bluuebunny/crossref_metadata_2025_split huggingface dataset:
Review of: Gene expression profiling identifies molecular subtypes of inflammatory breast cancer
Authors: Lønning P. E. 
Published: January 2006

Citation of original article:F. Bertucci, P. Finetti, J. Rougemont, E. Charafe-Jauffret, N. Cervera, C. Tarpin,et al. Gene expression profiling identifies molecular subtypes of inflammatory breast cancer.Cancer Research2005;65(6): 2170–8.Abstract of the original articleBreast cancer is a heterogeneous disease. Comprehensive gene expression profiles obtained using DNA microarrays have revealed previously indistinguishable subtypes of non-inflammatory breast cancer (NIBC) related to different features of mammary epithelial biology and significantly associated with survival. Inflammatory breast cancer (IBC) is a rare, particular, and aggressive form of disease. Here we have investigated whether the five molecular subtypes described for NIBC (luminal A and B, basal, ERBB2 overexpressing, and normal breast-like) were also present in IBC. We monitored the RNA expression of approximately 8,000 genes in 83 breast tissue samples including 37 IBC, 44 NIBC, and 2 normal breast samples. Hierarchical clustering identified the five subtypes of breast cancer in both NIBC and IBC samples. These subtypes were highly similar to those defined in previous studies and associated with similar histoclinical features. The robustness of this classification was confirmed by the use of both alternative gene set and analysis method, and the results were corroborated at the protein level. Furthermore, we show that the differences in gene expression between NIBC and IBC and between IBC with and without pathologic complete response that we have recently reported persist in each subtype. Our results show that the expression signatures defining molecular subtypes of NIBC are also present in IBC. Obtained using different patient series and different microarray platforms, they reinforce confidence in the expression-based molecular taxonomy but also give evidence for its universality in breast cancer, independently of a specific clinical form.
What Went Wrong? Church–State Relations in Socialist Yugoslavia
Authors: Buchenau Klaus 
Published: January 2006

Yugoslavia's socialism was always a special case when compared with other states in the eastern part of Europe, and so was its religious policy. In the 1960s, Yugoslavia adopted a rather liberal stance towards its religious communities. The state interfered less in the internal affairs of the churches than it did in most states in the Warsaw Pact. Even Croat Cardinal Franjo Kuharić, who was otherwise very critical towards Tito's Yugoslavia, had to admit in 1987,The Pope freely appoints bishops, without the intervention of the government. The church is free in its inner administration: there is no numerus clausus, neither for priests nor for the order's candidates. The bishops appoint and transfer priests without hindrance, without government interference. Bishops, priests and believers are free to gather in church rooms and don't have to apply for special permits. The orders can exist and function, although within the frames of law. The freedom of motion in- and outside the country is not hampered, though it may happen that-in our conviction, without justification-priests' passports are taken away. The freedom of the religious press is also one of the positive facts.
Seeing is believing? A beginners' guide to practical pitfalls in image acquisition
Authors: North Alison J. 
Published: January 2006

Imaging can be thought of as the most direct of experiments. You see something; you report what you see. If only things were truly this simple. Modern imaging technology has brought about a revolution in the kinds of questions we can approach, but this comes at the price of increasingly complex equipment. Moreover, in an attempt to market competing systems, the microscopes have often been inappropriately described as easy to use and suitable for near-beginners. Insufficient understanding of the experimental manipulations and equipment set-up leads to the introduction of errors during image acquisition. In this feature, I review some of the most common practical pitfalls faced by researchers during image acquisition, and how they can affect the interpretation of the experimental data.
This article is targeted neither to the microscopy gurus who push forward the frontiers of imaging technology nor to my imaging specialist colleagues who may wince at the overly simplistic comments and lack of detail. Instead, this is for beginners who gulp with alarm when they hear the word “confocal pinhole” or sigh as they watch their cells fade and die in front of their very eyes time and time again at the microscope. Take heart, beginners, if microscopes were actually so simple then many people (including myself) would suddenly be out of a job!
Carbon partitioning to mobile and structural fractions in poplar wood under elevated CO2 (EUROFACE) and N fertilization
Authors: LUO ZHI‐BIN , CALFAPIETRA CARLO , LIBERLOO MARION , SCARASCIA‐MUGNOZZA GIUSEPPE , POLLE ANDREA 
Published: January 2006

AbstractTo determine whether globally increasing atmospheric carbon dioxide (CO2) concentrations can affect carbon partitioning between nonstructural and structural carbon pools in agroforestry plantations, Populus nigra was grown in ambient air (about 370 μmol mol−1 CO2) and in air with elevated CO2 concentrations (about 550 μmol mol−1 CO2) using free‐air CO2 enrichment (FACE) technology. FACE was maintained for 5 years. After three growing seasons, the plantation was coppiced and one half of each experimental plot was fertilized with nitrogen. Carbon concentrations and stocks were measured in secondary sprouts in seasons of active growth and dormancy during 2 years after coppicing. Although FACE, N fertilization and season had significant tissue‐specific effects on carbon partitioning to the fractions of structural carbon, soluble sugars and starch as well as to residual soluble carbon, the overall magnitude of these shifts was small. The major effect of FACE and N fertilization was on cell wall biomass production, resulting in about 30% increased above ground stocks of both mobile and immobile carbon pools compared with fertilized trees under ambient CO2. Relative C partitioning between mobile and immobile C pools was not significantly affected by FACE or N fertilization. These data demonstrate high metabolic flexibility of P. nigra to maintain C‐homeostasis under changing environmental conditions and illustrate that nonstructural carbon compounds can be utilized more rapidly for structural growth under elevated atmospheric [CO2] in fertilized agroforestry systems. Thus, structural biomass production on abandoned agricultural land may contribute to achieving the goals of the Kyoto protocol.
Ecohydrological impacts of woody‐plant encroachment: seasonal patterns of water and carbon dioxide exchange within a semiarid riparian environment
Authors: SCOTT RUSSELL L. , HUXMAN TRAVIS E. , WILLIAMS DAVID G. , GOODRICH DAVID C. 
Published: January 2006

AbstractAcross many dryland regions, historically grass‐dominated ecosystems have been encroached upon by woody‐plant species. In this paper, we compare ecosystem water and carbon dioxide (CO2) fluxes over a grassland, a grassland–shrubland mosaic, and a fully developed woodland to evaluate potential consequences of woody‐plant encroachment on important ecosystem processes. All three sites were located in the riparian corridor of a river in the southwest US. As such, plants in these ecosystems may have access to moisture at the capillary fringe of the near‐surface water table. Using fluxes measured by eddy covariance in 2003 we found that ecosystem evapotranspiration (ET) and net ecosystem exchange of carbon dioxide (NEE) increased with increasing woody‐plant dominance. Growing season ET totals were 407, 450, and 639 mm in the grassland, shrubland, and woodland, respectively, and in excess of precipitation by 227, 265, and 473 mm. This excess was derived from groundwater, especially during the extremely dry premonsoon period when this was the only source of moisture available to plants. Access to groundwater by the deep‐rooted woody plants apparently decouples ecosystem ET from gross ecosystem production (GEP) with respect to precipitation. Compared with grasses, the woody plants were better able to use the stable groundwater source and had an increased net CO2 gain during the dry periods. This enhanced plant activity resulted in substantial accumulation of leaf litter on the soil surface that, during rainy periods, may lead to high microbial respiration rates that offset these photosynthetic fluxes. March–December (primary growing season) totals of NEE were −63, −212, and −233 g C m−2 in the grassland, shrubland, and woodland, respectively. Thus, there was a greater disparity between ecosystem water use and the strength of the CO2 sink as woody plants increased across the encroachment gradient. Despite a higher density of woody plants and a greater plant productivity in the woodland than in the shrubland, the woodland produced a larger respiration response to rainfall that largely offset its higher photosynthetic potential. These data suggest that the capacity for woody plants to exploit water resources in riparian areas results in enhanced carbon sequestration at the expense of increased groundwater use under current climate conditions, but the potential does not scale specifically as a function of woody‐plant abundance. These results highlight the important roles of water sources and ecosystem structure on the control of water and carbon balances in dryland areas.
Comparison of the rebound tonometer (ICare®) to the applanation tonometer (Tonopen XL®) in normotensive dogs
Authors: Leiva M. , Naranjo C. , Peña M. T. 
Published: January 2006

AbstractObjectiveTo compare intraocular pressure (IOP) measurements obtained by recently introduced rebound tonometer (ICare®) and the well‐known applanation tonometer Tonopen XL®in normal canine eyes.MethodsIn a prospective, randomized, single‐center study, IOP measurements by ICare®and Tonopen XL®tonometers were compared in 160 nonpathologic canine eyes (80 dogs). Complete slit‐lamp biomicroscopy and indirect ophthalmoscopy were performed on each dog. Rebound tonometry was performed first and immediately after topical anesthetic drops were instilled in both eyes. One minute after the application of the topical anesthetic, applanation tonometry was performed in both eyes. The intraocular pressures obtained by use of both techniques were compared by statistical analysis.ResultsThe mean IOP readings were 9.158 mmHg (SD 3.471 mmHg) for the ICare®tonometer (x) and 11.053 mmHg (SD 3.451 mmHg) for the Tonopen XL®readings (y). The mean difference in intraocular pressures (−1.905 mmHg) was within clinically acceptable limits. The correlation coefficient (r2) of the relationship within both tonometers wasr2 = 0.7477. The corresponding linear regression between the tonometers readings wasy = 0.6662x + 4.942.ConclusionsIntraocular pressures obtained with the ICare®rebound tonometer were concordant with the IOP readings obtained by applanation Tonopen XL®, but ICare®values were significantly (P < 0.0001) lower. Rebound tonometry could be an appropriate tonometry method for routine clinical use after its calibration for canine eyes.
Evolutionary and functional analysis of the tailless enhancer in Musca domestica and Drosophila melanogaster
Authors: Wratten Naomi S. , McGregor Alistair P. , Shaw Philip J. , Dover Gabriel A. 
Published: January 2006

SUMMARYTo further understand the evolutionary dynamics of the regulatory interactions underlying development, we expand on our previous analysis of hunchback and compare the structure and function of the tailless enhancer between Musca domestica and Drosophila melanogaster. Our analysis shows that although the expression patterns and functional protein domains of tll are conserved between Musca and Drosophila, the enhancer sequences are unalignable. Upon closer investigation, we find that these highly diverged enhancer sequences encode the same regulatory information necessary for Bicoid, Dorsal, and the terminal system to drive tll expression. The binding sites for these transcription factors differ in the sequence, number, spacing, and position between the Drosophila and Musca tll enhancers, and we were unable to establish homology between binding sites from each species. This implies that the Musca and Drosophila Bcd‐binding sites have evolved de novo in the 100 million years since these species diverged. However, in transgenic Drosophila embryos the Musca tll enhancer is able to drive the same expression pattern as endogenous Drosophila tll. Therefore, during the rapid evolution of enhancer sequences individual binding sites are continually lost and gained, but the transcriptional output is maintained by compensatory mutations in cis and in trans.
Production of Recombinant and Tagged Proteins in the Hyperthermophilic Archaeon
Sulfolobus solfataricus
Authors: Albers S.-V. , Jonuscheit M. , Dinkelaker S. , Urich T. , Kletzin A. , Tampé R. , Driessen A. J. M. , Schleper C. 
Published: January 2006

ABSTRACT

Many systems are available for the production of recombinant proteins in bacterial and eukaryotic model organisms, which allow us to study proteins in their native hosts and to identify protein-protein interaction partners. In contrast, only a few transformation systems have been developed for archaea, and no system for high-level gene expression existed for hyperthermophilic organisms. Recently, a virus-based shuttle vector with a reporter gene was developed for the crenarchaeote
Sulfolobus solfataricus
, a model organism of hyperthermophilic archaea that grows optimally at 80°C (M. Jonuscheit, E. Martusewitsch, K. M. Stedman, and C. Schleper, Mol. Microbiol.
48:
1241-1252, 2003). Here we have refined this system for high-level gene expression in
S. solfataricus
with the help of two different promoters, the heat-inducible promoter of the major chaperonin, thermophilic factor 55, and the arabinose-inducible promoter of the arabinose-binding protein AraS. Functional expression of heterologous and homologous genes was demonstrated, including production of the cytoplasmic sulfur oxygenase reductase from
Acidianus ambivalens
, an Fe-S protein of the ABC class from
S. solfataricus
, and two membrane-associated ATPases potentially involved in the secretion of proteins. Single-step purification of the proteins was obtained via fused His or Strep tags. To our knowledge, these are the first examples of the application of an expression vector system to produce large amounts of recombinant and also tagged proteins in a hyperthermophilic archaeon.
Biotransformation of 1,2,3-Tri- and 1,2,3,4,7,8-Hexachlorodibenzo-p- Dioxin bySphingomonas wittichiiStrain RW1
Authors: Nam In-Hyun , Kim Young-Mo , Schmidt Stefan , Chang Yoon-Seok 
Published: January 2006

ABSTRACTSphingomonas wittichiiRW1 is able to catabolize 1,2,3,4-tetrachlorodibenzo-p-dioxin (H. B. Hong, Y. S. Chang, I. H. Nam, P. Fortnagel, and S. Schmidt, Appl. Environ. Microbiol. 68:2584-2588, 2002). Here we demonstrate the aerobic bacterial catabolism of the ubiquitous toxic diaryl ether pollutant 1,2,3,4,7,8-hexachlorodibenzo-p-dioxin by this strain. The products of this biotransformation were identified as tetrachlorocatechol and 2-methoxy-3,4,5,6-tetrachlorophenol by comparing mass spectra recorded before and aftern-butylboronate andN,O-bis(trimethylsilyl)-trifluoroacetamide derivatization with those of authentic compounds. Additional experiments showed that the less-chlorinated 1,2,3,7,8-pentachlorodibenzo-p-dioxin was not transformed by the strain RW1. The importance of substitution patterns for the degradability of individual congeners was illustrated by the fact that the 1,2,3-trichlorodibenzo-p-dioxin was catabolized to yield 3,4,5-trichlorocatechol, whereas the 2,3,7-trichlorodibenzo-p-dioxin was not attacked.
Transposons Inactivate Biosynthesis of the Nonribosomal Peptide Microcystin in Naturally Occurring
Planktothrix
spp
Authors: Christiansen Guntram , Kurmayer Rainer , Liu Qian , Börner Thomas 
Published: January 2006

ABSTRACT

The filamentous cyanobacteria
Planktothrix
spp. occur in the temperate region of the Northern hemisphere. The red-pigmented
Planktothrix rubescens
bacteria occur in deep, physically stratified, and less eutrophic lakes.
Planktothrix
is a known producer of the toxic heptapeptide microcystin (MC), which is produced nonribosomally by a large enzyme complex consisting of peptide synthetases and polyketide synthases encoded by a total of nine genes (
mcy
genes).
Planktothrix
spp. differ in their cellular MC contents as well as the production of MC variants; however, the mechanisms favoring this diversity are not understood. Recently, the occurrence of
Planktothrix
strains containing all
mcy
genes but lacking MC has been reported. In this study, 29 such strains were analyzed to find out if mutations of the
mcy
genes lead to the inability to synthesize MC. Two deletions, spanning 400 bp (in
mcyB
; one strain) and 1,869 bp (in
mcyHA
; three strains), and three insertions (IS), spanning 1,429 bp (in
mcyD
; eight strains), 1,433 bp (in
mcyEG
; one strain), and 1,433 bp (in
mcyA
; one strain), were identified. Though found in different genes and different isolates and transcribed in opposite directions, IS were found to be identical and contained conserved domains assigned to transposable elements. Using mutation-specific primers, two insertions (in
mcyD
and
mcyA
) and one deletion (in
mcyHA
) were found regularly in populations of
P. rubescens
in different lakes. The results demonstrate for the first time that different mutations resulting in inactivation of MC synthesis do occur frequently and make up a stable proportion of the
mcy
gene pool in
Planktothrix
populations over several years.
Development of a Microbial Model for the Combined Effect of Temperature and pH on Spoilage of Ground Meat, and Validation of the Model under Dynamic Temperature Conditions
Authors: Koutsoumanis K. , Stamatiou A. , Skandamis P. , Nychas G.-J. E. 
Published: January 2006

ABSTRACT

The changes in microbial flora and sensory characteristics of fresh ground meat (beef and pork) with pH values ranging from 5.34 to 6.13 were monitored at different isothermal storage temperatures (0 to 20°C) under aerobic conditions. At all conditions tested, pseudomonads were the predominant bacteria, followed by
Brochothrix thermosphacta
, while the other members of the microbial association (e.g., lactic acid bacteria and
Enterobacteriaceae
) remained at lower levels. The results from microbiological and sensory analysis showed that changes in pseudomonad populations followed closely sensory changes during storage and could be used as a good index for spoilage of aerobically stored ground meat. The kinetic parameters (maximum specific growth rate [μ
max
] and the duration of lag phase [λ]) of the spoilage bacteria were modeled by using a modified Arrhenius equation for the combined effect of temperature and pH. Meat pH affected growth of all spoilage bacteria except that of lactic acid bacteria. The “adaptation work,” characterized by the product of μ
max
and λ(μ
max
× λ) was found to be unaffected by temperature for all tested bacteria but was affected by pH for pseudomonads and
B. thermosphacta
. For the latter bacteria, a negative linear correlation between ln(μ
max
× λ) and meat pH was observed. The developed models were further validated under dynamic temperature conditions using different fluctuating temperatures. Graphical comparison between predicted and observed growth and the examination of the relative errors of predictions showed that the model predicted satisfactorily growth under dynamic conditions. Predicted shelf life based on pseudomonads growth was slightly shorter than shelf life observed by sensory analysis with a mean difference of 13.1%. The present study provides a “ready-to-use,” well-validated model for predicting spoilage of aerobically stored ground meat. The use of the model by the meat industry can lead to effective management systems for the optimization of meat quality.
Identification of Eukaryotic Open Reading Frames in Metagenomic cDNA Libraries Made from Environmental Samples
Authors: Grant Susan , Grant William D. , Cowan Don A. , Jones Brian E. , Ma Yanhe , Ventosa Antonio , Heaphy Shaun 
Published: January 2006

ABSTRACT

Here we describe the application of metagenomic technologies to construct cDNA libraries from RNA isolated from environmental samples. RNAlater (Ambion) was shown to stabilize RNA in environmental samples for periods of at least 3 months at −20°C. Protocols for library construction were established on total RNA extracted from
Acanthamoeba polyphaga
trophozoites. The methodology was then used on algal mats from geothermal hot springs in Tengchong county, Yunnan Province, People's Republic of China, and activated sludge from a sewage treatment plant in Leicestershire, United Kingdom. The Tenchong libraries were dominated by RNA from prokaryotes, reflecting the mainly prokaryote microbial composition. The majority of these clones resulted from rRNA; only a few appeared to be derived from mRNA. In contrast, many clones from the activated sludge library had significant similarity to eukaryote mRNA-encoded protein sequences. A library was also made using polyadenylated RNA isolated from total RNA from activated sludge; many more clones in this library were related to eukaryotic mRNA sequences and proteins. Open reading frames (ORFs) up to 378 amino acids in size could be identified. Some resembled known proteins over their full length, e.g., 36% match to cystatin, 49% match to ribosomal protein L32, 63% match to ribosomal protein S16, 70% to CPC2 protein. The methodology described here permits the polyadenylated transcriptome to be isolated from environmental samples with no knowledge of the identity of the microorganisms in the sample or the necessity to culture them. It has many uses, including the identification of novel eukaryotic ORFs encoding proteins and enzymes.
Slugs: Potential Novel Vectors of
Escherichia coli
O157
Authors: Sproston Emma L. , Macrae M. , Ogden Iain D. , Wilson Michael J. , Strachan Norval J. C. 
Published: January 2006

ABSTRACT

Field and laboratory studies were performed to determine whether slugs could act as novel vectors for pathogen (e.g.,
Escherichia coli
O157) transfer from animal feces to salad vegetables.
Escherichia coli
O157 was isolated from 0.21% of field slugs from an Aberdeenshire sheep farm. These isolates carried the verocytotoxin genes (
vt1
and
vt2
) and the attaching and effacing gene (
eae
), suggesting that they are potentially pathogenic to humans. Strain typing using multilocus variable number tandem repeats analysis showed that slug and sheep isolates were indistinguishable. Laboratory experiments using an
E. coli
mutant resistant to nalidixic acid showed that the ubiquitous slug species
Deroceras reticulatum
could carry viable
E. coli
on its external surface for up to 14 days. Slugs that had been fed
E. coli
shed viable bacteria in their feces with numbers showing a short but statistically significant linear log decline. Further, it was found that
E. coli
persisted for up to 3 weeks in excreted slug feces, and hence, we conclude that slugs have the potential to act as novel vectors of
E. coli
O157.