bluuebunny/crossref_metadata_2025_split huggingface dataset:
The LCB Data Warehouse
Authors: Ameur Adam , Yankovski Vladimir , Enroth Stefan , Spjuth Ola , Komorowski Jan 
Published: February 2006

AbstractSummary: The Linnaeus Centre for Bioinformatics Data Warehouse (LCB-DWH) is a web-based infrastructure for reliable and secure microarray gene expression data management and analysis that provides an online service for the scientific community. The LCB-DWH is an effort towards a complete system for storage (using the BASE system), analysis and publication of microarray data. Important features of the system include: access to established methods within R/Bioconductor for data analysis, built-in connection to the Gene Ontology database and a scripting facility for automatic recording and re-play of all the steps of the analysis. The service is up and running on a high performance server. At present there are more than 150 registered users.Availability: An open functional version is available at . User accounts are created upon request. Additional facilities including plug-ins, user documentation and a password protected data storage system are available fromContact: Jan.Komorowski@lcb.uu.se
FANMOD: a tool for fast network motif detection
Authors: Wernicke Sebastian , Rasche Florian 
Published: February 2006

Abstract
Summary: Motifs are small connected subnetworks that a network displays in significantly higher frequencies than would be expected for a random network. They have recently gathered much attention as a concept to uncover structural design principles of complex biological networks. FANMOD is a tool for fast network motif detection; it relies on recently developed algorithms to improve the efficiency of network motif detection by some orders of magnitude over existing tools. This facilitates the detection of larger motifs in bigger networks than previously possible. Additional benefits of FANMOD are the ability to analyze colored networks, a graphical user interface and the ability to export results to a variety of machine- and human-readable file formats including comma-separated values and HTML.
Availability: The tool is freely available online at and runs under Linux, Mac OS and Windows.
Contact: wernicke@minet.uni-jena.de
Analysis of Phase of LUCIFERASE Expression Reveals Novel Circadian Quantitative Trait Loci in Arabidopsis
Authors: Darrah Chiarina , Taylor Bethan L. , Edwards Kieron D. , Brown Paul E. , Hall Anthony , McWatters Harriet G. 
Published: February 2006

Abstract
In response to exogenous rhythms of light and temperature, most organisms exhibit endogenous circadian rhythms (i.e. cycles of behavior and gene expression with a periodicity of approximately 24 h). One of the defining characteristics of the circadian clock is its ability to synchronize (entrain) to an environmental rhythm. Entrainment is arguably the most salient feature of the clock in evolutionary terms. Previous quantitative trait studies of circadian characteristics in Arabidopsis (Arabidopsis thaliana) considered leaf movement under constant (free-running) conditions. This study, however, addressed the important circadian parameter of phase, which reflects the entrained relationship between the clock and the external cycle. Here it is shown that, when exposed to the same photoperiod, Arabidopsis accessions differ dramatically in phase. Variation in the timing of circadian LUCIFERASE expression was used to map loci affecting the entrained phase of the clock in a recombinant population derived from two geographically distant accessions, Landsberg erecta and Cape Verde Islands. Four quantitative trait loci (QTL) were found with major effects on circadian phase. A QTL on chromosome 5 contained SIGNALING IN RED LIGHT REDUCED 1 and PSEUDORESPONSE REGULATOR 3, both genes known to affect the circadian clock. Previously unknown polymorphisms were found in both genes, making them candidates for the effect on phase. Fine mapping of two other QTL highlighted genomic regions not previously identified in any circadian screens, indicating their effects are likely due to genes not hitherto considered part of the circadian system.
Posttranslational Regulation of Nitrate Reductase Strongly Affects the Levels of Free Amino Acids and Nitrate, whereas Transcriptional Regulation Has Only Minor Influence
Authors: Lea Unni S. , Leydecker Marie-Thérèse , Quilleré Isabelle , Meyer Christian , Lillo Cathrine 
Published: February 2006

Abstract
Diurnal variations in nitrate reductase (NR) activity and nitrogen metabolites were examined in wild-type Nicotiana plumbaginifolia and transformants with various degrees of NR deregulation. In the C1 line, NR was only deregulated at the transcriptional level by placing the NR gene under the control of the cauliflower mosaic virus 35S RNA promoter. In the Del8 and S521D lines, NR was additionally deregulated at the posttranslational level either by a deletion mutation in the N-terminal domain or by a mutation of the regulatory phosphorylation site (serine-521). Posttranslational regulation was essential for pronounced diurnal variations in NR activity. Low nitrate content was related to deregulation of NR, whereas the level of total free amino acids was much higher in plants with fully deregulated NR. Abolishing transcriptional and posttranslational regulation (S521D plants) resulted in an increase of glutamine and asparagine by a factor of 9 and 14, respectively, compared with wild type, whereas abolishing transcriptional regulation (C1 plants) only resulted in increases of glutamine and asparagine by factors &lt;2. Among the minor amino acids, isoleucine and threonine, in particular, showed enhanced levels in S521D. Nitrate uptake rates were the same in S521D and wild type as determined with 15N feeding. Deregulation of NR appears to set the level of certain amino acids, whereas diurnal variations were still determined by light/dark. Generally, deregulation of NR at the transcriptional level did not have much influence on metabolite levels, but additional deregulation at the posttranslational level resulted in profound changes of nitrogen metabolite levels.
An Ankyrin Repeat-Containing Protein, Characterized as a Ubiquitin Ligase, Is Closely Associated with Membrane-Enclosed Organelles and Required for Pollen Germination and Pollen Tube Growth in Lily
Authors: Huang Jian , Chen Feng , Del Casino Cecilia , Autino Antonella , Shen Mouhua , Yuan Shuai , Peng Jia , Shi Hexin , Wang Chen , Cresti Mauro , Li Yiqin 
Published: February 2006

Abstract
Exhibiting rapid polarized growth, the pollen tube delivers the male gametes into the ovule for fertilization in higher plants. To get an overall picture of gene expression during pollen germination and pollen tube growth, we profiled the transcription patterns of 1,536 pollen cDNAs from lily (Lilium longiflorum) by microarray. Among those that exhibited significant differential expression, a cDNA named lily ankyrin repeat-containing protein (LlANK) was thoroughly studied. The full-length LlANK cDNA sequence predicts a protein containing five tandem ankyrin repeats and a RING zinc-finger domain. The LlANK protein possesses ubiquitin ligase activity in vitro. RNA blots demonstrated that LlANK transcript is present in mature pollen and its level, interestingly contrary to most pollen mRNAs, up-regulated significantly during pollen germination and pollen tube growth. When fused with green fluorescent protein and transiently expressed in pollen, LlANK was found dominantly associated with membrane-enclosed organelles as well as the generative cell. Overexpression of LlANK, however, led to abnormal growth of the pollen tube. On the other hand, transient silencing of LlANK impaired pollen germination and tube growth. Taken together, these results showed that LlANK is a ubiquitin ligase associated with membrane-enclosed organelles and required for polarized pollen tube growth.
Vacuolar H+-ATPase Activity Is Required for Endocytic and Secretory Trafficking inArabidopsis
Authors: Dettmer Jan , Hong-Hermesdorf Anne , Stierhof York-Dieter , Schumacher Karin 
Published: February 2006

AbstractIn eukaryotic cells, compartments of the highly dynamic endomembrane system are acidified to varying degrees by the activity of vacuolar H+-ATPases (V-ATPases). In the Arabidopsis thaliana genome, most V-ATPase subunits are encoded by small gene families, thus offering potential for a multitude of enzyme complexes with different kinetic properties and localizations. We have determined the subcellular localization of the three Arabidopsis isoforms of the membrane-integral V-ATPase subunit VHA-a. Colocalization experiments as well as immunogold labeling showed that VHA-a1 is preferentially found in the trans-Golgi network (TGN), the main sorting compartment of the secretory pathway. Uptake experiments with the endocytic tracer FM4-64 revealed rapid colocalization with VHA-a1, indicating that the TGN may act as an early endosomal compartment. Concanamycin A, a specific V-ATPase inhibitor, blocks the endocytic transport of FM4-64 to the tonoplast, causes the accumulation of FM4-64 together with newly synthesized plasma membrane proteins, and interferes with the formation of brefeldin A compartments. Furthermore, nascent cell plates are rapidly stained by FM4-64, indicating that endocytosed material is redirected into the secretory flow after reaching the TGN. Together, our results suggest the convergence of the early endocytic and secretory trafficking pathways in the TGN.
Transcriptome Profiling, Molecular Biological, and Physiological Studies Reveal a Major Role for Ethylene in Cotton Fiber Cell Elongation
Authors: Shi Yong-Hui , Zhu Sheng-Wei , Mao Xi-Zeng , Feng Jian-Xun , Qin Yong-Mei , Zhang Liang , Cheng Jing , Wei Li-Ping , Wang Zhi-Yong , Zhu Yu-Xian 
Published: February 2006

AbstractUpland cotton (Gossypium hirsutum) produces the most widely used natural fibers, yet the regulatory mechanisms governing fiber cell elongation are not well understood. Through sequencing of a cotton fiber cDNA library and subsequent microarray analysis, we found that ethylene biosynthesis is one of the most significantly upregulated biochemical pathways during fiber elongation. The 1-Aminocyclopropane-1-Carboxylic Acid Oxidase1-3 (ACO1-3) genes responsible for ethylene production were expressed at significantly higher levels during this growth stage. The amount of ethylene released from cultured ovules correlated with ACO expression and the rate of fiber growth. Exogenously applied ethylene promoted robust fiber cell expansion, whereas its biosynthetic inhibitor l-(2-aminoethoxyvinyl)-glycine (AVG) specifically suppressed fiber growth. The brassinosteroid (BR) biosynthetic pathway was modestly upregulated during this growth stage, and treatment with BR or its biosynthetic inhibitor brassinazole (BRZ) also promoted or inhibited, respectively, fiber growth. However, the effect of ethylene treatment was much stronger than that of BR, and the inhibitory effect of BRZ on fiber cells could be overcome by ethylene, but the AVG effect was much less reversed by BR. These results indicate that ethylene plays a major role in promoting cotton fiber elongation. Furthermore, ethylene may promote cell elongation by increasing the expression of sucrose synthase, tubulin, and expansin genes.
Evidence of a local spawning site of marine eels along northeastern Japan, based on the distribution of small leptocephali
Authors: KIMURA YOBUO , MILLER MICHAEL J. , MINAGAWA GEN , WATANABE SHUN , SHINODA AKIRA , AOYAMA JUN , INAGAKI TADASHI , TSUKAMOTO KATSUMI 
Published: February 2006

AbstractEvidence of recent spawning by several species of marine eels of the families Congridae, Ophichthidae, and Nettastomatidae was found over the continental shelf along the coast of northeastern Japan in October 2003. Sixty‐three leptocephali of at least three taxa that ranged from 3.8 to 12.3 mm total length were collected in a relatively small area, just to the south of Cape Shioya, primarily over the 100‐and 200‐m‐depth contours. The leptocephali of Gnathophis nystromi nystromi were the most abundant, followed by those of G. nystromi ginanago. This spawning area is located in an area that appeared to include water originating from the Tsugaru Warm Current and is further south than the typical latitude of the cold water of the Oyashio First Intrusion. These findings suggest that some species of marine eels may not migrate past the slope to spawn, and that the oceanographic features of the region may provide favorable conditions for the growth and retention of leptocephali in the area to the south of Cape Shioya.
Estimation of seasonal spawning ground locations and ambient sea surface temperatures for eggs and larvae of Pacific saury (Cololabis saira) in the western North Pacific
Authors: IWAHASHI MASAYUKI , ISODA YUTAKA , ITO SHIN‐ICHI , OOZEKI YOSHIOKI , SUYAMA SATOSHI 
Published: February 2006

AbstractSince there have been practically no surveys of the eggs of Pacific saury (Cololabis saira) in the western North Pacific (WNP), its spawning ground (SG) distribution has been poorly resolved, based mainly on the larval distribution. This means of estimating SG distribution is imprecise because saury eggs drift for more than a week before they hatch, in a region with intense western boundary currents and their extensions. To improve our understanding of the immature saury, a large number of larvae (body length <25 mm) collected in the WNP during 1993–96 were numerically backtracked to take into account the advection by geostrophic and wind‐forced Ekman currents, and the SG locations and ambient sea surface temperatures (SSTs) for the eggs and larvae on the backtracking trajectories were estimated. The resulting seasonal distributions of SGs indicated that both the locations and the intensities of spawning change from season to season. Moreover, the ambient SSTs for eggs just after fertilization ranged from a high of around 21.5°C in early autumn (September to October) to a low of around 15.0°C in late spring (May to June) with an intermediate of around 20.0°C in winter (January to February). The ambient SSTs showed seasonally different gradients while the individuals developed from eggs to early larvae: the SSTs decreased throughout the autumn (September to December), stayed rather constant in winter (January to February), and increased throughout the spring (March to June). The ambient SSTs for the early larvae were at around 19.0°C in autumn and winter (September to February) and around 16.5°C throughout the spring (March to June).
Environmental determinants of growth rates for larval Japanese anchovy Engraulis japonicus in different waters
Authors: TAKASUKA AKINORI , AOKI ICHIRO 
Published: February 2006

AbstractDo disparate mechanisms determine growth rates of fish larvae in the different regions? The relationship between growth rates and environmental factors (sea temperature and food availability) was examined for larval Japanese anchovy Engraulis japonicus in geographically and environmentally different waters, through sagittal otolith microstructure analysis. Recent 3‐day mean growth rates directly before capture were positively related with sea‐surface temperature (SST) but not with food availability (plankton density) for the larvae in the Kuroshio Extension and Kuroshio–Oyashio transition regions of the western North Pacific. On the contrary, variations in recent growth rates were attributed to food availability (plankton density) as well as SST for the larvae in the East China Sea. In the shirasu fishing ground in Sagami Bay, larval growth rates were variable under the influences of both SST and food availability (feeding incidence). On the surface, the growth–environment relationships seemed to differ among regions. However, a definite general pattern of the dome‐shaped relationship between recent growth rates and SST was observed when all the regions were combined. Growth rates were similar even among clearly different regions if at the same SST. Overall, growth rates roughly increased with SST until they reached the maximum at SST of 21–22°C (i.e. optimal growth temperature), and declined when SST went over 21–22°C. On the contrary, no clear relationship was observed between growth rate and plankton density or between SST and plankton density. Therefore, the apparent among‐region differences would be firstly caused by the differences in regional SST range. The systematic mechanism of growth determination for widespread pelagic fish species larvae would be run by primarily sea temperature and secondarily food availability, at the species level.
Distribution of the frankincense tree Boswellia papyrifera in Eritrea: the role of environment and land use
Authors: Ogbazghi Woldeselassie , Rijkers Toon , Wessel Marius , Bongers Frans 
Published: February 2006

AbstractAim  We determined the present and past distribution, and the abundance, of Boswellia papyrifera in Eritrea, and the environmental and land‐use factors determining its distribution limits.Location  Eritrea, in the Horn of Africa.Methods  In 1997 a Boswellia field survey was conducted in 113 village areas covering four administrative regions. Species occurrence was related to rainfall, air temperature and length of growing period. Additionally, the relationship between the abundance of Boswellia trees and selected physical and chemical soil factors, topography and land‐use types was determined for five study areas (with a total of 144 plots) situated along an altitude gradient of 800–2000 m a.s.l.Results  The geographical distribution of B. papyrifera was limited to the south‐western and southern parts of the country between 800 and 1850 m altitude receiving a mean annual rainfall of 375–700 mm, with a growing period of 45–100 days. Species abundance was affected by, in order of importance: altitude, land‐use intensity and soil organic matter. Most trees were found in hilly areas; tree density increased from the foot slope to the hill summit; no trees occurred in valleys. Land‐use intensity, especially agriculture, fallow and grazed areas, had a profound negative effect on tree abundance. Natural regeneration of the species was promoted in areas where grazing by livestock was not allowed or regulated.Main conclusions  The distribution of B. papyrifera in Eritrea has decreased during past decades, mainly due to an increasing human population, resulting in the conversion of woodlands into agricultural fields and increasing livestock pressure hindering natural regeneration. Consequently, Boswellia trees are found mainly in hilly areas on steep slopes with shallow soils of low fertility. The species appears to be able to adapt to these harsh growing conditions: in adjacent countries it was also found in comparable growth habitats.
Effect of N‐fixing and non N‐fixing trees and crops on NO and N2O emissions from Senegalese soils
Authors: Dick Jan , Skiba Ute , Munro Robert , Deans Douglas 
Published: February 2006

AbstractAim  Agroforestry systems incorporating N‐fixing trees have been shown to be socially beneficial and are thought to be environmentally friendly, both enriching and stabilizing soil. However, the effect of such systems on the emissions of the important greenhouse gas nitrous oxide (N2O) and the tropospheric ozone precursor nitric oxide (NO) is largely unknown.Location  Soil was collected from the research plots of Institut Sénégalais de Recherches Agricoles at Bandia and Bambey, Senegal, West Africa, and from neighbouring farmers’ fields. Trace gas flux measurements and chemical analysis of the soil were carried out at the Centre for Ecology and Hydrology (CEH), Edinburgh, UK.Methods  Nitric oxide (NO) and nitrous oxide (N2O) emissions were measured following simulated rainfall events (10 and 20 mm equivalents) from repacked soil cores collected under two tree species (Acacia raddiana) and Eucalyptus camaldulensis) in each of two provenance trails. In addition, soil samples were collected in local fields growing peanut (Arachis hypogaea) and Sorghum (Sorghum vulgare), close to the species trials in Bambey. NO was measured using a flow through system and was analysed by chemiluminescence. Nitrous oxide was measured from the repacked soil core headspace and was analysed by electron capture gas chromatography. Soil mineral N was extracted with KCl and analysed by colorimetric methods on separate soil columns.Results  Light rainfall, which increased the gravimetric soil moisture content to 20%, stimulated an increase in NO emission but there was no detectable N2O emission. A heavy rainfall event, which increased the gravimetric soil moisture to 30%, stimulated N2O emission with a subsequent peak in NO emissions when the soils became drier. Soil collected under the N‐fixing tree species emitted significantly more N2O than soil collected under the N‐fixing crop species (P < 0.01). NO and N2O emissions significantly correlated with soil available N (NH4 and NO3) (P < 0.05).Main conclusions  Rainfall intensity, supply of mineral N from organic matter and N fixation were the prime drivers of NO and N2O emissions from seasonally dry tropical soils. The improved soil fertility underneath the trees provided a larger pool of mineral N and yielded larger rates of NO and N2O emissions.
Obesity and cardiovascular risk factors in type 2 diabetes: results from the Swedish National Diabetes Register
Authors: RIDDERSTRÅLE M. , GUDBJÖRNSDOTTIR S. , ELIASSON B. , NILSSON P. M. , CEDERHOLM J. ,   FOR THE STEERING COMMITTEE OF THE SWEDISH NATIONAL DIABETES REGISTER (NDR)
Published: February 2006

Abstract.Objectives.  To compare obese with normal and overweight type 2 diabetic patients regarding body mass index (BMI) and cardiovascular risk factors, and to analyse changes in weight versus risk factors.Design and setting.  A cross‐sectional study of 44 042 type 2 patients, and a 6‐year prospective study of 4468 type 2 patients.Results.  Obese patients (BMI ≥ 30 kg m−2), 37% of all patients, had high frequencies of hypertension (88%), hyperlipidaemia (81%) and microalbuminuria (29%). Only 11% had blood pressure <130/80 mmHg. Their ratio of triglycerides to HDL cholesterol was considerably elevated, whilst the mean total and LDL cholesterol were similar as in normal weight subjects. Obese patients had elevated odds ratios for hypertension, hyperlipidaemia and microalbuminuria: 2.1, 1.8 and 1.4 in the cross‐sectional study, similarly confirmed in the prospective 6‐year study. BMI was an independent predictor of these risk factors (P < 0.001), although only slightly associated with HbA1c and not with total or LDL cholesterol. A change in BMI during the prospective study was related to a change in HbA1c in patients treated with diet and oral hypoglycaemic agents (OHAs) but not with insulin. In all patients, an increase in BMI was related to the development of hypertension, and a change in BMI to change in blood pressure, also mostly confirmed when treated with diet, OHAs or insulin.Conclusions.  The high frequencies of risk factors in obese type 2 patients implies an increased risk of cardiovascular disease and the need for therapeutic measures. The paradox that hypoglycaemic treatment accompanied by weight gain may increase cardiovascular risk factors seems to be verified here concerning hypertension but not concerning microalbuminuria.