNA words. The classifier has proven successful in identifying foreign genes in Neisseria meningitis. In this study we extend the classifier approach using either a fixed higher order Markov model (Mk) or a variable length Markov model (VLMk).

Results: We propose a simple algorithm to lock a variable length Markov model to a certain number of parameters and show that the use of Markov models greatly increases the flexibility and accuracy in prediction to that of a naïve model. We also test the integrity of classifiers in terms of false-negatives and give estimates of the minimal sizes of training data. We end the report by proposing a method to reject a false hypothesis of horizontal gene transfer.

Availability: Software and Supplementary information available at

Contact:  dalevi@cs.chalmers.se
IWoCS: analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships
Authors: D'Auria Giuseppe , Pushker Ravindra , Rodriguez-Valera Francisco
Published: January 2006

Motivation: Lately the use of 16S–23S Intergenic Transcribed Spacer (ITS) sequences for bacterial typing purposes has increased. The presence of conserved regions like tRNA genes or boxes together with hypervariable regions allows performing intraspecific discrimination of very close bacterial strains. On the other hand this mosaic of variability makes the ITS a sequence difficult to analyze and compare.

Results: A software to study ITSs by a Word Count based System (IWoCS) is proposed. A large dataset of ITS was created (comprising 7355 sequences). A database indicating all the occurrences of possible n-mers (tags), describing each ITS sequence, was created (with n going from 5 to 13) including 32 061 819 entries. The database allows to analyze ITS sequences submitted by users using a web-based interface. The abundance in the database of each n-mer is given in a one-base sliding frame. A dominance plot reflects how common the tags are within different taxonomic levels. The obtained profile identifies highly repeated tags as evolutionarily conserved regions (like tRNA or boxes) or low frequency tags as regions specifically associated to taxonomic groups. The study of the dominance and abundance profiles combined with the taxonomy reports provides a novel tool for the use of the ITS in bacteria typing and identification.

Availability: The database is freely accessible at

Contact:  gdauria@umh.es
A greedier approach for finding tag SNPs
Authors: Chang Chia-Jung , Huang Yao-Ting , Chao Kun-Mao
Published: January 2006

Motivation: Recent studies have shown that a small subset of Single Nucleotide Polymorphisms (SNPs) (called tag SNPs) is sufficient to capture the haplotype patterns in a high linkage disequilibrium region. To find the minimum set of tag SNPs, exact algorithms for finding the optimal solution could take exponential time. On the other hand, approximation algorithms are more efficient but may fail to find the optimal solution.

Results: We propose a hybrid method that combines the ideas of the branch-and-bound method and the greedy algorithm. This method explores larger solution space to obtain a better solution than a traditional greedy algorithm. It also allows the user to adjust the efficiency of the program and quality of solutions. This algorithm has been implemented and tested on a variety of simulated and biological data. The experimental results indicate that our program can find better solutions than previous methods. This approach is quite general since it can be used to adapt other greedy algorithms to solve their corresponding problems.

Availability: The program is available upon request.

Contact:  kmchao@csie.ntu.edu.tw
MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data
Authors: Katajamaa Mikko , Miettinen Jarkko , Orešič Matej
Published: January 2006

Summary: New additional methods are presented for processing and visualizing mass spectrometry based molecular profile data, implemented as part of the recently introduced MZmine software. They include new features and extensions such as support for mzXML data format, capability to perform batch processing for large number of files, support for parallel processing, new methods for calculating peak areas using post-alignment peak picking algorithm and implementation of Sammon's mapping and curvilinear distance analysis for data visualization and exploratory analysis.

Availability: MZmine is available under GNU Public license from

Contact:  matej.oresic@vtt.fi
GUUGle: a utility for fast exact matching under RNA complementary rules including G–U base pairing
Authors: Gerlach Wolfgang , Giegerich Robert
Published: January 2006

Motivation: RNA secondary structure analysis often requires searching for potential helices in large sequence data.

Results: We present a utility program GUUGle that efficiently locates potential helical regions under RNA base pairing rules, which include Watson–Crick as well as G–U pairs. It accepts a positive and a negative set of sequences, and determines all exact matches under RNA rules between positive and negative sequences that exceed a specified length. The GUUGle algorithm can also be adapted to use a precomputed suffix array of the positive sequence set. We show how this program can be effectively used as a filter preceding a more computationally expensive task such as miRNA target prediction.

Availability: GUUGle is available via the Bielefeld Bioinformatics Server at

Contact:  robert@TechFak.Uni-Bielefeld.DE
Haloferax volcanii PitA: an example of functional interaction between the Pfam chlorite dismutase and antibiotic biosynthesis monooxygenase families?
Authors: Bab-Dinitz Elizabeta , Shmuely Hagay , Maupin-Furlow Julie , Eichler Jerry , Shaanan Boaz
Published: January 2006

A curious fusion between chlorite dismutase-like and antibiotic biosynthesis monooxygenase-like domains within a single open reading frame has been revealed by both sequence homology and structural modeling in Haloferax volcanii PitA and its homologues in other halophilic archaea. While this fusion may reflect an environmental adaptation to life in hypersaline environments and hence one specific to haloarchaea, PitA and its homologues may represent a paradigm of biologically-relevant interplay between these two distinct activities in accordance with the Rosetta Stone approach.

Contact:  bshaanan@bgu.ac.il
As you reap, so shall you sow: coupling of harvesting and inoculating stabilizes the mutualism between termites and fungi
Authors: Aanen Duur K
Published: January 2006

At present there is no consensus theory explaining the evolutionary stability of mutualistic interactions. However, the question is whether there are general ‘rules’, or whether each particular mutualism needs a unique explanation. Here, I address the ultimate evolutionary stability of the ‘agricultural’ mutualism between fungus-growing termites andTermitomycesfungi, and provide a proximate mechanism for how stability is achieved. The key to the proposed mechanism is the within-nest propagation mode of fungal symbionts by termites. The termites suppress horizontal fungal transmission by consuming modified unripe mushrooms (nodules) for food. However, these nodules provide asexual gut-resistant spores that form the inoculum of new substrate. This within-nest propagation has two important consequences: (i) the mutualistic fungi undergo severe, recurrent bottlenecks, so that the fungus is likely to be in monoculture and (ii) the termites ‘artificially’ select for high nodule production, because their fungal food source also provides the inoculum for the next harvest. I also provide a brief comparison of the termite–fungus mutualism with the analogous agricultural mutualism between attine ants and fungi. This comparison shows that—although common factors for the ultimate evolutionary stability of mutualisms can be identified—the proximate mechanisms can be fundamentally different between different mutualisms.
Sex allocation theory aids species conservation
Authors: Robertson Bruce C , Elliott Graeme P , Eason Daryl K , Clout Mick N , Gemmell Neil J
Published: January 2006

Supplementary feeding is often a key tool in the intensive management of captive and threatened species. Although it can increase such parameters as breeding frequency and individual survival, supplementary feeding may produce undesirable side effects that increase overall extinction risk. Recent attempts to increase breeding frequency and success in the kakapo
Strigops habroptilus
using supplementary feeding inadvertently resulted in highly male-biased chick sex ratios. Here, we describe how the inclusion of sex allocation theory has remedied this conservation dilemma. Our study is the first to manipulate chick sex ratios in an endangered species by altering maternal condition and highlights the importance of incorporating evolutionary theory into modern conservation practice.
Inbreeding avoidance through non-random mating in sticklebacks
Authors: Frommen Joachim G , Bakker Theo C.M
Published: January 2006

Negative effects of inbreeding are well documented in a wide range of animal taxa. Hatching success and survival of inbred offspring is reduced in many species and inbred progeny are often less attractive to potential mates. Thus, individuals should avoid mating with close kin. However, experimental evidence for inbreeding avoidance through non-random mating in vertebrates is scarce. Here, we show that gravid female three-spined sticklebacks (
Gasterosteus aculeatus
) when given the choice between a courting familiar brother and a courting unfamiliar non-sib prefer to mate with the non-sib and thus avoid the disadvantages of incest. We controlled for differences in males' body size and red intensity of nuptial coloration. Thus, females adjust their courting behaviour to the risk of inbreeding.
A sharp interface reduction for multiphase transport in a porous fuel cell electrode
Authors: Promislow Keith , Stockie John , Wetton Brian
Published: January 2006

The gas diffusion layer in the electrode of a proton exchange membrane fuel cell is a highly porous material which acts to distribute reactant gases uniformly to the active catalyst sites. We analyse the conservation laws governing the multiphase flow of liquid, gas and heat within the electrode. The model is comprised of five nonlinear-degenerate parabolic differential equations strongly coupled through liquid–gas phase change. We identify a scaling regime in which the model reduces to a free boundary problem for a moving two-phase interface. On each side of the moving boundary the nonlinear system is well approximated by its linearization whose relaxation times are much shorter than the front evolution. Using a quasi-steady reduction, we obtain an explicit leading-order evolution equation for the free surface in terms of the prescribed boundary conditions.
The treatment of lubrication forces in boundary integral equations
Authors: Mammoli Andrea Alberto
Published: January 2006

Despite their many advantages over other numerical methods, boundary integral formulations still fail to provide accurate predictions of mesoscale motion in dense suspensions of rigid particles because the nearly singular flow between surfaces in close proximity cannot be resolved accurately. A procedure for incorporating analytical solutions for the lubrication flow within a large-scale boundary integral equation method is shown. Although the method is applied to the case of spherical particles, in conjunction with the completed double layer boundary integral equation, it can be developed further to treat more complex geometries and can be adapted to other numerical techniques. In contrast to other apparently similar approaches, the present method does not resort to effective medium approximations, and in principle retains all the advantages typical of boundary integral approaches. The framework also allows for forces other than those due to hydrodynamic lubrication between particles, provided that they are a linear function of the relative velocity or at least can be linearized; for example, forces due to sub-continuum fluid behaviour or forces resulting from surface chemistry. It is shown using several benchmarks that the relative motion between two particles in various flows is captured accurately, both statically and dynamically, in situations where uncorrected simulations fail. Moreover, the computational effort is reduced substantially by the application of the method.
Calculation of the slowness vector from the ray vector in anisotropic media
Authors: Vavryčuk Václav
Published: January 2006

The wave quantities needed in constructing wave fields propagating in anisotropic elastic media are usually calculated as a function of the slowness vector, or of its direction called the wave normal. In some applications, however, it is desirable to calculate the wave quantities as a function of the ray direction. In this paper, a method of calculating the slowness vector for a specified ray direction is proposed. The method is applicable to general anisotropy of arbitrary strength with arbitrary complex wave surface. The slowness vector is determined by numerically solving a system of multivariate polynomial equations of the sixth order. By solving the equations, we obtain a complete set of slowness vectors corresponding to all wave types and to all branches of the wave surface including the slowness vectors along the acoustic axes. The wave surface can be folded to any degree. The system of equations is further specified for rays shot in the symmetry plane of an orthorhombic medium and for a transversely isotropic medium. The system is decoupled into two polynomial equations of the fourth order for the
P
–SV
waves, and into equations for the
SH
wave, which yield an explicit closed-form solution. The presented approach is particularly advantageous in constructing ray fields, ray-theoretical Green functions, wavefronts and wave fields in strong anisotropy.
The hairless guinea‐pig as a model for treatment of cumulative irritation in humans
Authors: Andersen F. , Hedegaard K. , Petersen T. K. , Bindslev‐Jensen C. , Fullerton A. , Andersen K. E.
Published: January 2006

Background: The effect of six skin‐care formulations (SCFs) on experimentally induced cumulative irritation was studied in hairless guinea‐pigs (HLGPs) and in human volunteers (HVs). The formulations were a basic cream, a carbomer cream and four modifications of the carbomer cream, containing either 10% isopropyl palmitate (IPP cream), 10% glycerol (glycerol cream), 19.5% canola oil (canola oil cream) or 0.5% (‐)‐α‐bisabolol (bisabolol cream).

Methods: In HLGP, irritant dermatitis was induced with 30 min daily exposure for 4 days to 0.5% sodium lauryl sulfate aq. (SLS). In HVs, irritant dermatitis was induced with 10 min daily exposure for 5+4 days (no irritation on weekends) to 3% SLS aq. on the right and 30% nonanoic acid (NON) in n‐propanol on the left volar forearm. Clinical scoring was performed daily; evaporimetry (total epidermal water loss (TEWL)), hydration and colorimetry were measured at baseline (day 0) in the middle and at the end of treatment. Treatments were applied twice daily. The basic cream and the IPP cream were excluded from testing in HLGP because they were known from previous studies to be irritant in HLGP, while all formulations were known to be equally and well tolerated locally in humans.

Results: All formulations worsened the skin irritation in HLGP: the glycerol cream the least, the canola oil cream the most, while the bisabolol cream and the carbomer cream were indistinguishable. In humans, the glycerol cream was better than ‘No Treatment’ after cumulative irritation with both SLS and NON. The basic cream was better tolerated in humans than was expected from previous testing in HLGPs.

Conclusion: In conclusion, the results from the studies in HLGPs and HVs are in agreement with regard to ranking of the SCFs. Further, the glycerol cream showed a positive treatment effect on both SLS‐ and NON‐irritated skin in HVs.
Towards targeted therapy for infant acute lymphoblastic leukaemia
Authors: Stam Ronald W. , den Boer Monique L. , Pieters Rob
Published: January 2006

Despite the greatly improved treatment regimes for childhood acute lymphoblastic leukaemia (ALL) in general, resulting in long‐term survival in approximately 80% of cases, current therapies still fail in >50% of ALL cases diagnosed within the first year of life (i.e. in infants). Therefore, more adequate treatment strategies are urgently needed to also improve the prognosis for these very young patients with ALL. Here we review the current acquaintance with the biology of infant ALL and describe how this knowledge may lead to innovative therapeutic approaches.
Thalassaemia‐like carriers not linked to the β‐globin gene cluster
Authors: Faà Valeria , Meloni Alessandra , Moi Loredana , Ibba Giuseppe , Travi Maurizio , Vitucci Antonio , Cao Antonio , Rosatelli Maria Cristina
Published: January 2006

This study describes the largest series reported to date, of individuals belonging to unrelated families carrying a β‐thalassaemia‐like phenotype in whom the β‐globin gene was found to be structurally intact by sequence analysis. This genetic determinant appears haematologically heterogeneous, displaying either a silent β‐thalassaemia‐like phenotype or a typical β‐thalassaemia carrier‐like phenotype in different families. Compound heterozygosity for both β‐thalassaemia‐like determinant and typical β‐thalassaemia allele resulted either in thalassaemia intermedia or thalassaemia major. By linkage analysis both the silent and the typical β‐like determinants were found not to be linked to the β‐globin cluster. Sequence analysis of the hypersensitive site cores of locus control region and of the genes coding for the transcription factors erythroid Kruppel‐like factor and nuclear factor (erythroid‐derived 2) were normal. β‐globin mRNA levels determined by real‐time polymerase chain reaction were reduced in both types of β‐like carriers. These results indicate the existence of causative genetic determinants not yet molecularly defined, but most likely, resulting from either the reduction or loss of function of a gene coding for unknown transcriptional regulator(s) of the β‐globin gene. The knowledge of these rare β‐thalassaemia‐like determinants have implications for clinical and, especially, prenatal diagnosis of β‐thalassaemia.
Specific polymorphisms of cytokine genes are associated with different risks to develop single‐system or multi‐system childhood Langerhans cell histiocytosis
Authors: Filippi Paola De , Badulli Carla , Cuccia Mariaclara , Silvestri Annalisa De , Dametto Ennia , Pasi Annamaria , Garaventa Alberto , Prever Adalberto Brach del , Todesco Alessandra , Trizzino Antonino , Danesino Cesare , Martinetti Miryam , Aricò Maurizio
Published: January 2006

Cytokines and chemokines determine mobilisation of Langerhans cells and their dysregulation is implicated in the pathogenesis of Langerhans cell histiocytosis (LCH). Twenty point mutations of 12 different cytokine genes were studied in 41 Italian children, 15 with single‐system (SS) and 26 with multi‐system disease. The allele and genotype distributions of interleukin‐4 (IL‐4) and interferon‐γ (IFNγ) were significantly different in patients vs. 140 controls (P = 0.007, and P = 0.018). Older children with single‐system disease shared the ‘anti‐inflammatory profile’ determined by the intermediate producer genotype IFNγ +874A/T (P = 0.029) and the high‐producer genotypes IL‐4 –590C/T and T/T (P = 0.029). Our findings suggest that specific cytokine gene variants affect susceptibility to LCH and its clinical heterogeneity.